diff --git a/workflows/epigenetics/hic-hicup-cooler/.dockstore.yml b/workflows/epigenetics/hic-hicup-cooler/.dockstore.yml index 7c6c4b9a8..6d9404165 100644 --- a/workflows/epigenetics/hic-hicup-cooler/.dockstore.yml +++ b/workflows/epigenetics/hic-hicup-cooler/.dockstore.yml @@ -3,36 +3,36 @@ workflows: - name: hic-fastq-to-cool-hicup-cooler subclass: Galaxy publish: true - primaryDescriptorPath: /hic_fastq_to_cool_hicup_cooler.ga + primaryDescriptorPath: /hic-fastq-to-cool-hicup-cooler.ga testParameterFiles: - - /hic_fastq_to_cool_hicup_cooler-tests.yml + - /hic-fastq-to-cool-hicup-cooler-tests.yml authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 - name: chic-fastq-to-cool-hicup-cooler subclass: Galaxy publish: true - primaryDescriptorPath: /chic_fastq_to_cool_hicup_cooler.ga + primaryDescriptorPath: /chic-fastq-to-cool-hicup-cooler.ga testParameterFiles: - - /chic_fastq_to_cool_hicup_cooler-tests.yml + - /chic-fastq-to-cool-hicup-cooler-tests.yml authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 -- name: hic-juicermediumtabix-to_cool-cooler +- name: hic-juicermediumtabix-to-cool-cooler subclass: Galaxy publish: true - primaryDescriptorPath: /hic_juicermediumtabix_to_cool_cooler.ga + primaryDescriptorPath: /hic-juicermediumtabix-to-cool-cooler.ga testParameterFiles: - - /hic_juicermediumtabix_to_cool_cooler-tests.yml + - /hic-juicermediumtabix-to-cool-cooler-tests.yml authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 - name: hic-fastq-to-pairs-hicup subclass: Galaxy publish: true - primaryDescriptorPath: /hic_fastq_to_pairs_hicup.ga + primaryDescriptorPath: /hic-fastq-to-pairs-hicup.ga testParameterFiles: - - /hic_fastq_to_pairs_hicup-tests.yml + - /hic-fastq-to-pairs-hicup-tests.yml authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 diff --git a/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md b/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md index 93ba3a378..86f34616a 100644 --- a/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md +++ b/workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.3] 2023-09-08 + +### Update tools +- all cooler tools were updated from 0.8.11 to 0.9.3 +- pyGenomeTracks was updated from 3.7 to 3.8 + ## [0.2.1] 2023-09-01 Bug fix Fix dockstore (workflows are the same) diff --git a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler-tests.yml rename to workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml diff --git a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga similarity index 97% rename from workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga rename to workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga index c0d3968fa..903a8e783 100644 --- a/workflows/epigenetics/hic-hicup-cooler/chic_fastq_to_cool_hicup_cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.3", "name": "cHi-C_fastqToCool_hicup_cooler", "steps": { "0": { @@ -319,7 +319,7 @@ "outputs": [], "position": { "left": 520, - "top": 0.0 + "top": 0 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -741,23 +741,13 @@ } }, "tags": "", - "uuid": "4a815412-cadd-4df9-9559-15b365715f05" + "uuid": "9df7c037-6fe4-47e9-8311-e40bc5101b58" }, "tool_id": null, "type": "subworkflow", "uuid": "3584d879-0b7a-4a89-a5f6-8439db6f003e", "when": null, "workflow_outputs": [ - { - "label": "HiCUP report (txt)", - "output_name": "HiCUP report (tabular)", - "uuid": "b479e588-6d59-4b60-9dd7-036e58358eae" - }, - { - "label": "HiCUP report (html)", - "output_name": "HiCUP report (HTML)", - "uuid": "902f20ef-d51d-4fad-86a0-206cda2ef361" - }, { "label": "valid pairs in juicebox format", "output_name": "valid pairs in juicebox format", @@ -767,6 +757,16 @@ "label": "valid pairs in juicebox format MAPQ filtered", "output_name": "valid pairs in juicebox format MAPQ filtered", "uuid": "ec040a8e-883a-4cdb-b5bf-ea5a611a16a7" + }, + { + "label": "HiCUP report (html)", + "output_name": "HiCUP report (HTML)", + "uuid": "902f20ef-d51d-4fad-86a0-206cda2ef361" + }, + { + "label": "HiCUP report (txt)", + "output_name": "HiCUP report (tabular)", + "uuid": "b479e588-6d59-4b60-9dd7-036e58358eae" } ] }, @@ -933,7 +933,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1", "errors": null, "id": 14, "input_connections": { @@ -975,15 +975,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "d56db0e1555d", + "changeset_revision": "8c3cba559c99", "name": "cooler_csort_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "bbb479cd-c67c-4347-9c1d-ac8095d90aa9", "when": null, @@ -1170,7 +1170,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -1203,15 +1203,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "c3dc51297bf8", + "changeset_revision": "ebd2a52eb245", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -1219,7 +1219,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -1258,15 +1258,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "3ff6eeca667e", + "changeset_revision": "0641e1c892c6", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "d411eea7-7996-44f2-af2a-feecb854a067", "when": null, @@ -1280,7 +1280,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -1320,15 +1320,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "8f71aaf6e59d", + "changeset_revision": "8f9fe0667b89", "name": "cooler_balance", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"cistrans\": {\"__class__\": \"ConnectedValue\"}, \"convergencepolicy\": \"error\", \"ignorediags\": \"2\", \"ignoredist\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"madmax\": \"5\", \"maxiters\": \"200\", \"mincount\": \"0\", \"minnnz\": \"10\", \"name\": \"weight\", \"tol\": \"1e-05\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "44270887-1c96-4ede-8bb9-3db2a07eeb6e", "when": null, @@ -1342,28 +1342,28 @@ } }, "tags": "", - "uuid": "bb361160-3ee3-4f03-99a3-7870baee168e" + "uuid": "1a6f4422-8f82-4444-a30c-bde38d181e41" }, "tool_id": null, "type": "subworkflow", "uuid": "63c60960-bd33-436a-ac47-fdaf69c4bdfa", "when": null, "workflow_outputs": [ - { - "label": "matrix with raw values", - "output_name": "matrix with raw values", - "uuid": "606c3260-41a2-400e-a580-0db59b3bc11f" - }, { "label": "matrix with iced values", "output_name": "matrix with iced values", "uuid": "178c2801-e3b3-4398-8448-795d67ae5aa3" + }, + { + "label": "matrix with raw values", + "output_name": "matrix with raw values", + "uuid": "606c3260-41a2-400e-a580-0db59b3bc11f" } ] }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2", "errors": null, "id": 16, "input_connections": { @@ -1398,15 +1398,15 @@ "output_name": "outFileName" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.7+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2", "tool_shed_repository": { - "changeset_revision": "7dd841a32245", + "changeset_revision": "59fd173ac850", "name": "pygenometracks", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"global_args\": {\"title\": \"\", \"fontsize\": \"12\", \"dpi\": \"72\", \"width\": \"40.0\", \"plotWidth\": null, \"height\": null, \"trackLabelFraction\": \"0.05\", \"trackLabelHAlign\": \"left\", \"decreasingXAxis\": false}, \"image_file_format\": \"png\", \"region\": {\"__class__\": \"ConnectedValue\"}, \"tracks\": [{\"__index__\": 0, \"track_file_style_conditional\": {\"track_file_style_selector\": \"hic_matrix_option\", \"__current_case__\": 0, \"title\": \"\", \"matrix_h5_cooler_multiple\": {\"__class__\": \"ConnectedValue\"}, \"colormap\": \"RdYlBu_r\", \"min_value\": null, \"max_value\": null, \"depth\": \"8000000\", \"transform\": \"no\", \"height_matrix\": null, \"show_masked_bins\": false, \"boundaries_file\": {\"__class__\": \"RuntimeValue\"}, \"scale_factor\": \"1.0\", \"rasterize\": true, \"invert_orientation\": false, \"spacer_height\": null}}, {\"__index__\": 1, \"track_file_style_conditional\": {\"track_file_style_selector\": \"xaxis_option\", \"__current_case__\": 13, \"title\": \"\", \"fontsize\": null, \"xaxis_where\": \"bottom\", \"spacer_height\": null}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.7+galaxy0", + "tool_version": "3.8+galaxy2", "type": "tool", "uuid": "dfbe45de-b2a7-479e-b717-29ec5b31379e", "when": null, @@ -1422,6 +1422,6 @@ "tags": [ "Hi-C" ], - "uuid": "f310abac-4a50-41fa-a59a-84c51816a462", - "version": 1 + "uuid": "2a89cbe4-a69f-4bff-9465-2e04b0217e35", + "version": 4 } diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml similarity index 98% rename from workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler-tests.yml rename to workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml index ab9ed27a5..95a438d6b 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler-tests.yml +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml @@ -21,7 +21,7 @@ No fill-in: 'false' minimum MAPQ: 30 Bin size in bp: 1000000 - Interactions to consider to calculate weights in normalization step: --cis-only + Interactions to consider to calculate weights in normalization step: "" region for matrix plotting: chr2:175,689,620-178,604,461 outputs: HiCUP report (html): @@ -76,7 +76,7 @@ test_dataset: asserts: has_size: - value: 123613 + value: 149349 delta: 10000 plot with pyGenomeTracks: class: File diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga similarity index 96% rename from workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga rename to workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga index 2f34eb68d..71ea93dc9 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_cool_hicup_cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.3", "name": "Hi-C_fastqToCool_hicup_cooler", "steps": { "0": { @@ -592,16 +592,7 @@ "output_name": "dataset_hicup" } }, - "inputs": [ - { - "description": "runtime parameter for tool Hicup to juicer converter", - "name": "digester" - }, - { - "description": "runtime parameter for tool Hicup to juicer converter", - "name": "input_file" - } - ], + "inputs": [], "label": "valid pairs in juicebox format", "name": "Hicup to juicer converter", "outputs": [ @@ -630,7 +621,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"digester\": {\"provide_digester\": \"yes\", \"__current_case__\": 0, \"digester_file\": {\"__class__\": \"RuntimeValue\"}, \"usemid\": true}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"digester\": {\"provide_digester\": \"yes\", \"__current_case__\": 0, \"digester_file\": {\"__class__\": \"ConnectedValue\"}, \"usemid\": true}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.9.2+galaxy0", "type": "tool", "uuid": "659811cd-a212-4949-9693-074f6161ed11", @@ -696,7 +687,7 @@ } }, "tags": "", - "uuid": "48f579ea-eaac-49ee-b38f-93c82f8b7d76" + "uuid": "f6bb48d4-0392-4c89-825e-01b8523b0943" }, "tool_id": null, "type": "subworkflow", @@ -727,7 +718,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -769,15 +760,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "d56db0e1555d", + "changeset_revision": "8c3cba559c99", "name": "cooler_csort_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "bbb479cd-c67c-4347-9c1d-ac8095d90aa9", "when": null, @@ -964,7 +955,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -997,15 +988,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "c3dc51297bf8", + "changeset_revision": "ebd2a52eb245", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -1013,7 +1004,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -1052,15 +1043,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "3ff6eeca667e", + "changeset_revision": "0641e1c892c6", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy1", + "tool_version": "0.9.3+galaxy1", "type": "tool", "uuid": "d411eea7-7996-44f2-af2a-feecb854a067", "when": null, @@ -1074,7 +1065,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -1114,15 +1105,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "8f71aaf6e59d", + "changeset_revision": "8f9fe0667b89", "name": "cooler_balance", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"cistrans\": {\"__class__\": \"ConnectedValue\"}, \"convergencepolicy\": \"error\", \"ignorediags\": \"2\", \"ignoredist\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"madmax\": \"5\", \"maxiters\": \"200\", \"mincount\": \"0\", \"minnnz\": \"10\", \"name\": \"weight\", \"tol\": \"1e-05\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "44270887-1c96-4ede-8bb9-3db2a07eeb6e", "when": null, @@ -1136,7 +1127,7 @@ } }, "tags": "", - "uuid": "3b4cd11c-7937-4679-bb3c-9b067ad8f567" + "uuid": "d7fb120d-41f4-4a67-a6fe-2885dcd33ebf" }, "tool_id": null, "type": "subworkflow", @@ -1218,4 +1209,4 @@ ], "uuid": "2196fbff-317e-437d-a022-696a1f95a850", "version": 4 -} +} \ No newline at end of file diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup-tests.yml similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup-tests.yml rename to workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup-tests.yml diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup.ga similarity index 99% rename from workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga rename to workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup.ga index 9f5c219b3..28c9666b7 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic_fastq_to_pairs_hicup.ga +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.3", "name": "Hi-C_fastqToPairs_hicup", "steps": { "0": { diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler-tests.yml similarity index 100% rename from workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler-tests.yml rename to workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler-tests.yml diff --git a/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga similarity index 93% rename from workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga rename to workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga index 65ef368d5..408e5ca35 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic_juicermediumtabix_to_cool_cooler.ga +++ b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2.1", + "release": "0.3", "name": "Hi-C_juicermediumtabixToCool_cooler", "steps": { "0": { @@ -123,7 +123,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -156,15 +156,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.8.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "c3dc51297bf8", + "changeset_revision": "ebd2a52eb245", "name": "cooler_makebins", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"binsize\": {\"__class__\": \"ConnectedValue\"}, \"size_source\": {\"size_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_cached\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.8.11+galaxy0", + "tool_version": "0.9.3+galaxy0", "type": "tool", "uuid": "34e0a213-93e8-466e-b07b-ede1443ee7d6", "when": null, @@ -172,7 +172,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -211,15 +211,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.8.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "3ff6eeca667e", + "changeset_revision": "0641e1c892c6", "name": "cooler_cload_tabix", "owner": "lldelisle", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assembly\": {\"__class__\": \"ConnectedValue\"}, \"format_sel\": {\"format\": \"juicer_medium\", \"__current_case__\": 0, \"input_pairs\": {\"__class__\": \"ConnectedValue\"}}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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