diff --git a/.ci/jenkins.sh b/.ci/jenkins.sh index a1342fcc..e4e72d2f 100755 --- a/.ci/jenkins.sh +++ b/.ci/jenkins.sh @@ -10,7 +10,7 @@ GALAXY_URL="http://127.0.0.1:${LOCAL_PORT}" SSH_MASTER_SOCKET_DIR="${HOME}/.cache/usegalaxy-tools" # Set to 'centos:7' and set GALAXY_GIT_* below to use a clone -GALAXY_DOCKER_IMAGE='galaxy/galaxy-min:21.05' +GALAXY_DOCKER_IMAGE='galaxy/galaxy-min:23.0' # Disable if using a locally built image e.g. for debugging GALAXY_DOCKER_IMAGE_PULL=true @@ -22,8 +22,6 @@ GALAXY_TEMPLATE_DB='galaxy.sqlite' # Need to run dev until 0.10.4 #EPHEMERIS="git+https://github.com/galaxyproject/ephemeris.git" -# Fix for not installing Conda deps: https://github.com/galaxyproject/ephemeris/pull/181 -EPHEMERIS="git+https://github.com/mvdbeek/ephemeris.git@fix_option_parsing_and_tool_id_handling" # Should be set by Jenkins, so the default here is for development : ${GIT_COMMIT:=$(git rev-parse HEAD)} @@ -474,12 +472,14 @@ function run_mounted_galaxy() { -e "GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=sqlite:////galaxy/server/database/${GALAXY_TEMPLATE_DB}" \ -e "GALAXY_CONFIG_OVERRIDE_INTEGRATED_TOOL_PANEL_CONFIG=/tmp/integrated_tool_panel.xml" \ -e "GALAXY_CONFIG_OVERRIDE_SHED_TOOL_CONFIG_FILE=${SHED_TOOL_CONFIG}" \ + -e "GALAXY_CONFIG_OVERRIDE_MIGRATED_TOOLS_CONFIG=/abcdef" \ -e "GALAXY_CONFIG_OVERRIDE_TOOL_SHEDS_CONFIG_FILE=/tool_sheds_conf.xml" \ -e "GALAXY_CONFIG_OVERRIDE_SHED_TOOL_DATA_TABLE_CONFIG=${SHED_TOOL_DATA_TABLE_CONFIG}" \ -e "GALAXY_CONFIG_OVERRIDE_SHED_DATA_MANAGER_CONFIG_FILE=${SHED_DATA_MANAGER_CONFIG}" \ -e "GALAXY_CONFIG_TOOL_DATA_PATH=/tmp/tool-data" \ -e "GALAXY_CONFIG_INSTALL_DATABASE_CONNECTION=sqlite:///${INSTALL_DATABASE}" \ -e "GALAXY_CONFIG_MASTER_API_KEY=${API_KEY:=deadbeef}" \ + -e "GALAXY_CONFIG_FILE=config/galaxy.yml.sample" \ -e "${CONDA_ENV_OPTION}" \ ${CONDA_EXEC_OPTION} \ -v "${OVERLAYFS_MOUNT}:/cvmfs/${REPO}" \ @@ -488,7 +488,7 @@ function run_mounted_galaxy() { -v "${GALAXY_SOURCE_TMPDIR}:/galaxy/server" \ -v "${GALAXY_DATABASE_TMPDIR}:/galaxy/server/database" \ --workdir /galaxy/server \ - "$GALAXY_DOCKER_IMAGE" ./.venv/bin/uwsgi --yaml config/galaxy.yml.sample + "$GALAXY_DOCKER_IMAGE" ./.venv/bin/gunicorn 'galaxy.webapps.galaxy.fast_factory:factory\(\)' --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b 0.0.0.0:8080 GALAXY_CONTAINER_UP=true } @@ -511,29 +511,22 @@ function run_cloudve_galaxy() { -e "GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=sqlite:////galaxy/server/database/${GALAXY_TEMPLATE_DB}" \ -e "GALAXY_CONFIG_OVERRIDE_INTEGRATED_TOOL_PANEL_CONFIG=/tmp/integrated_tool_panel.xml" \ -e "GALAXY_CONFIG_OVERRIDE_SHED_TOOL_CONFIG_FILE=${SHED_TOOL_CONFIG}" \ + -e "GALAXY_CONFIG_OVERRIDE_MIGRATED_TOOLS_CONFIG=/abcdef" \ -e "GALAXY_CONFIG_OVERRIDE_TOOL_SHEDS_CONFIG_FILE=/tool_sheds_conf.xml" \ -e "GALAXY_CONFIG_OVERRIDE_SHED_TOOL_DATA_TABLE_CONFIG=${SHED_TOOL_DATA_TABLE_CONFIG}" \ -e "GALAXY_CONFIG_OVERRIDE_SHED_DATA_MANAGER_CONFIG_FILE=${SHED_DATA_MANAGER_CONFIG}" \ -e "GALAXY_CONFIG_TOOL_DATA_PATH=/tmp/tool-data" \ -e "GALAXY_CONFIG_INSTALL_DATABASE_CONNECTION=sqlite:///${INSTALL_DATABASE}" \ -e "GALAXY_CONFIG_MASTER_API_KEY=${API_KEY:=deadbeef}" \ + -e "GALAXY_CONFIG_FILE=/galaxy/server/lib/galaxy/config/sample/galaxy.yml.sample" \ -e "${CONDA_ENV_OPTION}" \ ${CONDA_EXEC_OPTION} \ -v "${OVERLAYFS_MOUNT}:/cvmfs/${REPO}" \ -v "${WORKDIR}/tool_sheds_conf.xml:/tool_sheds_conf.xml" \ -v "${WORKDIR}/condarc:${CONDARC_MOUNT_PATH}" \ -v "${GALAXY_DATABASE_TMPDIR}:/galaxy/server/database" \ - "$GALAXY_DOCKER_IMAGE" ./.venv/bin/uwsgi --http :8080 \ - --virtualenv /galaxy/server/.venv --pythonpath /galaxy/server/lib \ - --master --offload-threads 2 --processes 1 --threads 4 --enable-threads \ - --buffer-size 16384 --thunder-lock --die-on-term --py-call-osafterfork \ - --module 'galaxy.webapps.galaxy.buildapp:uwsgi_app\(\)' \ - --hook-master-start '"unix_signal:2 gracefully_kill_them_all"' \ - --hook-master-start '"unix_signal:15 gracefully_kill_them_all"' \ - --static-map '/static/style=/galaxy/server/static/style/blue' \ - --static-map '/static=/galaxy/server/static' \ - --set 'galaxy_config_file=/galaxy/server/config/galaxy.yml' \ - --set 'galaxy_root=/galaxy/server' + --workdir /galaxy/server \ + "$GALAXY_DOCKER_IMAGE" ./.venv/bin/gunicorn 'galaxy.webapps.galaxy.fast_factory:factory\(\)' --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b 0.0.0.0:8080 #"$GALAXY_DOCKER_IMAGE" ./.venv/bin/uwsgi --yaml config/galaxy.yml # TODO: double quoting above probably breaks non-local mode GALAXY_CONTAINER_UP=true @@ -642,7 +635,7 @@ function install_tools() { for tool_yaml in "${TOOL_YAMLS[@]}"; do log "Installing tools in ${tool_yaml}" # FIXME: after https://github.com/galaxyproject/ephemeris/pull/181 is merged you would need to remove - # --skip_install_resolver_dependencies for install_resolver_dependencies in tools.yaml to work + # --skip_install_resolver_dependencies for install_resolver_dependencies: true in tools.yaml to work log_exec shed-tools install --skip_install_resolver_dependencies -v -g "$GALAXY_URL" -a "$API_KEY" -t "$tool_yaml" || { log_error "Tool installation failed" show_logs diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 00000000..a002f316 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,7 @@ +TODO: Please replace this header with a description of your pull request. + +## Installation sequence for `tool-installers` +- [ ] Test using `@galaxybot test this` +- [ ] Inspect CI output for expected changes +- [ ] Deploy using `@galaxybot deploy this` if test install was successful +- [ ] Merge this PR diff --git a/.github/workflows/static.yml b/.github/workflows/static.yml new file mode 100644 index 00000000..ea881062 --- /dev/null +++ b/.github/workflows/static.yml @@ -0,0 +1,52 @@ +# Simple workflow for deploying static content to GitHub Pages +name: Deploy static content to Pages + +on: + # Runs on pushes targeting the default branch + push: + branches: ["master"] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +permissions: + contents: read + pages: write + id-token: write + +# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. +# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. +concurrency: + group: "pages" + cancel-in-progress: false + +jobs: + # Single deploy job since we're just deploying + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + steps: + - uses: actions/setup-python@v2 + with: + python-version: '3.11' + architecture: 'x64' + - name: Checkout + uses: actions/checkout@v3 + - name: Setup Pages + uses: actions/configure-pages@v3 + - name: Install pyyaml + run: pip install PyYAML + - name: Build API + run: + python scripts/api.py + - name: Upload artifact + uses: actions/upload-pages-artifact@v2 + with: + # Upload entire repository + path: '.' + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v2 diff --git a/Makefile b/Makefile index 0fc7332f..a6d96f11 100644 --- a/Makefile +++ b/Makefile @@ -1,22 +1,23 @@ GALAXY_SERVER := https://usegalaxy.* +TOOLSET := usegalaxy.org help: @egrep '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[94m%-16s\033[0m %s\n", $$1, $$2}' lint: ## Lint all yaml files - find ./$(TOOLSET) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/fix-lockfile.py - find ./$(TOOLSET) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 -I{} pykwalify -d '{}' -s .schema.yml + find ./$(TOOLSET) -name '*.yml' ! -path .//.schema.yml | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/fix-lockfile.py + find ./$(TOOLSET) -name '*.yml' ! -path .//.schema.yml | grep '^\./[^/]*/' | xargs -n 1 -P 8 -I{} pykwalify -d '{}' -s .schema.yml fix: ## Fix all lockfiles and add any missing revisions @# Generates the lockfile or updates it if it is missing tools - find ./$(TOOLSET) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/fix-lockfile.py + find ./$(TOOLSET) -name '*.yml' ! -path .//.schema.yml | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/fix-lockfile.py @# --without says only add those hashes for those missing hashes (zB new tools) - find ./$(TOOLSET) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update-tool.py --without + find ./$(TOOLSET) -name '*.yml' ! -path .//.schema.yml | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update-tool.py --without fix-no-deps: - find ./$(TOOLSET) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/fix-lockfile.py --no-install-repository-dependencies --no-install-resolver-dependencies - find ./$(TOOLSET) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update-tool.py --without + find ./$(TOOLSET) -name '*.yml'! -path .//.schema.yml | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/fix-lockfile.py --no-install-repository-dependencies --no-install-resolver-dependencies + find ./$(TOOLSET) -name '*.yml' ! -path .//.schema.yml | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update-tool.py --without #install: #@echo "Installing any updated versions of $<" @@ -25,9 +26,9 @@ fix-no-deps: update-trusted: ## Run the update script for a subset of repos @# Missing --without, so this updates all tools in the file. - find ./$(TOOLSET) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update-tool.py --owner $(OWNER) + find ./$(TOOLSET) -name '*.yml' ! -path .//.schema.yml | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update-tool.py --owner $(OWNER) update-all: ## Run the update script for all repos - find ./$(TOOLSET) -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update-tool.py + find ./$(TOOLSET) -name '*.yml' ! -path .//.schema.yml | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/update-tool.py .PHONY: lint update-trusted update-all help fix diff --git a/README.md b/README.md index 836f0f40..5000ff2a 100644 --- a/README.md +++ b/README.md @@ -32,10 +32,32 @@ In your destination you should set: - Only IUC tools are automatically updated with the latest version each week - Use the provided `requirements.txt` to install dependences needed for the make targets -### Updating an Existing Tool - -1. Edit the .yaml.lock file to add the latest/specific changeset revision for the tool. You can use `python scripts/update-tool.py --owner --name ` in order to do this if you just want to add the latest revision. -2. Open a pull request +## Requesting a new tool or updating a tool + +*Anyone* can request tool installations or updates on [usegalaxy.org](https://usegalaxy.org/) or [test.galaxyproject.org](https://test.galaxyproject.org). +In the commands below fill the `{server_name}` as appropriate (usegalaxy.org, test.galaxyproject.org) + +1. Fork and clone [usegalaxy-tools](https://github.com/galaxyproject/usegalaxy-tools) +1. Create/activate a virtualenv and `pip install -r requirements.txt` +1. You are either installing a new repo or updating existing repo + - **NEW REPO** + 1. If this is a new a section without an existing yml file create a new one like this: + 1. Determine the desired section label + 1. Normalize the section label to an ID/filename with [this process](https://github.com/galaxyproject/usegalaxy-tools/issues/9#issuecomment-500847395) + 1. Create `{server_name}/.yml` setting `tool_panel_section_label` from the section label obtained in previous step (see existing yml files for exact syntax) + 1. Continue with the steps below + 1. Add the entry for the new tool to the section yml (only the yml, not the yml.lock) [example](https://github.com/galaxyproject/usegalaxy-tools/pull/86/files#diff-7de70f8620e8ba71104b398d57087611R25-R26) + 1. Run `$ make TOOLSET={server_name} fix` (this will fill the yml.lock ) + 1. Then `$ git add ` only the updates that you care about. + - **UPDATE REPO** + 1. Find the yml and yml.lock files with the repository entries. Add the changeset hash of repo's desired *installable revision* to the yml.lock file [example](https://github.com/galaxyproject/usegalaxy-tools/pull/80/files#diff-2e7bd27ec27fa6be24b5689cebc77defR62-R64) + - Alternatively, run `make TOOLSET={server_name} OWNER={repo_owner} update-trusted` for every owner in your yml file, then run `$ make TOOLSET={server_name} fix`, and then `$ git add ` only the updates that you care about. +1. Run `make TOOLSET={server_name} lint` +1. Commit `{server_name}/.yaml{.lock}` +1. Create a PR against the `master` branch of [usegalaxy-tools](https://github.com/galaxyproject/usegalaxy-tools) + - Use PR labels as appropriate + - To aid PR mergers, you can include information on tools in the repo's use of `$GALAXY_SLOTS`, or even PR any needed update(s) to [Main's job_conf.xml](https://github.com/galaxyproject/usegalaxy-playbook/blob/master/env/main/templates/galaxy/config/job_conf.xml.j2) as explained in the "[Determine tool requirements](#determine-tool-requirements)" section once the test installation (via Travis) succeeds (see details below) +1. Once the PR is merged and the tool appears on [usegalaxy.org](https://usegalaxy.org/) or [test.galaxyproject.org](https://test.galaxyproject.org), test to ensure the tool works ### Requesting a New Tool @@ -43,7 +65,7 @@ In your destination you should set: - Edit the .yaml file to add name/owner/section - If you want a specific version: - Edit the .yaml file to add name/owner/section - - Run `make fix` (or `make fix-no-deps` for non-Conda toolsets like `cloud`) + - Run `make fix-no-deps` - Edit the .yaml.lock to correct the version number. - Open a pull request diff --git a/cloud/bed.yml.lock b/cloud/bed.yml.lock index 47e33d07..8b9fd2da 100644 --- a/cloud/bed.yml.lock +++ b/cloud/bed.yml.lock @@ -7,5 +7,6 @@ tools: owner: iuc revisions: - ce3c7f062223 + - 07e8b80f278c tool_panel_section_id: bed tool_panel_section_label: BED diff --git a/cloud/collection_operations.yml.lock b/cloud/collection_operations.yml.lock index fb2b76ea..e09fdcd8 100644 --- a/cloud/collection_operations.yml.lock +++ b/cloud/collection_operations.yml.lock @@ -25,5 +25,6 @@ tools: owner: iuc revisions: - 071084070619 + - 58228a4d58fe tool_panel_section_id: collection_operations tool_panel_section_label: Collection Operations diff --git a/cloud/convert_formats.yml b/cloud/convert_formats.yml new file mode 100644 index 00000000..b2e4d664 --- /dev/null +++ b/cloud/convert_formats.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Convert Formats +tools: +- name: gtftobed12 + owner: iuc diff --git a/cloud/convert_formats.yml.lock b/cloud/convert_formats.yml.lock new file mode 100644 index 00000000..5bd06e1b --- /dev/null +++ b/cloud/convert_formats.yml.lock @@ -0,0 +1,10 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Convert Formats +tools: +- name: gtftobed12 + owner: iuc + revisions: + - b026dae67fba + tool_panel_section_label: Convert Formats diff --git a/cloud/datamash.yml.lock b/cloud/datamash.yml.lock index 04f2e335..2a6310bf 100644 --- a/cloud/datamash.yml.lock +++ b/cloud/datamash.yml.lock @@ -6,18 +6,20 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 0f1724dd59d2 + - f198773344e4 tool_panel_section_id: datamash tool_panel_section_label: Datamash - name: datamash_transpose owner: iuc revisions: + - 374cb875d38a + - ac092723240d - 22c2a1ac7ae3 tool_panel_section_id: datamash tool_panel_section_label: Datamash - name: datamash_ops owner: iuc revisions: - - 562f3c677828 + - 746e8e4bf929 tool_panel_section_id: datamash tool_panel_section_label: Datamash diff --git a/cloud/expressiontools.yml b/cloud/expressiontools.yml new file mode 100644 index 00000000..aa1f9b5d --- /dev/null +++ b/cloud/expressiontools.yml @@ -0,0 +1,6 @@ +tool_panel_section_label: Expression Tools +tools: +- name: map_param_value + owner: iuc +- name: compose_text_param + owner: iuc diff --git a/cloud/expressiontools.yml.lock b/cloud/expressiontools.yml.lock new file mode 100644 index 00000000..55f84f4b --- /dev/null +++ b/cloud/expressiontools.yml.lock @@ -0,0 +1,15 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Expression Tools +tools: +- name: map_param_value + owner: iuc + revisions: + - a01f088d0e5e + tool_panel_section_label: Expression Tools +- name: compose_text_param + owner: iuc + revisions: + - e188c9826e0f + tool_panel_section_label: Expression Tools diff --git a/cloud/fasta_fastq.yml b/cloud/fasta_fastq.yml index 79542ee2..e1eeaac2 100644 --- a/cloud/fasta_fastq.yml +++ b/cloud/fasta_fastq.yml @@ -18,3 +18,11 @@ tools: owner: iuc - name: trim_galore owner: bgruening +- name: umi_tools_count + owner: iuc +- name: umi_tools_extract + owner: iuc +- name: seq_filter_by_id + owner: peterjc +- name: length_and_gc_content + owner: iuc diff --git a/cloud/fasta_fastq.yml.lock b/cloud/fasta_fastq.yml.lock index 535ae889..f27cd622 100644 --- a/cloud/fasta_fastq.yml.lock +++ b/cloud/fasta_fastq.yml.lock @@ -7,6 +7,9 @@ tools: owner: lparsons revisions: - 093678460093 + - 135b80fb1ac2 + - c5e2e5902201 + - 660cffd8d92a tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fastq_filter @@ -57,3 +60,32 @@ tools: - 084bbd8ba7b8 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ +- name: umi_tools_count + owner: iuc + revisions: + - 8250ea3a1501 + - b557acca0b56 + - a535cf1e5da4 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: umi_tools_extract + owner: iuc + revisions: + - 6a675c3aa610 + - 99aea37a7ff7 + - f3759eec3018 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: seq_filter_by_id + owner: peterjc + revisions: + - 141612f8c3e3 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: length_and_gc_content + owner: iuc + revisions: + - e3ba567abdf5 + - f088370d2a3c + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ diff --git a/cloud/fastq_quality_control.yml.lock b/cloud/fastq_quality_control.yml.lock index 332a1ded..ee99a7bf 100644 --- a/cloud/fastq_quality_control.yml.lock +++ b/cloud/fastq_quality_control.yml.lock @@ -8,19 +8,25 @@ tools: revisions: - 75c93c70d094 - 9a913cdee30e + - df99138d2776 + - abfd8a6544d7 + - 5e33b465d8d5 + - 1c2db0054039 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: fastp owner: iuc revisions: + - 65b93b623c77 - dbf9c561ef29 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: fastqc owner: devteam revisions: - - e7b2202befea - 3d0c7bdf12f5 + - e7b2202befea + - 9da02be9c6cc tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: trimmomatic diff --git a/cloud/gemini.yml b/cloud/gemini.yml new file mode 100644 index 00000000..b2b22492 --- /dev/null +++ b/cloud/gemini.yml @@ -0,0 +1,8 @@ +tool_panel_section_label: GEMINI +tools: +- name: gemini_load + owner: iuc +- name: gemini_db_info + owner: iuc +- name: gemini_query + owner: iuc diff --git a/cloud/gemini.yml.lock b/cloud/gemini.yml.lock new file mode 100644 index 00000000..efee7ba5 --- /dev/null +++ b/cloud/gemini.yml.lock @@ -0,0 +1,23 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: GEMINI +tools: +- name: gemini_load + owner: iuc + revisions: + - 2270a8b83c12 + - cf61daf064fe + tool_panel_section_label: GEMINI +- name: gemini_db_info + owner: iuc + revisions: + - c2a413e47fe9 + - 4c5f4e9b1931 + tool_panel_section_label: GEMINI +- name: gemini_query + owner: iuc + revisions: + - 77a1e60fd1de + - 666f60a9331a + tool_panel_section_label: GEMINI diff --git a/cloud/get_data.yml.lock b/cloud/get_data.yml.lock index ed0e39cb..d406f524 100644 --- a/cloud/get_data.yml.lock +++ b/cloud/get_data.yml.lock @@ -6,8 +6,7 @@ tools: - name: sra_tools owner: iuc revisions: - - 69ebb7f46e45 - - e08a7ad4378b + - 83c7d564b128 tool_panel_section_id: get_data tool_panel_section_label: Get Data - name: ncbi_acc_download diff --git a/cloud/graph_display_data.yml b/cloud/graph_display_data.yml index 92518162..6056dfbd 100644 --- a/cloud/graph_display_data.yml +++ b/cloud/graph_display_data.yml @@ -8,3 +8,7 @@ tools: owner: iuc - name: volcanoplot owner: iuc +- name: pathview + owner: iuc +- name: ggplot2_heatmap2 + owner: iuc diff --git a/cloud/graph_display_data.yml.lock b/cloud/graph_display_data.yml.lock index b6794cd7..9bb0af2a 100644 --- a/cloud/graph_display_data.yml.lock +++ b/cloud/graph_display_data.yml.lock @@ -25,6 +25,22 @@ tools: - name: volcanoplot owner: iuc revisions: + - 83c573f2e73c - 73b8cb5bddcd tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data +- name: pathview + owner: iuc + revisions: + - f1691de443a7 + - fe154a7af404 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: ggplot2_heatmap2 + owner: iuc + revisions: + - 53460afd5115 + - 566197475670 + - 4955e9bb96d1 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data diff --git a/cloud/mapping.yml b/cloud/mapping.yml index df6e8b1b..19f61388 100644 --- a/cloud/mapping.yml +++ b/cloud/mapping.yml @@ -10,3 +10,7 @@ tools: owner: iuc - name: lastz owner: devteam +- name: rgrnastar + owner: iuc +- name: rna_starsolo + owner: iuc diff --git a/cloud/mapping.yml.lock b/cloud/mapping.yml.lock index df085613..3ba7e81e 100644 --- a/cloud/mapping.yml.lock +++ b/cloud/mapping.yml.lock @@ -18,6 +18,7 @@ tools: - name: bwa owner: devteam revisions: + - e188dc7a68e6 - 3fe632431b68 tool_panel_section_id: mapping tool_panel_section_label: Mapping @@ -33,3 +34,18 @@ tools: - e7f19d6a9af8 tool_panel_section_id: mapping tool_panel_section_label: Mapping +- name: rgrnastar + owner: iuc + revisions: + - c772497b2c32 + - 2055c2667eb3 + - 980d2a2e1180 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: rna_starsolo + owner: iuc + revisions: + - eec9494fdafa + - 79b885ce78d7 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping diff --git a/cloud/picard.yml.lock b/cloud/picard.yml.lock index b9fff8a4..43de521c 100644 --- a/cloud/picard.yml.lock +++ b/cloud/picard.yml.lock @@ -6,6 +6,8 @@ tools: - name: picard owner: devteam revisions: + - b502c227b5e6 - a1f0b3f4b781 + - b9fbec5ac6b2 tool_panel_section_id: picard tool_panel_section_label: Picard diff --git a/cloud/qiime2.yml b/cloud/qiime2.yml new file mode 100644 index 00000000..8258f75b --- /dev/null +++ b/cloud/qiime2.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: QIIME2 +tools: +- name: suite_qiime2_core + owner: q2d2 \ No newline at end of file diff --git a/cloud/qiime2.yml.lock b/cloud/qiime2.yml.lock new file mode 100644 index 00000000..07ddd228 --- /dev/null +++ b/cloud/qiime2.yml.lock @@ -0,0 +1,10 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: QIIME2 +tools: +- name: suite_qiime2_core + owner: q2d2 + revisions: + - 3f011fac899d + tool_panel_section_label: QIIME2 \ No newline at end of file diff --git a/cloud/rna_seq.yml b/cloud/rna_seq.yml index 5aac245b..07a71a81 100644 --- a/cloud/rna_seq.yml +++ b/cloud/rna_seq.yml @@ -18,3 +18,15 @@ tools: owner: iuc - name: stringtie owner: iuc +- name: featurecounts + owner: iuc +- name: cufflinks + owner: devteam +- name: deg_annotate + owner: iuc +- name: goseq + owner: iuc +- name: egsea + owner: iuc +- name: fgsea + owner: iuc diff --git a/cloud/rna_seq.yml.lock b/cloud/rna_seq.yml.lock index 69776778..ff854f22 100644 --- a/cloud/rna_seq.yml.lock +++ b/cloud/rna_seq.yml.lock @@ -24,6 +24,8 @@ tools: - name: deseq2 owner: iuc revisions: + - 8fe98f7094de + - cd9874cb9019 - 6a3a025714d3 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq @@ -31,6 +33,8 @@ tools: owner: iuc revisions: - 0921444c832d + - d6f5fa4ee473 + - d5a940112511 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: edger @@ -49,6 +53,8 @@ tools: owner: iuc revisions: - 26371a1df031 + - f4af63aaf57a + - 61ee47027bd3 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: stringtie @@ -57,3 +63,42 @@ tools: - 1ebd14235b92 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq +- name: featurecounts + owner: iuc + revisions: + - 38b6d12edc68 + - f3a5f075498f + - 1759d845181e + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: cufflinks + owner: devteam + revisions: + - d080005cffe1 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: deg_annotate + owner: iuc + revisions: + - e98d4ab5b5bc + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: goseq + owner: iuc + revisions: + - 602de62d995b + - ef2ad746b589 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: egsea + owner: iuc + revisions: + - fba1660fb717 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: fgsea + owner: iuc + revisions: + - 17eb1e0d711f + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq diff --git a/cloud/rseqc.yml.lock b/cloud/rseqc.yml.lock index 3efbf8a4..927bce22 100644 --- a/cloud/rseqc.yml.lock +++ b/cloud/rseqc.yml.lock @@ -7,5 +7,6 @@ tools: owner: nilesh revisions: - 1a052c827e88 + - dbedfc5f5a3c tool_panel_section_id: rseqc tool_panel_section_label: RSeQC diff --git a/cloud/sam_bam.yml b/cloud/sam_bam.yml index 88b47b31..c2788637 100644 --- a/cloud/sam_bam.yml +++ b/cloud/sam_bam.yml @@ -62,3 +62,5 @@ tools: owner: boris - name: sam_merge owner: devteam +- name: revertr2orientationinbam + owner: lldelisle diff --git a/cloud/sam_bam.yml.lock b/cloud/sam_bam.yml.lock index 4061e047..2a0a9941 100644 --- a/cloud/sam_bam.yml.lock +++ b/cloud/sam_bam.yml.lock @@ -18,6 +18,8 @@ tools: - name: samtools_view owner: iuc revisions: + - 5826298f6a73 + - 0dbf49c414ae - b72793637686 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM @@ -61,18 +63,21 @@ tools: owner: devteam revisions: - b5c3b1856370 + - 1e5880498f52 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_merge owner: iuc revisions: - 740ce0a18f0d + - 36677f429310 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_markdup owner: iuc revisions: - 83b8e36e9cbe + - b5527cc104ab tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_fixmate @@ -97,6 +102,7 @@ tools: owner: devteam revisions: - 145f6d74ff5e + - 24c5d43cb545 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_split @@ -121,6 +127,8 @@ tools: owner: devteam revisions: - 7a6034296ae9 + - 7def34e6cf4d + - 811fc2d75ad4 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtool_filter2 @@ -157,6 +165,8 @@ tools: owner: devteam revisions: - cb20f99fd45b + - bd735cae4ce6 + - 108db6635177 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: sam_to_bam @@ -189,3 +199,9 @@ tools: - 1977f1637890 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM +- name: revertr2orientationinbam + owner: lldelisle + revisions: + - 21ddefab2e4f + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM diff --git a/cloud/single_cell.yml b/cloud/single_cell.yml new file mode 100644 index 00000000..11f96bfa --- /dev/null +++ b/cloud/single_cell.yml @@ -0,0 +1,169 @@ +tool_panel_section_label: Single-cell +tools: + - name: music_compare + owner: bgruening + + - name: music_manipulate_eset + owner: bgruening + + - name: music_inspect_eset + owner: bgruening + + - name: music_deconvolution + owner: bgruening + + - name: music_construct_eset + owner: bgruening + + - name: 10x_bamtofastq + owner: bgruening + + - name: anndata_import + owner: iuc + + - name: anndata_export + owner: iuc + + - name: anndata_manipulate + owner: iuc + + - name: chromeister + owner: iuc + + - name: anndata_inspect + owner: iuc + + - name: modify_loom + owner: iuc + + - name: dropletutils + owner: iuc + + - name: dropletutils_read_10x + owner: ebi-gxa + + - name: dropletutils_empty_drops + owner: ebi-gxa + + - name: droplet_barcode_plot + owner: ebi-gxa + + - name: raceid_inspectclusters + owner: iuc + + - name: raceid_filtnormconf + owner: iuc + + - name: raceid_clustering + owner: iuc + + - name: raceid_trajectory + owner: iuc + + - name: raceid_inspecttrajectory + owner: iuc + + - name: alevin + owner: bgruening + + - name: salmonquantmerge + owner: bgruening + + - name: slice_image + owner: imgteam + + - name: scater_create_qcmetric_ready_sce + owner: iuc + + - name: scater_plot_tsne + owner: iuc + + - name: scater_filter + owner: iuc + + - name: scater_normalize + owner: iuc + + - name: scater_plot_dist_scatter + owner: iuc + + - name: scater_plot_exprs_freq + owner: iuc + + - name: scater_plot_pca + owner: iuc + + - name: scanpy_cluster_reduce_dimension + owner: iuc + + - name: scanpy_filter + owner: iuc + + - name: scanpy_inspect + owner: iuc + + - name: scanpy_normalize + owner: iuc + + - name: scanpy_plot + owner: iuc + + - name: scanpy_remove_confounders + owner: iuc + + - name: scanpy_read_10x + owner: ebi-gxa + + - name: gtf2gene_list + owner: ebi-gxa + + - name: salmon_kallisto_mtx_to_10x + owner: ebi-gxa + + - name: sceasy_convert + owner: ebi-gxa + + - name: anndata_ops + owner: ebi-gxa + + - name: retrieve_scxa + owner: ebi-gxa + + - name: scanpy_parameter_iterator + owner: ebi-gxa + + - name: scanpy_filter_cells + owner: ebi-gxa + + - name: scanpy_filter_genes + owner: ebi-gxa + + - name: scanpy_normalise_data + owner: ebi-gxa + + - name: scanpy_find_variable_genes + owner: ebi-gxa + + - name: scanpy_scale_data + owner: ebi-gxa + + - name: scanpy_run_pca + owner: ebi-gxa + + - name: scanpy_compute_graph + owner: ebi-gxa + + - name: scanpy_run_tsne + owner: ebi-gxa + + - name: scanpy_run_umap + owner: ebi-gxa + + - name: scanpy_find_cluster + owner: ebi-gxa + + - name: scanpy_find_markers + owner: ebi-gxa + + - name: scanpy_plot_embed + owner: ebi-gxa diff --git a/cloud/single_cell.yml.lock b/cloud/single_cell.yml.lock new file mode 100644 index 00000000..9c72c162 --- /dev/null +++ b/cloud/single_cell.yml.lock @@ -0,0 +1,375 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Single-cell +tools: +- name: music_compare + owner: bgruening + revisions: + - 4447ed460308 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_manipulate_eset + owner: bgruening + revisions: + - 22232092be53 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_inspect_eset + owner: bgruening + revisions: + - 2fed32b5aa02 + - 7705cc75ac18 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_deconvolution + owner: bgruening + revisions: + - 2ba99a52bd44 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_construct_eset + owner: bgruening + revisions: + - 282819d09a4f + - 2cfd0db49bbc + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: 10x_bamtofastq + owner: bgruening + revisions: + - f71fd828c126 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: anndata_import + owner: iuc + revisions: + - 55e35e9203cf + - fb9e030ffae4 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: anndata_export + owner: iuc + revisions: + - 707023fa62fe + - 0cb889db0910 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: anndata_manipulate + owner: iuc + revisions: + - 9bd945a03d7b + - 3d748954434b + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: chromeister + owner: iuc + revisions: + - e483be1014b6 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: anndata_inspect + owner: iuc + revisions: + - 688357ad5e61 + - 286a24ac079c + - ee98d611afc6 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: modify_loom + owner: iuc + revisions: + - 05631436cdf1 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: dropletutils + owner: iuc + revisions: + - a9caad671439 + - 2c1200fba922 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: dropletutils_read_10x + owner: ebi-gxa + revisions: + - ca62f52e0d7f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: dropletutils_empty_drops + owner: ebi-gxa + revisions: + - fa662ca7ae7f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: droplet_barcode_plot + owner: ebi-gxa + revisions: + - 8f605643ccfd + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: raceid_inspectclusters + owner: iuc + revisions: + - 2b0d3e2f402a + - 41f34e925bd5 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: raceid_filtnormconf + owner: iuc + revisions: + - c891d8b33ede + - 43c146e25a43 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: raceid_clustering + owner: iuc + revisions: + - a4b734cd253b + - f911a64454fb + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: raceid_trajectory + owner: iuc + revisions: + - 72979cac22b2 + - c92d0f9338c5 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: raceid_inspecttrajectory + owner: iuc + revisions: + - c8434a623268 + - df8e4e54d367 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: alevin + owner: bgruening + revisions: + - 04b494623f8e + - e4c01dcece8b + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: salmonquantmerge + owner: bgruening + revisions: + - 88c07fc4024c + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: slice_image + owner: imgteam + revisions: + - 8856a7c85e4c + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_create_qcmetric_ready_sce + owner: iuc + revisions: + - 8f333f90d8d6 + - fd808de478b1 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_plot_tsne + owner: iuc + revisions: + - 99f912d5af9f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_filter + owner: iuc + revisions: + - 652923ce664f + - b7ea9f09c02f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_normalize + owner: iuc + revisions: + - 946179ef029c + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_plot_dist_scatter + owner: iuc + revisions: + - 2e41b35b5bdd + - ef4c80837bc5 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_plot_exprs_freq + owner: iuc + revisions: + - 058b40656107 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_plot_pca + owner: iuc + revisions: + - 46fc6751d746 + - c99ba278dfa9 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_cluster_reduce_dimension + owner: iuc + revisions: + - aaa5da8e73a9 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_filter + owner: iuc + revisions: + - b409c2486353 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_inspect + owner: iuc + revisions: + - c5d3684f7c4c + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_normalize + owner: iuc + revisions: + - ab55fe8030b6 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_plot + owner: iuc + revisions: + - aa0c474463c2 + - a8f865950ac4 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_remove_confounders + owner: iuc + revisions: + - bf2017df9837 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_read_10x + owner: ebi-gxa + revisions: + - c8391a25dee3 + - d92e6f12b790 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: gtf2gene_list + owner: ebi-gxa + revisions: + - 1a642de6db01 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: salmon_kallisto_mtx_to_10x + owner: ebi-gxa + revisions: + - 88f5a0a6a818 + - e42c217a450f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: sceasy_convert + owner: ebi-gxa + revisions: + - f62bc418173f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: anndata_ops + owner: ebi-gxa + revisions: + - 54f1212d26ac + - 6aa025ea64d3 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: retrieve_scxa + owner: ebi-gxa + revisions: + - 72b6e1747e37 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_parameter_iterator + owner: ebi-gxa + revisions: + - 0387a2179f88 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_filter_cells + owner: ebi-gxa + revisions: + - 4c42e5d8cb7c + - ba64b91ed2b9 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_filter_genes + owner: ebi-gxa + revisions: + - 7857ea93a011 + - a1698b43abeb + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_normalise_data + owner: ebi-gxa + revisions: + - 439f7f939d46 + - 463d4fa8f5ec + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_find_variable_genes + owner: ebi-gxa + revisions: + - 0edb75c411a4 + - 5c62f39aab8f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_scale_data + owner: ebi-gxa + revisions: + - 9664a6c00fd1 + - c6e52529260e + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_run_pca + owner: ebi-gxa + revisions: + - 988edd5fa902 + - ce93e630b55a + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_compute_graph + owner: ebi-gxa + revisions: + - 2401808e20e8 + - a58d4166805b + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_run_tsne + owner: ebi-gxa + revisions: + - 384cacc40611 + - 8eff7ec034e3 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_run_umap + owner: ebi-gxa + revisions: + - 0f98603d0116 + - abae3d11d920 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_find_cluster + owner: ebi-gxa + revisions: + - 35caf3c27c91 + - 9e4f79e40b84 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_find_markers + owner: ebi-gxa + revisions: + - eb01a7e59e9a + - f04dd4e5b6a7 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_plot_embed + owner: ebi-gxa + revisions: + - 99dd7baf9e23 + - a8ef4bc35839 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell diff --git a/cloud/text_manipulation.yml b/cloud/text_manipulation.yml index f2c1ab50..49461ad5 100644 --- a/cloud/text_manipulation.yml +++ b/cloud/text_manipulation.yml @@ -38,3 +38,5 @@ tools: owner: bgruening - name: diff owner: bgruening +- name: merge_cols + owner: devteam diff --git a/cloud/text_manipulation.yml.lock b/cloud/text_manipulation.yml.lock index 87172605..4965bf71 100644 --- a/cloud/text_manipulation.yml.lock +++ b/cloud/text_manipulation.yml.lock @@ -12,12 +12,13 @@ tools: - name: query_tabular owner: iuc revisions: - - 83069b38aa85 + - cf34c344508d tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: column_maker owner: devteam revisions: + - 6595517c2dd8 - 02026300aa45 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation @@ -30,7 +31,10 @@ tools: - name: annotatemyids owner: iuc revisions: + - 133f36c29579 - 44018dd6b447 + - fe3ca740a485 + - 1a125daea0d8 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: concatenate_multiple_datasets @@ -48,6 +52,7 @@ tools: - name: table_compute owner: iuc revisions: + - 3bf5661c0280 - 60ff16842fcd tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation @@ -66,7 +71,10 @@ tools: - name: text_processing owner: bgruening revisions: + - d698c222f354 - ddf54b12c295 + - 9ff72e942410 + - 74a8bef53a00 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: reshape2_melt @@ -117,3 +125,10 @@ tools: - 156d0908e232 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation +- name: merge_cols + owner: devteam + revisions: + - ae7843d06f8f + - f2aac0c5c60d + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation diff --git a/cloud/variant_calling.yml.lock b/cloud/variant_calling.yml.lock index f4d9410e..9e7bd2eb 100644 --- a/cloud/variant_calling.yml.lock +++ b/cloud/variant_calling.yml.lock @@ -6,13 +6,16 @@ tools: - name: snpfreqplot owner: iuc revisions: + - 3d0adeee3f2b - e362b3143cde tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: lofreq_call owner: iuc revisions: + - 4805fe3d8fda - e1461b5c52a0 + - 65432c3abf6c tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: lofreq_viterbi @@ -42,7 +45,9 @@ tools: - name: freebayes owner: devteam revisions: + - a5937157062f - ef2c525bd8cd + - 156b60c1530f tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: snpsift_genesets @@ -60,8 +65,10 @@ tools: - name: snpeff owner: iuc revisions: + - 5b80f544c67f - 74aebe30fb52 - cfcf33df7fc0 + - 68693743661e tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: snpsift diff --git a/cloud/vcf_bcf.yml.lock b/cloud/vcf_bcf.yml.lock index e2300469..eb159bac 100644 --- a/cloud/vcf_bcf.yml.lock +++ b/cloud/vcf_bcf.yml.lock @@ -199,6 +199,7 @@ tools: owner: devteam revisions: - 57a16b310fe8 + - f49b23b41a12 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: vcfannotate diff --git a/common_toolset/annotation.yml b/common_toolset/annotation.yml deleted file mode 100644 index 7e0411ae..00000000 --- a/common_toolset/annotation.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: Annotation -tools: -- name: prokka - owner: crs4 -- name: busco - owner: iuc -- name: mlst - owner: iuc -- name: abricate - owner: iuc -- name: hammock - owner: hammock -- name: roary - owner: iuc -- name: gubbins - owner: iuc -- name: probmetab - owner: mmonsoor -- name: lcmsmatching - owner: prog diff --git a/common_toolset/annotation.yml.lock b/common_toolset/annotation.yml.lock deleted file mode 100644 index 8782d430..00000000 --- a/common_toolset/annotation.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Annotation -tools: -- name: prokka - owner: crs4 - revisions: - - eaee459f3d69 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: busco - owner: iuc - revisions: - - 1440ae06552f - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: mlst - owner: iuc - revisions: - - 1f5641a52664 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: abricate - owner: iuc - revisions: - - 78c75f134c16 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: hammock - owner: hammock - revisions: - - afddbcbc8ee8 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: roary - owner: iuc - revisions: - - f1ccc8a6eb05 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: gubbins - owner: iuc - revisions: - - 637ec5d5368c - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: probmetab - owner: mmonsoor - revisions: - - 52b222a626b0 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation -- name: lcmsmatching - owner: prog - revisions: - - f86fec07f392 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation diff --git a/common_toolset/assembly.yml b/common_toolset/assembly.yml deleted file mode 100644 index 840bc09e..00000000 --- a/common_toolset/assembly.yml +++ /dev/null @@ -1,14 +0,0 @@ -tool_panel_section_label: Assembly -tools: -- name: unicycler - owner: iuc -- name: quast - owner: iuc -- name: spades - owner: nml -- name: shovill - owner: iuc -- name: velvetoptimiser - owner: simon-gladman -- name: pilon - owner: iuc diff --git a/common_toolset/assembly.yml.lock b/common_toolset/assembly.yml.lock deleted file mode 100644 index af625809..00000000 --- a/common_toolset/assembly.yml.lock +++ /dev/null @@ -1,41 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Assembly -tools: -- name: unicycler - owner: iuc - revisions: - - 0a3a602cd1e3 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: quast - owner: iuc - revisions: - - f30d03867854 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: spades - owner: nml - revisions: - - b8d633fbf5f5 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: shovill - owner: iuc - revisions: - - 865119fcb694 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: velvetoptimiser - owner: simon-gladman - revisions: - - 37d88f41c810 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly -- name: pilon - owner: iuc - revisions: - - 11e5408fd238 - tool_panel_section_id: assembly - tool_panel_section_label: Assembly diff --git a/common_toolset/bed.yml b/common_toolset/bed.yml deleted file mode 100644 index a97a3e41..00000000 --- a/common_toolset/bed.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: BED -tools: -- name: bedtools - owner: iuc diff --git a/common_toolset/bed.yml.lock b/common_toolset/bed.yml.lock deleted file mode 100644 index b58e983f..00000000 --- a/common_toolset/bed.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: BED -tools: -- name: bedtools - owner: iuc - revisions: - - dde39ba9c031 - tool_panel_section_id: bed - tool_panel_section_label: BED diff --git a/common_toolset/chip_seq.yml b/common_toolset/chip_seq.yml deleted file mode 100644 index 3eb9692d..00000000 --- a/common_toolset/chip_seq.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: ChIP-seq -tools: -- name: chipseeker - owner: rnateam -- name: macs2 - owner: iuc -- name: sicer - owner: devteam -- name: ngsutils_bam_filter - owner: iuc -- name: diffbind - owner: bgruening -- name: tag_pileup_frequency - owner: iuc -- name: fasta_nucleotide_color_plot - owner: iuc -- name: resize_coordinate_window - owner: iuc -- name: macs - owner: devteam diff --git a/common_toolset/chip_seq.yml.lock b/common_toolset/chip_seq.yml.lock deleted file mode 100644 index eb26d727..00000000 --- a/common_toolset/chip_seq.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: ChIP-seq -tools: -- name: chipseeker - owner: rnateam - revisions: - - 1b9a9409831d - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: macs2 - owner: iuc - revisions: - - 424aefbd7777 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: sicer - owner: devteam - revisions: - - 74c9214cc8e6 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: ngsutils_bam_filter - owner: iuc - revisions: - - 2e957d4c4b95 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: diffbind - owner: bgruening - revisions: - - c97a786e8fb5 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: tag_pileup_frequency - owner: iuc - revisions: - - 6432735cdb22 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: fasta_nucleotide_color_plot - owner: iuc - revisions: - - e4b5401adcec - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: resize_coordinate_window - owner: iuc - revisions: - - 9ba78e8985dc - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq -- name: macs - owner: devteam - revisions: - - f6319b0b4391 - tool_panel_section_id: chip_seq - tool_panel_section_label: ChIP-seq diff --git a/common_toolset/chromosome_conformation.yml b/common_toolset/chromosome_conformation.yml deleted file mode 100644 index 3a0dd5e3..00000000 --- a/common_toolset/chromosome_conformation.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Chromosome Conformation -tools: -- name: hifive - owner: sauria diff --git a/common_toolset/chromosome_conformation.yml.lock b/common_toolset/chromosome_conformation.yml.lock deleted file mode 100644 index 30cd3d9e..00000000 --- a/common_toolset/chromosome_conformation.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Chromosome Conformation -tools: -- name: hifive - owner: sauria - revisions: - - cc95aa05f643 - tool_panel_section_id: chromosome_conformation - tool_panel_section_label: Chromosome Conformation diff --git a/common_toolset/collection_operations.yml b/common_toolset/collection_operations.yml deleted file mode 100644 index a6a37c4a..00000000 --- a/common_toolset/collection_operations.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Collection Operations -tools: -- name: collection_column_join - owner: iuc -- name: collapse_collections - owner: nml diff --git a/common_toolset/collection_operations.yml.lock b/common_toolset/collection_operations.yml.lock deleted file mode 100644 index cbb61c3b..00000000 --- a/common_toolset/collection_operations.yml.lock +++ /dev/null @@ -1,17 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Collection Operations -tools: -- name: collection_column_join - owner: iuc - revisions: - - 071084070619 - tool_panel_section_id: collection_operations - tool_panel_section_label: Collection Operations -- name: collapse_collections - owner: nml - revisions: - - 25136a2b0cfe - tool_panel_section_id: collection_operations - tool_panel_section_label: Collection Operations diff --git a/common_toolset/convert_formats.yml b/common_toolset/convert_formats.yml deleted file mode 100644 index 5b996965..00000000 --- a/common_toolset/convert_formats.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: Convert Formats -tools: -- name: tabular_to_fasta - owner: devteam -- name: fasta_to_tabular - owner: devteam -- name: intermine_galaxy_exchange - owner: iuc -- name: bam_to_scidx - owner: iuc -- name: fastq_to_fasta - owner: devteam -- name: tabular_to_fastq - owner: devteam -- name: fastqtofasta - owner: devteam -- name: fastq_to_tabular - owner: devteam -- name: idpquery - owner: galaxyp diff --git a/common_toolset/convert_formats.yml.lock b/common_toolset/convert_formats.yml.lock deleted file mode 100644 index db897873..00000000 --- a/common_toolset/convert_formats.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Convert Formats -tools: -- name: tabular_to_fasta - owner: devteam - revisions: - - 0b4e36026794 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: fasta_to_tabular - owner: devteam - revisions: - - 7e801ab2b70e - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: intermine_galaxy_exchange - owner: iuc - revisions: - - c24014d80001 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: bam_to_scidx - owner: iuc - revisions: - - 408520e1ae1a - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: fastq_to_fasta - owner: devteam - revisions: - - 02a5f43cd5d1 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: tabular_to_fastq - owner: devteam - revisions: - - b8cdc0507586 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: fastqtofasta - owner: devteam - revisions: - - 4844c1810c16 - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: fastq_to_tabular - owner: devteam - revisions: - - ccf4e1d1fcbe - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats -- name: idpquery - owner: galaxyp - revisions: - - 66c38e74d1ae - tool_panel_section_id: convert_formats - tool_panel_section_label: Convert Formats diff --git a/common_toolset/datamash.yml b/common_toolset/datamash.yml deleted file mode 100644 index 662eb7df..00000000 --- a/common_toolset/datamash.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Datamash -tools: -- name: datamash_ops - owner: iuc -- name: datamash_transpose - owner: iuc -- name: datamash_reverse - owner: iuc diff --git a/common_toolset/datamash.yml.lock b/common_toolset/datamash.yml.lock deleted file mode 100644 index c70a8d8f..00000000 --- a/common_toolset/datamash.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Datamash -tools: -- name: datamash_ops - owner: iuc - revisions: - - 562f3c677828 - tool_panel_section_id: datamash - tool_panel_section_label: Datamash -- name: datamash_transpose - owner: iuc - revisions: - - 22c2a1ac7ae3 - tool_panel_section_id: datamash - tool_panel_section_label: Datamash -- name: datamash_reverse - owner: iuc - revisions: - - 0f1724dd59d2 - tool_panel_section_id: datamash - tool_panel_section_label: Datamash diff --git a/common_toolset/deeptools.yml b/common_toolset/deeptools.yml deleted file mode 100644 index 446f542a..00000000 --- a/common_toolset/deeptools.yml +++ /dev/null @@ -1,36 +0,0 @@ -tool_panel_section_label: deepTools -tools: -- name: deeptools_plot_profile - owner: bgruening -- name: deeptools_bam_coverage - owner: bgruening -- name: deeptools_plot_pca - owner: bgruening -- name: deeptools_plot_heatmap - owner: bgruening -- name: deeptools_plot_fingerprint - owner: bgruening -- name: deeptools_plot_enrichment - owner: bgruening -- name: deeptools_plot_coverage - owner: bgruening -- name: deeptools_plot_correlation - owner: bgruening -- name: deeptools_multi_bigwig_summary - owner: bgruening -- name: deeptools_multi_bam_summary - owner: bgruening -- name: deeptools_correct_gc_bias - owner: bgruening -- name: deeptools_compute_matrix - owner: bgruening -- name: deeptools_compute_gc_bias - owner: bgruening -- name: deeptools_bigwig_compare - owner: bgruening -- name: deeptools_bam_pe_fragmentsize - owner: bgruening -- name: deeptools_bam_compare - owner: bgruening -- name: deeptools_compute_matrix_operations - owner: bgruening diff --git a/common_toolset/deeptools.yml.lock b/common_toolset/deeptools.yml.lock deleted file mode 100644 index fee67610..00000000 --- a/common_toolset/deeptools.yml.lock +++ /dev/null @@ -1,107 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: deepTools -tools: -- name: deeptools_plot_profile - owner: bgruening - revisions: - - d806504e96d9 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_bam_coverage - owner: bgruening - revisions: - - 7a7fd0f5f15d - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_pca - owner: bgruening - revisions: - - aa200e4f3939 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_heatmap - owner: bgruening - revisions: - - a7849312d328 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_fingerprint - owner: bgruening - revisions: - - d57251071381 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_enrichment - owner: bgruening - revisions: - - d9114ef1c8a5 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_coverage - owner: bgruening - revisions: - - 4e12ea27f788 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_plot_correlation - owner: bgruening - revisions: - - bd7db9e2f2cb - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_multi_bigwig_summary - owner: bgruening - revisions: - - 2f9e4843f480 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_multi_bam_summary - owner: bgruening - revisions: - - 69a8621ca2f0 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_correct_gc_bias - owner: bgruening - revisions: - - c34d11ea4ba6 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_compute_matrix - owner: bgruening - revisions: - - b73e213add0c - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_compute_gc_bias - owner: bgruening - revisions: - - b8858746dc1f - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_bigwig_compare - owner: bgruening - revisions: - - 71aa86af6762 - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_bam_pe_fragmentsize - owner: bgruening - revisions: - - 1d848bc4585f - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_bam_compare - owner: bgruening - revisions: - - 268e91e540ee - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools -- name: deeptools_compute_matrix_operations - owner: bgruening - revisions: - - c3e012dfe21f - tool_panel_section_id: deeptools - tool_panel_section_label: deepTools diff --git a/common_toolset/emboss.yml b/common_toolset/emboss.yml deleted file mode 100644 index a6f95ed2..00000000 --- a/common_toolset/emboss.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: EMBOSS -tools: -- name: emboss_5 - owner: devteam diff --git a/common_toolset/emboss.yml.lock b/common_toolset/emboss.yml.lock deleted file mode 100644 index 04676c6d..00000000 --- a/common_toolset/emboss.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: EMBOSS -tools: -- name: emboss_5 - owner: devteam - revisions: - - dc492eb6a4fc - tool_panel_section_id: emboss - tool_panel_section_label: EMBOSS diff --git a/common_toolset/epigenetics.yml b/common_toolset/epigenetics.yml deleted file mode 100644 index 0335c7a4..00000000 --- a/common_toolset/epigenetics.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Epigenetics -tools: -- name: vcf_filter - owner: devteam -- name: hicup_deduplicator - owner: bgruening diff --git a/common_toolset/epigenetics.yml.lock b/common_toolset/epigenetics.yml.lock deleted file mode 100644 index de7b5503..00000000 --- a/common_toolset/epigenetics.yml.lock +++ /dev/null @@ -1,17 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Epigenetics -tools: -- name: vcf_filter - owner: devteam - revisions: - - da1a6f33b504 - tool_panel_section_id: epigenetics - tool_panel_section_label: Epigenetics -- name: hicup_deduplicator - owner: bgruening - revisions: - - 46e5b4782715 - tool_panel_section_id: epigenetics - tool_panel_section_label: Epigenetics diff --git a/common_toolset/evolution.yml b/common_toolset/evolution.yml deleted file mode 100644 index a19b0471..00000000 --- a/common_toolset/evolution.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Evolution -tools: -- name: iqtree - owner: iuc diff --git a/common_toolset/evolution.yml.lock b/common_toolset/evolution.yml.lock deleted file mode 100644 index 4ec72870..00000000 --- a/common_toolset/evolution.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Evolution -tools: -- name: iqtree - owner: iuc - revisions: - - d1c340a5664b - tool_panel_section_id: evolution - tool_panel_section_label: Evolution diff --git a/common_toolset/fastafastq.yml b/common_toolset/fastafastq.yml deleted file mode 100644 index df05370a..00000000 --- a/common_toolset/fastafastq.yml +++ /dev/null @@ -1,72 +0,0 @@ -tool_panel_section_label: FASTA/FASTQ -tools: -- name: find_subsequences - owner: bgruening -- name: cutadapt - owner: lparsons -- name: flash - owner: iuc -- name: fastx_trimmer - owner: devteam -- name: fastx_reverse_complement - owner: devteam -- name: fastx_clipper - owner: devteam -- name: fastq_quality_filter - owner: devteam -- name: length_and_gc_content - owner: iuc -- name: fastx_renamer - owner: devteam -- name: fastx_barcode_splitter - owner: devteam -- name: fastx_artifacts_filter - owner: devteam -- name: fastq_quality_converter - owner: devteam -- name: fastq_paired_end_joiner - owner: devteam -- name: fastq_paired_end_interlacer - owner: devteam -- name: fastq_paired_end_deinterlacer - owner: devteam -- name: fastq_join - owner: lparsons -- name: fastq_paired_end_splitter - owner: devteam -- name: fastq_masker_by_quality - owner: devteam -- name: fastq_manipulation - owner: devteam -- name: fastq_groomer - owner: devteam -- name: fastq_filter - owner: devteam -- name: fastq_combiner - owner: devteam -- name: trim_galore - owner: bgruening -- name: short_reads_trim_seq - owner: devteam -- name: short_reads_figure_score - owner: devteam -- name: fastx_collapser - owner: devteam -- name: fastq_trimmer - owner: devteam -- name: fastq_trimmer_by_quality - owner: devteam -- name: fasta_nucleotide_changer - owner: devteam -- name: fasta_formatter - owner: devteam -- name: fasta_filter_by_length - owner: devteam -- name: fasta_concatenate_by_species - owner: devteam -- name: fasta_compute_length - owner: devteam -- name: fastp - owner: iuc -- name: fasta_stats - owner: iuc diff --git a/common_toolset/fastafastq.yml.lock b/common_toolset/fastafastq.yml.lock deleted file mode 100644 index b2d9ad52..00000000 --- a/common_toolset/fastafastq.yml.lock +++ /dev/null @@ -1,215 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: FASTA/FASTQ -tools: -- name: find_subsequences - owner: bgruening - revisions: - - d882a0a75759 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: cutadapt - owner: lparsons - revisions: - - e4691e1589d3 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: flash - owner: iuc - revisions: - - a27654fc4270 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_trimmer - owner: devteam - revisions: - - 547e8d00f11c - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_reverse_complement - owner: devteam - revisions: - - 0c2907307ba4 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_clipper - owner: devteam - revisions: - - 736b8f6ee456 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_quality_filter - owner: devteam - revisions: - - 7b4468117008 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: length_and_gc_content - owner: iuc - revisions: - - f088370d2a3c - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_renamer - owner: devteam - revisions: - - 3599f5451ee2 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_barcode_splitter - owner: devteam - revisions: - - 4bedca26c133 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_artifacts_filter - owner: devteam - revisions: - - 567d5b3c52b1 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_quality_converter - owner: devteam - revisions: - - 54053ea6c77e - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_paired_end_joiner - owner: devteam - revisions: - - 822cc1e6274e - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_paired_end_interlacer - owner: devteam - revisions: - - ef49268ee579 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_paired_end_deinterlacer - owner: devteam - revisions: - - b7ce72b00e62 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_join - owner: lparsons - revisions: - - 8ec3dfde378b - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_paired_end_splitter - owner: devteam - revisions: - - 9bbe5b7ffa12 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_masker_by_quality - owner: devteam - revisions: - - eb592e9ec47a - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_manipulation - owner: devteam - revisions: - - 4ac14b275aca - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_groomer - owner: devteam - revisions: - - 71e5fa25b8a2 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_filter - owner: devteam - revisions: - - 06934412f56d - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_combiner - owner: devteam - revisions: - - 56389130cb63 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: trim_galore - owner: bgruening - revisions: - - 949f01671246 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: short_reads_trim_seq - owner: devteam - revisions: - - 25e6fe525306 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: short_reads_figure_score - owner: devteam - revisions: - - b52b9c7aabd9 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastx_collapser - owner: devteam - revisions: - - 7ce1891db6f5 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_trimmer - owner: devteam - revisions: - - 2d0d13b0b0f1 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastq_trimmer_by_quality - owner: devteam - revisions: - - c64d534a763c - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_nucleotide_changer - owner: devteam - revisions: - - 091ca73f5804 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_formatter - owner: devteam - revisions: - - 859422bcb689 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_filter_by_length - owner: devteam - revisions: - - 2fd6033d0e9c - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_concatenate_by_species - owner: devteam - revisions: - - 717aee069681 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_compute_length - owner: devteam - revisions: - - de2db1bdfbf8 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fastp - owner: iuc - revisions: - - 1d8fe9bc4cb0 - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ -- name: fasta_stats - owner: iuc - revisions: - - 9c620a950d3a - tool_panel_section_id: fasta_fastq - tool_panel_section_label: FASTA/FASTQ diff --git a/common_toolset/fastq_quality_control.yml b/common_toolset/fastq_quality_control.yml deleted file mode 100644 index 7262b15b..00000000 --- a/common_toolset/fastq_quality_control.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: FASTQ Quality Control -tools: -- name: fastqc - owner: devteam -- name: trimmomatic - owner: pjbriggs -- name: multiqc - owner: iuc -- name: fastq_stats - owner: devteam -- name: fastx_quality_statistics - owner: devteam -- name: fastx_nucleotides_distribution - owner: devteam -- name: fastq_quality_boxplot - owner: devteam diff --git a/common_toolset/fastq_quality_control.yml.lock b/common_toolset/fastq_quality_control.yml.lock deleted file mode 100644 index cdb752dc..00000000 --- a/common_toolset/fastq_quality_control.yml.lock +++ /dev/null @@ -1,47 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: FASTQ Quality Control -tools: -- name: fastqc - owner: devteam - revisions: - - e7b2202befea - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: trimmomatic - owner: pjbriggs - revisions: - - 51b771646466 - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: multiqc - owner: iuc - revisions: - - b2f1f75d49c4 - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: fastq_stats - owner: devteam - revisions: - - e2cf940128d5 - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: fastx_quality_statistics - owner: devteam - revisions: - - 59003d0543cd - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: fastx_nucleotides_distribution - owner: devteam - revisions: - - 21796f46e0ba - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control -- name: fastq_quality_boxplot - owner: devteam - revisions: - - 3987db70a4b0 - tool_panel_section_id: fastq_quality_control - tool_panel_section_label: FASTQ Quality Control diff --git a/common_toolset/fetch_sequencesalignments.yml b/common_toolset/fetch_sequencesalignments.yml deleted file mode 100644 index 9ddda79a..00000000 --- a/common_toolset/fetch_sequencesalignments.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Fetch Sequences/Alignments -tools: -- name: extract_genomic_dna - owner: iuc diff --git a/common_toolset/fetch_sequencesalignments.yml.lock b/common_toolset/fetch_sequencesalignments.yml.lock deleted file mode 100644 index a8bd6870..00000000 --- a/common_toolset/fetch_sequencesalignments.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Fetch Sequences/Alignments -tools: -- name: extract_genomic_dna - owner: iuc - revisions: - - e400dcbc60d0 - tool_panel_section_id: fetch_sequences_alignments - tool_panel_section_label: Fetch Sequences/Alignments diff --git a/common_toolset/filter_and_sort.yml b/common_toolset/filter_and_sort.yml deleted file mode 100644 index 89ef7a6d..00000000 --- a/common_toolset/filter_and_sort.yml +++ /dev/null @@ -1,10 +0,0 @@ -tool_panel_section_label: Filter and Sort -tools: -- name: column_arrange_by_header - owner: bgruening -- name: sample_seqs - owner: peterjc -- name: sqlite_to_tabular - owner: jjohnson -- name: query_tabular - owner: jjohnson diff --git a/common_toolset/filter_and_sort.yml.lock b/common_toolset/filter_and_sort.yml.lock deleted file mode 100644 index 9137579d..00000000 --- a/common_toolset/filter_and_sort.yml.lock +++ /dev/null @@ -1,29 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Filter and Sort -tools: -- name: column_arrange_by_header - owner: bgruening - revisions: - - 6c6d26ff01ff - tool_panel_section_id: filter_and_sort - tool_panel_section_label: Filter and Sort -- name: sample_seqs - owner: peterjc - revisions: - - 7c40a1fbc82e - tool_panel_section_id: filter_and_sort - tool_panel_section_label: Filter and Sort -- name: sqlite_to_tabular - owner: jjohnson - revisions: - - 123b9ca5e26a - tool_panel_section_id: filter_and_sort - tool_panel_section_label: Filter and Sort -- name: query_tabular - owner: jjohnson - revisions: - - 5bb148ee644a - tool_panel_section_id: filter_and_sort - tool_panel_section_label: Filter and Sort diff --git a/common_toolset/gatk.yml b/common_toolset/gatk.yml deleted file mode 100644 index 9bc16af1..00000000 --- a/common_toolset/gatk.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: GATK -tools: -- name: count_covariates - owner: devteam diff --git a/common_toolset/gatk.yml.lock b/common_toolset/gatk.yml.lock deleted file mode 100644 index 6050d29d..00000000 --- a/common_toolset/gatk.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: GATK -tools: -- name: count_covariates - owner: devteam - revisions: - - 14e304b70425 - tool_panel_section_id: gatk - tool_panel_section_label: GATK diff --git a/common_toolset/gatk_tools.yml b/common_toolset/gatk_tools.yml deleted file mode 100644 index 1a5907fd..00000000 --- a/common_toolset/gatk_tools.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: GATK Tools -tools: -- name: gatk2 - owner: iuc diff --git a/common_toolset/gatk_tools.yml.lock b/common_toolset/gatk_tools.yml.lock deleted file mode 100644 index 839b4105..00000000 --- a/common_toolset/gatk_tools.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: GATK Tools -tools: -- name: gatk2 - owner: iuc - revisions: - - 35c00763cb5c - tool_panel_section_id: gatk_tools - tool_panel_section_label: GATK Tools diff --git a/common_toolset/gemini.yml b/common_toolset/gemini.yml deleted file mode 100644 index 0f8df51a..00000000 --- a/common_toolset/gemini.yml +++ /dev/null @@ -1,36 +0,0 @@ -tool_panel_section_label: Gemini -tools: -- name: gemini_load - owner: iuc -- name: gemini_db_info - owner: iuc -- name: gemini_windower - owner: iuc -- name: gemini_pathways - owner: iuc -- name: gemini_annotate - owner: iuc -- name: gemini_interactions - owner: iuc -- name: gemini_qc - owner: iuc -- name: gemini_set_somatic - owner: iuc -- name: gemini_roh - owner: iuc -- name: gemini_fusions - owner: iuc -- name: gemini_query - owner: iuc -- name: gemini_lof_sieve - owner: iuc -- name: gemini_actionable_mutations - owner: iuc -- name: gemini_amend - owner: iuc -- name: gemini_stats - owner: iuc -- name: gemini_gene_wise - owner: iuc -- name: gemini_burden - owner: iuc diff --git a/common_toolset/gemini.yml.lock b/common_toolset/gemini.yml.lock deleted file mode 100644 index 1969ba49..00000000 --- a/common_toolset/gemini.yml.lock +++ /dev/null @@ -1,107 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Gemini -tools: -- name: gemini_load - owner: iuc - revisions: - - b2c25142267e - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_db_info - owner: iuc - revisions: - - bc8b01d1b496 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_windower - owner: iuc - revisions: - - 3b5b1ebc8423 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_pathways - owner: iuc - revisions: - - c63b7eefb07a - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_annotate - owner: iuc - revisions: - - 0c8f7322f8fc - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_interactions - owner: iuc - revisions: - - 7028ca3cac1c - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_qc - owner: iuc - revisions: - - 8414eecc3828 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_set_somatic - owner: iuc - revisions: - - '991049484627' - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_roh - owner: iuc - revisions: - - d65ca2fa673b - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_fusions - owner: iuc - revisions: - - 6e3d2bd01a96 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_query - owner: iuc - revisions: - - cd00221d67cb - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_lof_sieve - owner: iuc - revisions: - - dda378a72430 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_actionable_mutations - owner: iuc - revisions: - - 643a9ad97f08 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_amend - owner: iuc - revisions: - - bff8fad3fb69 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_stats - owner: iuc - revisions: - - 86d4303cc3ca - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_gene_wise - owner: iuc - revisions: - - 4b26f6c99227 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini -- name: gemini_burden - owner: iuc - revisions: - - 699ce2631e79 - tool_panel_section_id: gemini - tool_panel_section_label: Gemini diff --git a/common_toolset/genome_diversity.yml b/common_toolset/genome_diversity.yml deleted file mode 100644 index 62e10bfa..00000000 --- a/common_toolset/genome_diversity.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Genome Diversity -tools: -- name: genome_diversity - owner: miller-lab -- name: fasttree - owner: iuc diff --git a/common_toolset/genome_diversity.yml.lock b/common_toolset/genome_diversity.yml.lock deleted file mode 100644 index 87fb88f2..00000000 --- a/common_toolset/genome_diversity.yml.lock +++ /dev/null @@ -1,17 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Genome Diversity -tools: -- name: genome_diversity - owner: miller-lab - revisions: - - e56023008e36 - tool_panel_section_id: genome_diversity - tool_panel_section_label: Genome Diversity -- name: fasttree - owner: iuc - revisions: - - c7e73acfa3eb - tool_panel_section_id: genome_diversity - tool_panel_section_label: Genome Diversity diff --git a/common_toolset/get_data.yml b/common_toolset/get_data.yml deleted file mode 100644 index 325bbaac..00000000 --- a/common_toolset/get_data.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Get Data -tools: -- name: sra_tools - owner: iuc -- name: trinity_define_clusters_by_cutting_tree - owner: iuc diff --git a/common_toolset/get_data.yml.lock b/common_toolset/get_data.yml.lock deleted file mode 100644 index 00a67ad2..00000000 --- a/common_toolset/get_data.yml.lock +++ /dev/null @@ -1,17 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Get Data -tools: -- name: sra_tools - owner: iuc - revisions: - - 1790dcf3c32d - tool_panel_section_id: get_data - tool_panel_section_label: Get Data -- name: trinity_define_clusters_by_cutting_tree - owner: iuc - revisions: - - 6fa08f46db8c - tool_panel_section_id: get_data - tool_panel_section_label: Get Data diff --git a/common_toolset/graphdisplay_data.yml b/common_toolset/graphdisplay_data.yml deleted file mode 100644 index ad76b7fc..00000000 --- a/common_toolset/graphdisplay_data.yml +++ /dev/null @@ -1,28 +0,0 @@ -tool_panel_section_label: Graph/Display Data -tools: -- name: ggplot2_heatmap2 - owner: iuc -- name: xy_plot - owner: devteam -- name: circos - owner: iuc -- name: venn_list - owner: peterjc -- name: ucsc_custom_track - owner: devteam -- name: scatterplot - owner: devteam -- name: histogram - owner: devteam -- name: gmaj - owner: devteam -- name: bandage - owner: iuc -- name: jbrowse - owner: iuc -- name: ggplot2_heatmap - owner: iuc -- name: krona_text - owner: saskia-hiltemann -- name: mummer - owner: peterjc diff --git a/common_toolset/graphdisplay_data.yml.lock b/common_toolset/graphdisplay_data.yml.lock deleted file mode 100644 index f917348f..00000000 --- a/common_toolset/graphdisplay_data.yml.lock +++ /dev/null @@ -1,83 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Graph/Display Data -tools: -- name: ggplot2_heatmap2 - owner: iuc - revisions: - - ca7cb0eaad62 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: xy_plot - owner: devteam - revisions: - - ecb437f1d298 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: circos - owner: iuc - revisions: - - ae9994cf526f - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: venn_list - owner: peterjc - revisions: - - e13206029a72 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: ucsc_custom_track - owner: devteam - revisions: - - 760f588e8a26 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: scatterplot - owner: devteam - revisions: - - efda9a4a50e7 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: histogram - owner: devteam - revisions: - - cdb9e89e2970 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: gmaj - owner: devteam - revisions: - - 2cd5ee197ec7 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: bandage - owner: iuc - revisions: - - 58124285e462 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: jbrowse - owner: iuc - revisions: - - 2bb2e07a7a21 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: ggplot2_heatmap - owner: iuc - revisions: - - de002ba2b849 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: krona_text - owner: saskia-hiltemann - revisions: - - b14f1444e464 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data -- name: mummer - owner: peterjc - revisions: - - d9f3d4779507 - tool_panel_section_id: graph_display_data - tool_panel_section_label: Graph/Display Data diff --git a/common_toolset/iwtomics.yml b/common_toolset/iwtomics.yml deleted file mode 100644 index 11366df8..00000000 --- a/common_toolset/iwtomics.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: IWTomics -tools: -- name: iwtomics_loadandplot - owner: iuc -- name: iwtomics_testandplot - owner: iuc -- name: iwtomics_plotwithscale - owner: iuc diff --git a/common_toolset/iwtomics.yml.lock b/common_toolset/iwtomics.yml.lock deleted file mode 100644 index 8ac920a6..00000000 --- a/common_toolset/iwtomics.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: IWTomics -tools: -- name: iwtomics_loadandplot - owner: iuc - revisions: - - ce633cc8f5f9 - tool_panel_section_id: iwtomics - tool_panel_section_label: IWTomics -- name: iwtomics_testandplot - owner: iuc - revisions: - - 94965e369be4 - tool_panel_section_id: iwtomics - tool_panel_section_label: IWTomics -- name: iwtomics_plotwithscale - owner: iuc - revisions: - - 1bc9150ed125 - tool_panel_section_id: iwtomics - tool_panel_section_label: IWTomics diff --git a/common_toolset/join_subtract_and_group.yml b/common_toolset/join_subtract_and_group.yml deleted file mode 100644 index cedfb0cd..00000000 --- a/common_toolset/join_subtract_and_group.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Join, Subtract and Group -tools: -- name: subtract_query - owner: devteam diff --git a/common_toolset/join_subtract_and_group.yml.lock b/common_toolset/join_subtract_and_group.yml.lock deleted file mode 100644 index 9386136f..00000000 --- a/common_toolset/join_subtract_and_group.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Join, Subtract and Group -tools: -- name: subtract_query - owner: devteam - revisions: - - ff3901618482 - tool_panel_section_id: join__subtract_and_group - tool_panel_section_label: Join, Subtract and Group diff --git a/common_toolset/mapping.yml b/common_toolset/mapping.yml deleted file mode 100644 index fd7fc040..00000000 --- a/common_toolset/mapping.yml +++ /dev/null @@ -1,18 +0,0 @@ -tool_panel_section_label: Mapping -tools: -- name: bowtie2 - owner: devteam -- name: lastz - owner: devteam -- name: bwa - owner: devteam -- name: star_fusion - owner: iuc -- name: megablast_xml_parser - owner: devteam -- name: megablast_wrapper - owner: devteam -- name: bowtie_wrappers - owner: devteam -- name: lastz_paired_reads - owner: devteam diff --git a/common_toolset/mapping.yml.lock b/common_toolset/mapping.yml.lock deleted file mode 100644 index 1fd477ec..00000000 --- a/common_toolset/mapping.yml.lock +++ /dev/null @@ -1,53 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Mapping -tools: -- name: bowtie2 - owner: devteam - revisions: - - 017aba02828d - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: lastz - owner: devteam - revisions: - - e7f19d6a9af8 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: bwa - owner: devteam - revisions: - - 01ac0a5fedc3 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: star_fusion - owner: iuc - revisions: - - 04b73d626680 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: megablast_xml_parser - owner: devteam - revisions: - - 03ca082aeb2e - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: megablast_wrapper - owner: devteam - revisions: - - fb2e0e1dac89 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: bowtie_wrappers - owner: devteam - revisions: - - b46e7d48076a - tool_panel_section_id: mapping - tool_panel_section_label: Mapping -- name: lastz_paired_reads - owner: devteam - revisions: - - ecc974513241 - tool_panel_section_id: mapping - tool_panel_section_label: Mapping diff --git a/common_toolset/metagenomic_analysis.yml b/common_toolset/metagenomic_analysis.yml deleted file mode 100644 index 6c44ba39..00000000 --- a/common_toolset/metagenomic_analysis.yml +++ /dev/null @@ -1,34 +0,0 @@ -tool_panel_section_label: Metagenomic Analysis -tools: -- name: diamond - owner: bgruening -- name: vsearch - owner: iuc -- name: vegan_rarefaction - owner: iuc -- name: vegan_fisher_alpha - owner: iuc -- name: vegan_diversity - owner: iuc -- name: kraken_report - owner: devteam -- name: kraken - owner: devteam -- name: taxonomy_krona_chart - owner: crs4 -- name: metagenomeseq_normalization - owner: iuc -- name: kraken_taxonomy_report - owner: iuc -- name: biom_add_metadata - owner: iuc -- name: biom_convert - owner: iuc -- name: kraken_translate - owner: devteam -- name: kraken_filter - owner: devteam -- name: kraken2tax - owner: devteam -- name: poisson2test - owner: devteam diff --git a/common_toolset/metagenomic_analysis.yml.lock b/common_toolset/metagenomic_analysis.yml.lock deleted file mode 100644 index faf2f050..00000000 --- a/common_toolset/metagenomic_analysis.yml.lock +++ /dev/null @@ -1,101 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Metagenomic Analysis -tools: -- name: diamond - owner: bgruening - revisions: - - 64be1ac21109 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: vsearch - owner: iuc - revisions: - - b3c7199d8786 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: vegan_rarefaction - owner: iuc - revisions: - - b0d5976540e3 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: vegan_fisher_alpha - owner: iuc - revisions: - - f9966e11885b - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: vegan_diversity - owner: iuc - revisions: - - a2c047a2c380 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken_report - owner: devteam - revisions: - - 6c09bed3444f - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken - owner: devteam - revisions: - - 8ba2174315aa - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: taxonomy_krona_chart - owner: crs4 - revisions: - - c9f8fef1df74 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: metagenomeseq_normalization - owner: iuc - revisions: - - d16f7cc26516 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken_taxonomy_report - owner: iuc - revisions: - - b11b3ac48bb9 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: biom_add_metadata - owner: iuc - revisions: - - 367b1ed91207 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: biom_convert - owner: iuc - revisions: - - 501c21cce614 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken_translate - owner: devteam - revisions: - - 9bdcba262627 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken_filter - owner: devteam - revisions: - - 5bee9adae474 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: kraken2tax - owner: devteam - revisions: - - f03c7ba8d8bc - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis -- name: poisson2test - owner: devteam - revisions: - - 5ff18ec88181 - tool_panel_section_id: metagenomic_analysis - tool_panel_section_label: Metagenomic Analysis diff --git a/common_toolset/mimodd.yml b/common_toolset/mimodd.yml deleted file mode 100644 index 50da3c14..00000000 --- a/common_toolset/mimodd.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: MiModD -tools: -- name: mimodd_main - owner: wolma diff --git a/common_toolset/mimodd.yml.lock b/common_toolset/mimodd.yml.lock deleted file mode 100644 index 90858eba..00000000 --- a/common_toolset/mimodd.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: MiModD -tools: -- name: mimodd_main - owner: wolma - revisions: - - bfcd121b99bf - tool_panel_section_id: mimodd - tool_panel_section_label: MiModD diff --git a/common_toolset/mothur.yml b/common_toolset/mothur.yml deleted file mode 100644 index ed3e970d..00000000 --- a/common_toolset/mothur.yml +++ /dev/null @@ -1,264 +0,0 @@ -tool_panel_section_label: Mothur -tools: -- name: mothur_taxonomy_to_krona - owner: iuc -- name: mothur_merge_count - owner: iuc -- name: mothur_chimera_vsearch - owner: iuc -- name: mothur_rename_seqs - owner: iuc -- name: mothur_biom_info - owner: iuc -- name: mothur_venn - owner: iuc -- name: mothur_unique_seqs - owner: iuc -- name: mothur_unifrac_weighted - owner: iuc -- name: mothur_unifrac_unweighted - owner: iuc -- name: mothur_trim_seqs - owner: iuc -- name: mothur_trim_flows - owner: iuc -- name: mothur_tree_shared - owner: iuc -- name: mothur_summary_tax - owner: iuc -- name: mothur_summary_single - owner: iuc -- name: mothur_summary_shared - owner: iuc -- name: mothur_summary_seqs - owner: iuc -- name: mothur_summary_qual - owner: iuc -- name: mothur_sub_sample - owner: iuc -- name: mothur_split_groups - owner: iuc -- name: mothur_split_abund - owner: iuc -- name: mothur_sort_seqs - owner: iuc -- name: mothur_shhh_seqs - owner: iuc -- name: mothur_shhh_flows - owner: iuc -- name: mothur_sffinfo - owner: iuc -- name: mothur_seq_error - owner: iuc -- name: mothur_sens_spec - owner: iuc -- name: mothur_screen_seqs - owner: iuc -- name: mothur_reverse_seqs - owner: iuc -- name: mothur_remove_seqs - owner: iuc -- name: mothur_remove_rare - owner: iuc -- name: mothur_remove_otus - owner: iuc -- name: mothur_remove_otulabels - owner: iuc -- name: mothur_remove_lineage - owner: iuc -- name: mothur_remove_groups - owner: iuc -- name: mothur_remove_dists - owner: iuc -- name: mothur_rarefaction_single - owner: iuc -- name: mothur_rarefaction_shared - owner: iuc -- name: mothur_primer_design - owner: iuc -- name: mothur_pre_cluster - owner: iuc -- name: mothur_phylotype - owner: iuc -- name: mothur_phylo_diversity - owner: iuc -- name: mothur_pcr_seqs - owner: iuc -- name: mothur_pcoa - owner: iuc -- name: mothur_pca - owner: iuc -- name: mothur_parsimony - owner: iuc -- name: mothur_parse_list - owner: iuc -- name: mothur_pairwise_seqs - owner: iuc -- name: mothur_otu_hierarchy - owner: iuc -- name: mothur_otu_association - owner: iuc -- name: mothur_normalize_shared - owner: iuc -- name: mothur_nmds - owner: iuc -- name: mothur_mimarks_attributes - owner: iuc -- name: mothur_metastats - owner: iuc -- name: mothur_merge_taxsummary - owner: iuc -- name: mothur_merge_sfffiles - owner: iuc -- name: mothur_merge_groups - owner: iuc -- name: mothur_merge_files - owner: iuc -- name: mothur_mantel - owner: iuc -- name: mothur_make_sra - owner: iuc -- name: mothur_make_shared - owner: iuc -- name: mothur_make_lookup - owner: iuc -- name: mothur_make_lefse - owner: iuc -- name: mothur_make_group - owner: iuc -- name: mothur_make_fastq - owner: iuc -- name: mothur_make_design - owner: iuc -- name: mothur_make_contigs - owner: iuc -- name: mothur_make_biom - owner: iuc -- name: mothur_list_seqs - owner: iuc -- name: mothur_list_otulabels - owner: iuc -- name: mothur_libshuff - owner: iuc -- name: mothur_lefse - owner: iuc -- name: mothur_indicator - owner: iuc -- name: mothur_homova - owner: iuc -- name: mothur_heatmap_sim - owner: iuc -- name: mothur_heatmap_bin - owner: iuc -- name: mothur_get_sharedseqs - owner: iuc -- name: mothur_get_seqs - owner: iuc -- name: mothur_get_sabund - owner: iuc -- name: mothur_get_relabund - owner: iuc -- name: mothur_get_rabund - owner: iuc -- name: mothur_get_otus - owner: iuc -- name: mothur_get_oturep - owner: iuc -- name: mothur_get_otulist - owner: iuc -- name: mothur_get_otulabels - owner: iuc -- name: mothur_get_mimarkspackage - owner: iuc -- name: mothur_get_lineage - owner: iuc -- name: mothur_get_label - owner: iuc -- name: mothur_get_group - owner: iuc -- name: mothur_get_groups - owner: iuc -- name: mothur_get_dists - owner: iuc -- name: mothur_get_coremicrobiome - owner: iuc -- name: mothur_get_communitytype - owner: iuc -- name: mothur_filter_shared - owner: iuc -- name: mothur_filter_seqs - owner: iuc -- name: mothur_fastq_info - owner: iuc -- name: mothur_dist_shared - owner: iuc -- name: mothur_dist_seqs - owner: iuc -- name: mothur_deunique_tree - owner: iuc -- name: mothur_deunique_seqs - owner: iuc -- name: mothur_degap_seqs - owner: iuc -- name: mothur_create_database - owner: iuc -- name: mothur_count_seqs - owner: iuc -- name: mothur_count_groups - owner: iuc -- name: mothur_corr_axes - owner: iuc -- name: mothur_cooccurrence - owner: iuc -- name: mothur_consensus_seqs - owner: iuc -- name: mothur_collect_single - owner: iuc -- name: mothur_collect_shared - owner: iuc -- name: mothur_cluster - owner: iuc -- name: mothur_cluster_split - owner: iuc -- name: mothur_cluster_fragments - owner: iuc -- name: mothur_cluster_classic - owner: iuc -- name: mothur_clearcut - owner: iuc -- name: mothur_classify_tree - owner: iuc -- name: mothur_classify_seqs - owner: iuc -- name: mothur_classify_otu - owner: iuc -- name: mothur_chop_seqs - owner: iuc -- name: mothur_chimera_uchime - owner: iuc -- name: mothur_chimera_slayer - owner: iuc -- name: mothur_chimera_pintail - owner: iuc -- name: mothur_chimera_perseus - owner: iuc -- name: mothur_chimera_check - owner: iuc -- name: mothur_chimera_ccode - owner: iuc -- name: mothur_chimera_bellerophon - owner: iuc -- name: mothur_bin_seqs - owner: iuc -- name: mothur_anosim - owner: iuc -- name: mothur_amova - owner: iuc -- name: mothur_align_seqs - owner: iuc -- name: mothur_align_check - owner: iuc -- name: mothur_hcluster - owner: iuc -- name: mothur_classify_rf - owner: iuc diff --git a/common_toolset/mothur.yml.lock b/common_toolset/mothur.yml.lock deleted file mode 100644 index be4da916..00000000 --- a/common_toolset/mothur.yml.lock +++ /dev/null @@ -1,791 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Mothur -tools: -- name: mothur_taxonomy_to_krona - owner: iuc - revisions: - - 71e7d93a593e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_merge_count - owner: iuc - revisions: - - ccba5bd49390 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_chimera_vsearch - owner: iuc - revisions: - - d531f28e8266 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_rename_seqs - owner: iuc - revisions: - - 03b326e1f6a1 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_biom_info - owner: iuc - revisions: - - 3b426f118175 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_venn - owner: iuc - revisions: - - e4f4c1c0d193 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_unique_seqs - owner: iuc - revisions: - - 7c3f9c0850ac - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_unifrac_weighted - owner: iuc - revisions: - - 136cb4f4b996 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_unifrac_unweighted - owner: iuc - revisions: - - 3597ca9089a5 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_trim_seqs - owner: iuc - revisions: - - c49a6454726c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_trim_flows - owner: iuc - revisions: - - 4d56c7e82ba6 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_tree_shared - owner: iuc - revisions: - - 40d8938eaa24 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_tax - owner: iuc - revisions: - - 5eb0f670aa35 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_single - owner: iuc - revisions: - - 2857a688a7e9 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_shared - owner: iuc - revisions: - - 74c8ebee088c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_seqs - owner: iuc - revisions: - - 411ddfefe041 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_summary_qual - owner: iuc - revisions: - - d50fdfdc2a0c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_sub_sample - owner: iuc - revisions: - - 34e1fbd32a04 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_split_groups - owner: iuc - revisions: - - 68c20caae797 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_split_abund - owner: iuc - revisions: - - d850b4b9659d - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_sort_seqs - owner: iuc - revisions: - - cbe644faff63 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_shhh_seqs - owner: iuc - revisions: - - 6ee54b761c3c - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_shhh_flows - owner: iuc - revisions: - - 7cca6773bc2a - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_sffinfo - owner: iuc - revisions: - - 12507ed33710 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_seq_error - owner: iuc - revisions: - - a03c9ebf1959 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_sens_spec - owner: iuc - revisions: - - ddda05cfccb4 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_screen_seqs - owner: iuc - revisions: - - 94d8dbac60d8 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_reverse_seqs - owner: iuc - revisions: - - 03450507aa98 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_seqs - owner: iuc - revisions: - - 2fa446f85b18 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_rare - owner: iuc - revisions: - - 196b1583580a - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_otus - owner: iuc - revisions: - - ce3c9cb04314 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_otulabels - owner: iuc - revisions: - - ba9df7320629 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_lineage - owner: iuc - revisions: - - 2f633c057c0d - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_groups - owner: iuc - revisions: - - 7c5b7dddd02e - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_remove_dists - owner: iuc - revisions: - - ea7b70e1a61b - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_rarefaction_single - owner: iuc - revisions: - - 8091da04fbac - tool_panel_section_id: mothur - tool_panel_section_label: Mothur -- name: mothur_rarefaction_shared - owner: iuc - 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tool_panel_section_label: Mothur -- name: mothur_classify_rf - owner: iuc - revisions: - - 010296966465 - tool_panel_section_id: mothur - tool_panel_section_label: Mothur diff --git a/common_toolset/motif.yml b/common_toolset/motif.yml deleted file mode 100644 index 20f2d510..00000000 --- a/common_toolset/motif.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Motif -tools: -- name: meme_meme - owner: iuc -- name: meme_fimo - owner: iuc -- name: weblogo3 - owner: devteam diff --git a/common_toolset/motif.yml.lock b/common_toolset/motif.yml.lock deleted file mode 100644 index 77d1faa1..00000000 --- a/common_toolset/motif.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Motif -tools: -- name: meme_meme - owner: iuc - revisions: - - 57e5d9382f36 - tool_panel_section_id: motif - tool_panel_section_label: Motif -- name: meme_fimo - owner: iuc - revisions: - - c1a9a297ba8b - tool_panel_section_id: motif - tool_panel_section_label: Motif -- name: weblogo3 - owner: devteam - revisions: - - dc25a5169a91 - tool_panel_section_id: motif - tool_panel_section_label: Motif diff --git a/common_toolset/multiple_alignments.yml b/common_toolset/multiple_alignments.yml deleted file mode 100644 index e46f7ad0..00000000 --- a/common_toolset/multiple_alignments.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Multiple Alignments -tools: -- name: mafft - owner: rnateam -- name: clustalw - owner: devteam -- name: cdhit - owner: bebatut diff --git a/common_toolset/multiple_alignments.yml.lock b/common_toolset/multiple_alignments.yml.lock deleted file mode 100644 index 2b678693..00000000 --- a/common_toolset/multiple_alignments.yml.lock +++ /dev/null @@ -1,23 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Multiple Alignments -tools: -- name: mafft - owner: rnateam - revisions: - - c5908940967d - tool_panel_section_id: multiple_alignments - tool_panel_section_label: Multiple Alignments -- name: clustalw - owner: devteam - revisions: - - d6694932c5e0 - tool_panel_section_id: multiple_alignments - tool_panel_section_label: Multiple Alignments -- name: cdhit - owner: bebatut - revisions: - - 93f25d52cfa5 - tool_panel_section_id: multiple_alignments - tool_panel_section_label: Multiple Alignments diff --git a/common_toolset/nanopore.yml b/common_toolset/nanopore.yml deleted file mode 100644 index 67cd9c30..00000000 --- a/common_toolset/nanopore.yml +++ /dev/null @@ -1,28 +0,0 @@ -tool_panel_section_label: Nanopore -tools: -- name: poretools_yield_plot - owner: iuc -- name: poretools_winner - owner: iuc -- name: poretools_times - owner: iuc -- name: poretools_tabular - owner: iuc -- name: poretools_stats - owner: iuc -- name: poretools_squiggle - owner: iuc -- name: poretools_qualpos - owner: iuc -- name: poretools_qualdist - owner: iuc -- name: poretools_occupancy - owner: iuc -- name: poretools_nucdist - owner: iuc -- name: poretools_hist - owner: iuc -- name: poretools_extract - owner: iuc -- name: poretools_events - owner: iuc diff --git a/common_toolset/nanopore.yml.lock b/common_toolset/nanopore.yml.lock deleted file mode 100644 index 95df9dc6..00000000 --- a/common_toolset/nanopore.yml.lock +++ /dev/null @@ -1,83 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Nanopore -tools: -- name: poretools_yield_plot - owner: iuc - revisions: - - 64a83664b814 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_winner - owner: iuc - revisions: - - 9d8f41103cc6 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_times - owner: iuc - revisions: - - e5072f0d3772 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_tabular - owner: iuc - revisions: - - 7f0b324de883 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_stats - owner: iuc - revisions: - - ae4c8446ce30 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_squiggle - owner: iuc - revisions: - - ce8af9373061 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_qualpos - owner: iuc - revisions: - - 2e22ebec211a - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_qualdist - owner: iuc - revisions: - - 44111014e7c1 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_occupancy - owner: iuc - revisions: - - 336791b5665f - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_nucdist - owner: iuc - revisions: - - 3ae7ccba16cf - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_hist - owner: iuc - revisions: - - 47936349f3e9 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_extract - owner: iuc - revisions: - - 7593f94691fb - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_events - owner: iuc - revisions: - - 1d835c691480 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore diff --git a/common_toolset/ncbi_blast.yml b/common_toolset/ncbi_blast.yml deleted file mode 100644 index b03bebe9..00000000 --- a/common_toolset/ncbi_blast.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: NCBI BLAST+ -tools: -- name: ncbi_blast_plus - owner: devteam diff --git a/common_toolset/ncbi_blast.yml.lock b/common_toolset/ncbi_blast.yml.lock deleted file mode 100644 index 58637735..00000000 --- a/common_toolset/ncbi_blast.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: NCBI BLAST+ -tools: -- name: ncbi_blast_plus - owner: devteam - revisions: - - e25d3acf6e68 - tool_panel_section_id: ncbi_blast_ - tool_panel_section_label: NCBI BLAST+ diff --git a/common_toolset/operate_on_genomic_intervals.yml b/common_toolset/operate_on_genomic_intervals.yml deleted file mode 100644 index ffab8d91..00000000 --- a/common_toolset/operate_on_genomic_intervals.yml +++ /dev/null @@ -1,26 +0,0 @@ -tool_panel_section_label: Operate on Genomic Intervals -tools: -- name: merge - owner: devteam -- name: concat - owner: devteam -- name: subtract - owner: devteam -- name: join - owner: devteam -- name: intersect - owner: devteam -- name: coverage - owner: devteam -- name: complement - owner: devteam -- name: cluster - owner: devteam -- name: basecoverage - owner: devteam -- name: annotation_profiler - owner: devteam -- name: flanking_features - owner: devteam -- name: get_flanks - owner: devteam diff --git a/common_toolset/operate_on_genomic_intervals.yml.lock b/common_toolset/operate_on_genomic_intervals.yml.lock deleted file mode 100644 index b7bf75aa..00000000 --- a/common_toolset/operate_on_genomic_intervals.yml.lock +++ /dev/null @@ -1,77 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Operate on Genomic Intervals -tools: -- name: merge - owner: devteam - revisions: - - 381cd27bf67a - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: concat - owner: devteam - revisions: - - 35a89f8cc96e - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: subtract - owner: devteam - revisions: - - 0145969324c4 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: join - owner: devteam - revisions: - - a10f49d9218a - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: intersect - owner: devteam - revisions: - - 33b3f3688db4 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: coverage - owner: devteam - revisions: - - 4ef9819dc7fb - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: complement - owner: devteam - revisions: - - 38c8bb402872 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: cluster - owner: devteam - revisions: - - 05696474ee89 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: basecoverage - owner: devteam - revisions: - - 2cedec3759e4 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: annotation_profiler - owner: devteam - revisions: - - 3b33da018e74 - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: flanking_features - owner: devteam - revisions: - - a09d13b108fd - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals -- name: get_flanks - owner: devteam - revisions: - - 077f404ae1bb - tool_panel_section_id: operate_on_genomic_intervals - tool_panel_section_label: Operate on Genomic Intervals diff --git a/common_toolset/phenotype_association.yml b/common_toolset/phenotype_association.yml deleted file mode 100644 index a21cf8b0..00000000 --- a/common_toolset/phenotype_association.yml +++ /dev/null @@ -1,12 +0,0 @@ -tool_panel_section_label: Phenotype Association -tools: -- name: vcf2pgsnp - owner: devteam -- name: snpfreq - owner: devteam -- name: divide_pg_snp - owner: devteam -- name: hgv_fundo - owner: devteam -- name: hgv_hilbertvis - owner: devteam diff --git a/common_toolset/phenotype_association.yml.lock b/common_toolset/phenotype_association.yml.lock deleted file mode 100644 index b42b82bb..00000000 --- a/common_toolset/phenotype_association.yml.lock +++ /dev/null @@ -1,35 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Phenotype Association -tools: -- name: vcf2pgsnp - owner: devteam - revisions: - - 5fca46616675 - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association -- name: snpfreq - owner: devteam - revisions: - - 5c3ac057608b - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association -- name: divide_pg_snp - owner: devteam - revisions: - - f74fdfc17143 - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association -- name: hgv_fundo - owner: devteam - revisions: - - ca3fcd18dc3e - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association -- name: hgv_hilbertvis - owner: devteam - revisions: - - e1a9ad05dced - tool_panel_section_id: phenotype_association - tool_panel_section_label: Phenotype Association diff --git a/common_toolset/phylogenetics.yml b/common_toolset/phylogenetics.yml deleted file mode 100644 index a29a8293..00000000 --- a/common_toolset/phylogenetics.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Phylogenetics -tools: -- name: phyml - owner: iuc diff --git a/common_toolset/phylogenetics.yml.lock b/common_toolset/phylogenetics.yml.lock deleted file mode 100644 index 9a65e8ab..00000000 --- a/common_toolset/phylogenetics.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Phylogenetics -tools: -- name: phyml - owner: iuc - revisions: - - 850e213bee26 - tool_panel_section_id: phylogenetics - tool_panel_section_label: Phylogenetics diff --git a/common_toolset/picard.yml b/common_toolset/picard.yml deleted file mode 100644 index 44fb2253..00000000 --- a/common_toolset/picard.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Picard -tools: -- name: picard - owner: devteam diff --git a/common_toolset/picard.yml.lock b/common_toolset/picard.yml.lock deleted file mode 100644 index ebb9051d..00000000 --- a/common_toolset/picard.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Picard -tools: -- name: picard - owner: devteam - revisions: - - 7d34178f2812 - tool_panel_section_id: picard - tool_panel_section_label: Picard diff --git a/common_toolset/presto.yml b/common_toolset/presto.yml deleted file mode 100644 index 8e73367c..00000000 --- a/common_toolset/presto.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: pRESTO -tools: -- name: migmap - owner: iuc diff --git a/common_toolset/presto.yml.lock b/common_toolset/presto.yml.lock deleted file mode 100644 index dadc1ab1..00000000 --- a/common_toolset/presto.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: pRESTO -tools: -- name: migmap - owner: iuc - revisions: - - 6ad9d48a512e - tool_panel_section_id: presto - tool_panel_section_label: pRESTO diff --git a/common_toolset/proteomics.yml b/common_toolset/proteomics.yml deleted file mode 100644 index fb0b4e91..00000000 --- a/common_toolset/proteomics.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Proteomics -tools: -- name: protease_prediction - owner: bgruening diff --git a/common_toolset/proteomics.yml.lock b/common_toolset/proteomics.yml.lock deleted file mode 100644 index ccb45409..00000000 --- a/common_toolset/proteomics.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Proteomics -tools: -- name: protease_prediction - owner: bgruening - revisions: - - c7a363d7ab26 - tool_panel_section_id: proteomics - tool_panel_section_label: Proteomics diff --git a/common_toolset/regional_variation.yml b/common_toolset/regional_variation.yml deleted file mode 100644 index 26a9f15c..00000000 --- a/common_toolset/regional_variation.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: Regional Variation -tools: -- name: substitution_rates - owner: devteam -- name: indels_3way - owner: devteam -- name: featurecounter - owner: devteam -- name: karyotype_plot - owner: guru-ananda -- name: heatmap - owner: guru-ananda -- name: draw_stacked_barplots - owner: devteam -- name: compute_motifs_frequency - owner: devteam -- name: compute_motif_frequencies_for_all_motifs - owner: devteam -- name: categorize_elements_satisfying_criteria - owner: devteam diff --git a/common_toolset/regional_variation.yml.lock b/common_toolset/regional_variation.yml.lock deleted file mode 100644 index eed4cfe0..00000000 --- a/common_toolset/regional_variation.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Regional Variation -tools: -- name: substitution_rates - owner: devteam - revisions: - - 3d9544198582 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: indels_3way - owner: devteam - revisions: - - 5ad24b81dd10 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: featurecounter - owner: devteam - revisions: - - ac6218e2b686 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: karyotype_plot - owner: guru-ananda - revisions: - - d810aa84ee6a - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: heatmap - owner: guru-ananda - revisions: - - dbd447fcd3e4 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: draw_stacked_barplots - owner: devteam - revisions: - - e997b710e38a - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: compute_motifs_frequency - owner: devteam - revisions: - - 1f8ee7f9701b - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: compute_motif_frequencies_for_all_motifs - owner: devteam - revisions: - - 5319efa51514 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation -- name: categorize_elements_satisfying_criteria - owner: devteam - revisions: - - 586c1f0e1515 - tool_panel_section_id: regional_variation - tool_panel_section_label: Regional Variation diff --git a/common_toolset/rna_seq.yml b/common_toolset/rna_seq.yml deleted file mode 100644 index bca72b72..00000000 --- a/common_toolset/rna_seq.yml +++ /dev/null @@ -1,74 +0,0 @@ -tool_panel_section_label: RNA-seq -tools: -- name: limma_voom - owner: iuc -- name: edger - owner: iuc -- name: hisat2 - owner: iuc -- name: featurecounts - owner: iuc -- name: dexseq - owner: iuc -- name: stringtie - owner: iuc -- name: salmon - owner: bgruening -- name: kallisto_quant - owner: iuc -- name: kallisto_pseudo - owner: iuc -- name: sailfish - owner: bgruening -- name: goseq - owner: iuc -- name: deseq2 - owner: iuc -- name: rgrnastar - owner: iuc -- name: cummerbund - owner: devteam -- name: htseq_count - owner: lparsons -- name: gffcompare - owner: iuc -- name: cuffmerge - owner: devteam -- name: filter_transcripts_via_tracking - owner: devteam -- name: structurefold - owner: tyty -- name: express - owner: devteam -- name: trinotate - owner: iuc -- name: trinity_analyze_diff_expr - owner: iuc -- name: selectsequencesfrommsa - owner: rnateam -- name: trinity_gene_to_trans_map - owner: iuc -- name: trinity_samples_qccheck - owner: iuc -- name: describe_samples - owner: iuc -- name: trinity_run_de_analysis - owner: iuc -- name: trinity_filter_low_expr_transcripts - owner: iuc -- name: trinity_contig_exn50_statistic - owner: iuc -- name: trinity_abundance_estimates_to_matrix - owner: iuc -- name: trinity_align_and_estimate_abundance - owner: iuc -- name: trinity - owner: iuc -- name: transdecoder - owner: iuc -- name: infernal - owner: bgruening -- name: tophat_fusion_post - owner: devteam -- name: rsem - owner: jjohnson diff --git a/common_toolset/rna_seq.yml.lock b/common_toolset/rna_seq.yml.lock deleted file mode 100644 index aa9ffc40..00000000 --- a/common_toolset/rna_seq.yml.lock +++ /dev/null @@ -1,221 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: RNA-seq -tools: -- name: limma_voom - owner: iuc - revisions: - - 0921444c832d - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: edger - owner: iuc - revisions: - - 555659de7321 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: hisat2 - owner: iuc - revisions: - - 3fb01a8c902d - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: featurecounts - owner: iuc - revisions: - - 9301937c9037 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: dexseq - owner: iuc - revisions: - - 9fd8b69e6e68 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: stringtie - owner: iuc - revisions: - - eba36e001f45 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: salmon - owner: bgruening - revisions: - - 6b0ba6de1424 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: kallisto_quant - owner: iuc - revisions: - - 10c98fab6c5a - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: kallisto_pseudo - owner: iuc - revisions: - - 1c75aa5de15e - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: sailfish - owner: bgruening - revisions: - - a8f343909c17 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: goseq - owner: iuc - revisions: - - 67c29afac85f - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: deseq2 - owner: iuc - revisions: - - 0696db066a5b - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: rgrnastar - owner: iuc - revisions: - - 0a563fd2f22e - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: cummerbund - owner: devteam - revisions: - - 78fcfc04fcfe - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: htseq_count - owner: lparsons - revisions: - - 7f5a8d427b39 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: gffcompare - owner: iuc - revisions: - - 2bb86e2c417f - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: cuffmerge - owner: devteam - revisions: - - cf747d1bd79a - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: filter_transcripts_via_tracking - owner: devteam - revisions: - - 45f89dcf0b4c - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: structurefold - owner: tyty - revisions: - - 7bb98e9296e9 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: express - owner: devteam - revisions: - - 7b0708761d05 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinotate - owner: iuc - revisions: - - 6fd16fad465d - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_analyze_diff_expr - owner: iuc - revisions: - - dc0f01791c9b - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: selectsequencesfrommsa - owner: rnateam - revisions: - - 876c70c6ecad - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_gene_to_trans_map - owner: iuc - revisions: - - 37a1129c89d2 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_samples_qccheck - owner: iuc - revisions: - - 9871104ea630 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: describe_samples - owner: iuc - revisions: - - 0693ccd171c4 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_run_de_analysis - owner: iuc - revisions: - - 1d689e4e1caf - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_filter_low_expr_transcripts - owner: iuc - revisions: - - e406ac71165d - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_contig_exn50_statistic - owner: iuc - revisions: - - 34a018cbee9c - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_abundance_estimates_to_matrix - owner: iuc - revisions: - - d6a479fd4281 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity_align_and_estimate_abundance - owner: iuc - revisions: - - 478f36effca1 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: trinity - owner: iuc - revisions: - - c9cfec002f71 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: transdecoder - owner: iuc - revisions: - - 0db979fead3a - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: infernal - owner: bgruening - revisions: - - 477d829d3250 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: tophat_fusion_post - owner: devteam - revisions: - - f83394a2c2da - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq -- name: rsem - owner: jjohnson - revisions: - - 14267d364365 - tool_panel_section_id: rna_seq - tool_panel_section_label: RNA-seq diff --git a/common_toolset/rseqc.yml b/common_toolset/rseqc.yml deleted file mode 100644 index d3d15522..00000000 --- a/common_toolset/rseqc.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: RSeQC -tools: -- name: rseqc - owner: nilesh diff --git a/common_toolset/rseqc.yml.lock b/common_toolset/rseqc.yml.lock deleted file mode 100644 index 35ccb93a..00000000 --- a/common_toolset/rseqc.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: RSeQC -tools: -- name: rseqc - owner: nilesh - revisions: - - f437057e46f1 - tool_panel_section_id: rseqc - tool_panel_section_label: RSeQC diff --git a/common_toolset/sambam.yml b/common_toolset/sambam.yml deleted file mode 100644 index db5117cd..00000000 --- a/common_toolset/sambam.yml +++ /dev/null @@ -1,50 +0,0 @@ -tool_panel_section_label: SAM/BAM -tools: -- name: samtools_sort - owner: devteam -- name: samtools_mpileup - owner: devteam -- name: samtools_flagstat - owner: devteam -- name: samtool_filter2 - owner: devteam -- name: bam_to_sam - owner: devteam -- name: samtools_idxstats - owner: devteam -- name: sam_to_bam - owner: devteam -- name: samtools_calmd - owner: devteam -- name: samtools_bedcov - owner: devteam -- name: samtools_split - owner: devteam -- name: samtools_stats - owner: devteam -- name: samtools_slice_bam - owner: devteam -- name: samtools_reheader - owner: devteam -- name: samtools_rmdup - owner: devteam -- name: sam_merge - owner: devteam -- name: pileup_interval - owner: devteam -- name: pileup_parser - owner: devteam -- name: sam2interval - owner: devteam -- name: sam_bitwise_flag_filter - owner: devteam -- name: sam_pileup - owner: devteam -- name: bamtools_split - owner: devteam -- name: bamtools - owner: devteam -- name: bamtools_filter - owner: devteam -- name: samtools_phase - owner: devteam diff --git a/common_toolset/sambam.yml.lock b/common_toolset/sambam.yml.lock deleted file mode 100644 index 7b30df0f..00000000 --- a/common_toolset/sambam.yml.lock +++ /dev/null @@ -1,149 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: SAM/BAM -tools: -- name: samtools_sort - owner: devteam - revisions: - - e613c1ad4c4c - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_mpileup - owner: devteam - revisions: - - fa7ad9b89f4a - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_flagstat - owner: devteam - revisions: - - 4e404acfafa6 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtool_filter2 - owner: devteam - revisions: - - 56c31114ad4a - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: bam_to_sam - owner: devteam - revisions: - - 88eedb4abea0 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_idxstats - owner: devteam - revisions: - - 04d5581db1f5 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam_to_bam - owner: devteam - revisions: - - f7a0d41036c7 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_calmd - owner: devteam - revisions: - - e65c2cd0964c - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_bedcov - owner: devteam - revisions: - - 12749212f61b - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_split - owner: devteam - revisions: - - b7f7826ef1cd - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_stats - owner: devteam - revisions: - - 793ad847121d - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_slice_bam - owner: devteam - revisions: - - a4a10c7924d1 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_reheader - owner: devteam - revisions: - - db000c6007a0 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_rmdup - owner: devteam - revisions: - - 9129584416e2 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam_merge - owner: devteam - revisions: - - 1977f1637890 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: pileup_interval - owner: devteam - revisions: - - ef11139d4545 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: pileup_parser - owner: devteam - revisions: - - 85bedbea8a12 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam2interval - owner: devteam - revisions: - - 8c737b8ddc45 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam_bitwise_flag_filter - owner: devteam - revisions: - - 0b2424a404d9 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: sam_pileup - owner: devteam - revisions: - - 890d97772e2a - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: bamtools_split - owner: devteam - revisions: - - e2c1b62e1db1 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: bamtools - owner: devteam - revisions: - - 04866f817daa - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: bamtools_filter - owner: devteam - revisions: - - 4fe8a75334c8 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM -- name: samtools_phase - owner: devteam - revisions: - - 6166013090c0 - tool_panel_section_id: sam_bam - tool_panel_section_label: SAM/BAM diff --git a/common_toolset/seqtk.yml b/common_toolset/seqtk.yml deleted file mode 100644 index a2885d11..00000000 --- a/common_toolset/seqtk.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Seqtk -tools: -- name: seqtk - owner: iuc diff --git a/common_toolset/seqtk.yml.lock b/common_toolset/seqtk.yml.lock deleted file mode 100644 index 2f182149..00000000 --- a/common_toolset/seqtk.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Seqtk -tools: -- name: seqtk - owner: iuc - revisions: - - a09586d5149a - tool_panel_section_id: seqtk - tool_panel_section_label: Seqtk diff --git a/common_toolset/statistics.yml b/common_toolset/statistics.yml deleted file mode 100644 index 91809ff3..00000000 --- a/common_toolset/statistics.yml +++ /dev/null @@ -1,28 +0,0 @@ -tool_panel_section_label: Statistics -tools: -- name: count_gff_features - owner: devteam -- name: t_test_two_samples - owner: devteam -- name: mine - owner: devteam -- name: plot_from_lda - owner: devteam -- name: lda_analysis - owner: devteam -- name: generate_pc_lda_matrix - owner: devteam -- name: correlation - owner: devteam -- name: best_regression_subsets - owner: devteam -- name: canonical_correlation_analysis - owner: devteam -- name: kernel_canonical_correlation_analysis - owner: devteam -- name: kernel_principal_component_analysis - owner: devteam -- name: principal_component_analysis - owner: devteam -- name: dwt_var_perfeature - owner: devteam diff --git a/common_toolset/statistics.yml.lock b/common_toolset/statistics.yml.lock deleted file mode 100644 index 875a6013..00000000 --- a/common_toolset/statistics.yml.lock +++ /dev/null @@ -1,83 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Statistics -tools: -- name: count_gff_features - owner: devteam - revisions: - - 188392a0d0a8 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: t_test_two_samples - owner: devteam - revisions: - - c2ffc9885b5a - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: mine - owner: devteam - revisions: - - 5e2c89443c44 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: plot_from_lda - owner: devteam - revisions: - - 08affc5d2aef - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: lda_analysis - owner: devteam - revisions: - - f0b6217f4a0c - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: generate_pc_lda_matrix - owner: devteam - revisions: - - 04cdbd00dcec - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: correlation - owner: devteam - revisions: - - 24e01abf9e34 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: best_regression_subsets - owner: devteam - revisions: - - 4f33ec73e445 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: canonical_correlation_analysis - owner: devteam - revisions: - - 9bc0c48a027f - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: kernel_canonical_correlation_analysis - owner: devteam - revisions: - - 5ce5a2adb875 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: kernel_principal_component_analysis - owner: devteam - revisions: - - 3d58aa83e4a3 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: principal_component_analysis - owner: devteam - revisions: - - f568051cdf2e - tool_panel_section_id: statistics - tool_panel_section_label: Statistics -- name: dwt_var_perfeature - owner: devteam - revisions: - - 7a15159140d1 - tool_panel_section_id: statistics - tool_panel_section_label: Statistics diff --git a/common_toolset/text_manipulation.yml b/common_toolset/text_manipulation.yml deleted file mode 100644 index 78bf4d90..00000000 --- a/common_toolset/text_manipulation.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: Text Manipulation -tools: -- name: column_maker - owner: devteam -- name: annotatemyids - owner: iuc -- name: uniprot_rest_interface - owner: bgruening -- name: add_input_name_as_column - owner: mvdbeek -- name: replace_column_by_key_value_file - owner: bgruening -- name: text_processing - owner: bgruening -- name: regex_find_replace - owner: galaxyp diff --git a/common_toolset/text_manipulation.yml.lock b/common_toolset/text_manipulation.yml.lock deleted file mode 100644 index d7955877..00000000 --- a/common_toolset/text_manipulation.yml.lock +++ /dev/null @@ -1,47 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Text Manipulation -tools: -- name: column_maker - owner: devteam - revisions: - - 464b9305180e - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: annotatemyids - owner: iuc - revisions: - - 1aae04680c4b - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: uniprot_rest_interface - owner: bgruening - revisions: - - 054483e27a35 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: add_input_name_as_column - owner: mvdbeek - revisions: - - 06061aa49527 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: replace_column_by_key_value_file - owner: bgruening - revisions: - - d533e4b75800 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: text_processing - owner: bgruening - revisions: - - 0a8c6b61f0f4 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation -- name: regex_find_replace - owner: galaxyp - revisions: - - 209b7c5ee9d7 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation diff --git a/common_toolset/variant_calling.yml b/common_toolset/variant_calling.yml deleted file mode 100644 index 2136906b..00000000 --- a/common_toolset/variant_calling.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: Variant Calling -tools: -- name: varscan_version_2 - owner: devteam -- name: snpeff - owner: iuc -- name: naive_variant_caller - owner: blankenberg -- name: snpsift - owner: iuc -- name: freebayes - owner: devteam -- name: mutate_snp_codon - owner: devteam -- name: allele_counts - owner: nick diff --git a/common_toolset/variant_calling.yml.lock b/common_toolset/variant_calling.yml.lock deleted file mode 100644 index d9c63088..00000000 --- a/common_toolset/variant_calling.yml.lock +++ /dev/null @@ -1,47 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: Variant Calling -tools: -- name: varscan_version_2 - owner: devteam - revisions: - - bc1e0cd41241 - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: snpeff - owner: iuc - revisions: - - 8f92c2b26e6d - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: naive_variant_caller - owner: blankenberg - revisions: - - 07e71cf6c8ef - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: snpsift - owner: iuc - revisions: - - 2b3e65a4252f - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: freebayes - owner: devteam - revisions: - - 156b60c1530f - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: mutate_snp_codon - owner: devteam - revisions: - - 8f0af7251167 - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: allele_counts - owner: nick - revisions: - - 411adeff1eec - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling diff --git a/common_toolset/vcfbcf.yml b/common_toolset/vcfbcf.yml deleted file mode 100644 index 68aa018b..00000000 --- a/common_toolset/vcfbcf.yml +++ /dev/null @@ -1,122 +0,0 @@ -tool_panel_section_label: VCF/BCF -tools: -- name: vcffilter - owner: devteam -- name: vcfdistance - owner: devteam -- name: vcfselectsamples - owner: devteam -- name: vcfvcfintersect - owner: devteam -- name: vcfsort - owner: devteam -- name: vcfrandomsample - owner: devteam -- name: vcfprimers - owner: devteam -- name: vcfleftalign - owner: devteam -- name: vcfhethom - owner: devteam -- name: vcfgenotypes - owner: devteam -- name: vcfgeno2haplo - owner: devteam -- name: vcfflatten - owner: devteam -- name: vcffixup - owner: devteam -- name: vcfcommonsamples - owner: devteam -- name: vcfcombine - owner: devteam -- name: vcfcheck - owner: devteam -- name: vcfbreakcreatemulti - owner: devteam -- name: vcfbedintersect - owner: devteam -- name: vcfannotategenotypes - owner: devteam -- name: vcfannotate - owner: devteam -- name: vcfallelicprimitives - owner: devteam -- name: vcfaddinfo - owner: devteam -- name: vcf2tsv - owner: devteam -- name: vcftools_annotate - owner: devteam -- name: vcftools_slice - owner: devteam -- name: bcftools_plugin_tag2tag - owner: iuc -- name: bcftools_query - owner: iuc -- name: bcftools_plugin_dosage - owner: iuc -- name: bcftools_annotate - owner: iuc -- name: bcftools_csq - owner: iuc -- name: bcftools_filter - owner: iuc -- name: bcftools_view - owner: iuc -- name: bcftools_call - owner: iuc -- name: bcftools_roh - owner: iuc -- name: bcftools_merge - owner: iuc -- name: bcftools_isec - owner: iuc -- name: bcftools_plugin_fill_tags - owner: iuc -- name: bcftools_plugin_fill_an_ac - owner: iuc -- name: bcftools_stats - owner: iuc -- name: bcftools_reheader - owner: iuc -- name: bcftools_plugin_impute_info - owner: iuc -- name: bcftools_convert_from_vcf - owner: iuc -- name: bcftools_consensus - owner: iuc -- name: bcftools_concat - owner: iuc -- name: bcftools_plugin_mendelian - owner: iuc -- name: bcftools_mpileup - owner: iuc -- name: bcftools_plugin_counts - owner: iuc -- name: bcftools_plugin_setgt - owner: iuc -- name: bcftools_cnv - owner: iuc -- name: bcftools_plugin_missing2ref - owner: iuc -- name: bcftools_query_list_samples - owner: iuc -- name: bcftools_norm - owner: iuc -- name: bcftools_convert_to_vcf - owner: iuc -- name: bcftools_plugin_fixploidy - owner: iuc -- name: bcftools_gtcheck - owner: iuc -- name: snippy - owner: iuc -- name: varscan_somatic - owner: iuc -- name: vcftools_merge - owner: devteam -- name: vcftools_isec - owner: devteam -- name: vcftools_subset - owner: devteam diff --git a/common_toolset/vcfbcf.yml.lock b/common_toolset/vcfbcf.yml.lock deleted file mode 100644 index e03801e1..00000000 --- a/common_toolset/vcfbcf.yml.lock +++ /dev/null @@ -1,365 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_label: VCF/BCF -tools: -- name: vcffilter - owner: devteam - revisions: - - 81972652519c - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfdistance - owner: devteam - revisions: - - 48e458c721b3 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfselectsamples - owner: devteam - revisions: - - 958b6484a7f1 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfvcfintersect - owner: devteam - revisions: - - 6f6bf10618d7 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfsort - owner: devteam - revisions: - - 5b7120c66efc - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfrandomsample - owner: devteam - revisions: - - 12b570dd0bc5 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfprimers - owner: devteam - revisions: - - d226a7327946 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfleftalign - owner: devteam - revisions: - - d2406f98a782 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfhethom - owner: devteam - revisions: - - b07ef36cf7e6 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfgenotypes - owner: devteam - revisions: - - f5653ed90dfd - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfgeno2haplo - owner: devteam - revisions: - - b890055e07bd - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfflatten - owner: devteam - revisions: - - b24e368ae7b1 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcffixup - owner: devteam - revisions: - - fc5a64fdd5b2 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfcommonsamples - owner: devteam - revisions: - - 254f285dbaaa - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfcombine - owner: devteam - revisions: - - 53edb91ed051 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfcheck - owner: devteam - revisions: - - 5e850c85ba32 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfbreakcreatemulti - owner: devteam - revisions: - - 690b1d846263 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfbedintersect - owner: devteam - revisions: - - 9edfe5145ba8 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfannotategenotypes - owner: devteam - revisions: - - 70bc6ced57f7 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfannotate - owner: devteam - revisions: - - 6faa2c4c71d2 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfallelicprimitives - owner: devteam - revisions: - - a8a4f94aa321 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcfaddinfo - owner: devteam - revisions: - - afc0ba768690 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcf2tsv - owner: devteam - revisions: - - e92b3c0f9224 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_annotate - owner: devteam - revisions: - - 57a6550df582 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_slice - owner: devteam - revisions: - - 1363e5d4a8b8 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_tag2tag - owner: iuc - revisions: - - 2f8261ee0ea9 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_query - owner: iuc - revisions: - - 0770b1203e90 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_dosage - owner: iuc - revisions: - - 67bb9fcc0d96 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_annotate - owner: iuc - revisions: - - 2f09d9744e0b - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_csq - owner: iuc - revisions: - - 40388f544e5d - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_filter - owner: iuc - revisions: - - c01a175420f5 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_view - owner: iuc - revisions: - - ed94a3dccad0 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_call - owner: iuc - revisions: - - cb30a39055d0 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_roh - owner: iuc - revisions: - - f213f57dde66 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_merge - owner: iuc - revisions: - - beb87637bee3 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_isec - owner: iuc - revisions: - - 611f4cab1289 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_fill_tags - owner: iuc - revisions: - - 32f524fdc096 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_fill_an_ac - owner: iuc - revisions: - - d4a497619edf - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_stats - owner: iuc - revisions: - - e3c64225cbe6 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_reheader - owner: iuc - revisions: - - 3e9e03b3107a - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_impute_info - owner: iuc - revisions: - - 9b298d4d10c2 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_convert_from_vcf - owner: iuc - revisions: - - a7db83715075 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_consensus - owner: iuc - revisions: - - 70b8e9908ea8 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_concat - owner: iuc - revisions: - - 398d2ccc4233 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_mendelian - owner: iuc - revisions: - - 8c5c747e2bb4 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_mpileup - owner: iuc - revisions: - - 256e65e460b7 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_counts - owner: iuc - revisions: - - ed2ebaaded62 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_setgt - owner: iuc - revisions: - - 5ecd5f91b501 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_cnv - owner: iuc - revisions: - - 13fe14c56f6d - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_missing2ref - owner: iuc - revisions: - - ed003195e914 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_query_list_samples - owner: iuc - revisions: - - be337120b496 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_norm - owner: iuc - revisions: - - 76655fe2c70e - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_convert_to_vcf - owner: iuc - revisions: - - 843e008b15fd - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_plugin_fixploidy - owner: iuc - revisions: - - 2978f7d1f150 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: bcftools_gtcheck - owner: iuc - revisions: - - 833ad3665419 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: snippy - owner: iuc - revisions: - - feb7e635c6af - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: varscan_somatic - owner: iuc - revisions: - - b79bb8b09822 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_merge - owner: devteam - revisions: - - 71e19ddf52f5 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_isec - owner: devteam - revisions: - - aa232e38338f - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF -- name: vcftools_subset - owner: devteam - revisions: - - 23436d1d0fa1 - tool_panel_section_id: vcf_bcf - tool_panel_section_label: VCF/BCF diff --git a/scripts/api.py b/scripts/api.py new file mode 100644 index 00000000..eea4b948 --- /dev/null +++ b/scripts/api.py @@ -0,0 +1,16 @@ +#!/usr/bin/env python +import glob +import yaml +import json +import os + +data = {} +for fn in sorted(glob.glob("usegalaxy.org/*.yml")): + with open(fn, 'r') as handle: + tools = yaml.safe_load(handle) + for x in tools['tools']: + data[f"{x['owner']}/{x['name']}"] = tools['tool_panel_section_label'] + +os.makedirs('api/', exist_ok=True) +with open('api/labels.json', 'w') as handle: + json.dump(data, handle) diff --git a/scripts/fix-lockfile.py b/scripts/fix-lockfile.py index d79cb77a..63051567 100644 --- a/scripts/fix-lockfile.py +++ b/scripts/fix-lockfile.py @@ -96,7 +96,7 @@ def update_file(fn, install_repository_dependencies, install_resolver_dependenci parser = argparse.ArgumentParser() parser.add_argument('--no-install-repository-dependencies', action='store_true', default=False, help="Don't install TS repository dependencies") - parser.add_argument('--no-install-resolver-dependencies', action='store_true', default=False, + parser.add_argument('--no-install-resolver-dependencies', action='store_true', default=True, help="Don't install tool dependencies via Galaxy dependency resolver (e.g. conda)") parser.add_argument('fn', type=argparse.FileType('r'), help="Tool.yaml file") args = parser.parse_args() diff --git a/scripts/merge_versions.py b/scripts/merge_versions.py new file mode 100755 index 00000000..306eeef8 --- /dev/null +++ b/scripts/merge_versions.py @@ -0,0 +1,73 @@ +#!/usr/bin/env python +# +# given an input yaml and a toolset, find tools in existing sections and add versions + +import yaml +import glob +import re +import os +import sys +import argparse + +def main(): + + VERSION = 0.1 + + parser = argparse.ArgumentParser(description="") + parser.add_argument("-t", "--tools", default="tools.yaml", help="Input tools.yaml") + parser.add_argument("-s", "--toolset", default="usegalaxy.org", help="The toolset dir to add versions to") + parser.add_argument("-l", "--leftovers-file", default="leftovers.yaml", help="The file to store leftover (uninstalled) repos in.") + parser.add_argument("--version", action='store_true') + parser.add_argument("--verbose", action='store_true') + + args = parser.parse_args() + + if args.version: + print("merge_versions.py version: %.1f" % VERSION) + return + + tools_yaml = args.tools + toolset = args.toolset + + lock_files = glob.glob(os.path.join(args.toolset, "*.lock")) + + revisions = {} + leftover_tools = [] + + for lock_file in lock_files: + if args.verbose: + print(f"Reading lock file: {lock_file}") + a = yaml.safe_load(open(lock_file, 'r')) + tools = a['tools'] + for tool in tools: + tool_key = (tool['name'], tool['owner']) + revisions[tool_key] = tool['revisions'] + + if args.verbose: + print(f"Processing input tools.yaml: {tools_yaml}") + a = yaml.safe_load(open(tools_yaml, 'r')) + tools = a['tools'] + for tool in tools: + tool_key = (tool['name'], tool['owner']) + if tool_key in revisions: + revisions[tool_key] = sorted(list(set(tool['revisions']).union(set(revisions[tool_key])))) + else: + leftover_tools.append(tool) + + for lock_file in lock_files: + if args.verbose: + print(f"Updating lock file: {lock_file}") + a = yaml.safe_load(open(lock_file, 'r')) + tools = a['tools'] + for tool in tools: + tool_key = (tool['name'], tool['owner']) + tool['revisions'] = revisions[tool_key] + + with open(lock_file, 'w') as out: + yaml.dump(a, out, default_flow_style=False) + + with open(args.leftovers_file, 'w') as out: + yaml.dump({'tools': leftover_tools}, out, default_flow_style=False) + +if __name__ == "__main__": + main() diff --git a/scripts/steal_sections.py b/scripts/steal_sections.py new file mode 100755 index 00000000..331c9757 --- /dev/null +++ b/scripts/steal_sections.py @@ -0,0 +1,106 @@ +#!/usr/bin/env python +# +# given an input yaml and a toolset, find tools in sections on another server and add to toolset + +import yaml +import glob +import re +import os +import string +import sys +import argparse +import requests + +def main(): + + VERSION = 0.1 + + parser = argparse.ArgumentParser(description="") + parser.add_argument("-t", "--tools", default="tools.yaml", help="Input tools.yaml") + parser.add_argument("-s", "--toolset", default="usegalaxy.org", help="The toolset dir to add versions to") + parser.add_argument("-l", "--leftovers-file", default="leftovers.yaml", help="The file to store leftover (unmatched) repos in.") + parser.add_argument("-g", "--galaxy-url", default="https://usegalaxy.eu", help="The Galaxy server to steal from") + parser.add_argument("--version", action='store_true') + parser.add_argument("--verbose", action='store_true') + + args = parser.parse_args() + + if args.version: + print("merge_versions.py version: %.1f" % VERSION) + return + + tools_yaml = args.tools + toolset = args.toolset + + section_files = glob.glob(os.path.join(args.toolset, "*.yml")) + + other_tools = {} + other_labels = {} + + url = f"{args.galaxy_url}/api/tools?in_panel=false" + if args.verbose: + print(f"Loading tools from: {url}") + for tool in requests.get(url).json(): + if 'tool_shed_repository' not in tool: + continue + # this overwrites multi-tool repos but that's not a biggie + tool_key = (tool['tool_shed_repository']['name'], tool['tool_shed_repository']['owner']) + section_label = tool['panel_section_name'] + section_id = ''.join(c if c in string.ascii_letters + string.digits else '_' for c in section_label).lower() + other_tools[tool_key] = section_id + other_labels[section_id] = section_label + + existing = {} + leftover_tools = [] + new = {} + + for section_file in section_files: + if args.verbose: + print(f"Reading section file: {section_file}") + a = yaml.safe_load(open(section_file, 'r')) + tools = a['tools'] + for tool in tools: + tool_key = (tool['name'], tool['owner']) + existing[tool_key] = section_file + + if args.verbose: + print(f"Processing input tools.yaml: {tools_yaml}") + a = yaml.safe_load(open(tools_yaml, 'r')) + tools = a['tools'] + for tool in tools: + tool_key = (tool['name'], tool['owner']) + if tool_key in existing: + if args.verbose: + print(f"Skipping existing tool: {tool['owner']}/{tool['name']}") + continue + elif tool_key in other_tools: + try: + new[other_tools[tool_key]].append(tool_key) + except: + new[other_tools[tool_key]] = [tool_key] + else: + leftover_tools.append(tool) + + print(f"Found sections for {len(new)} tools ({len(leftover_tools)} left over)") + + for section, repos in new.items(): + section_file = os.path.join(toolset, section + ".yml") + if not os.path.exists(section_file): + a = {'tool_panel_section_label': other_labels[section], 'tools': []} + if args.verbose: + print(f"Adding to new section file: {section_file}") + else: + a = yaml.safe_load(open(section_file, 'r')) + if args.verbose: + print(f"Adding to existing section file: {section_file}") + tools = a['tools'] + tools.extend({"name": t[0], "owner": t[1]} for t in repos) + + with open(section_file, 'w') as out: + yaml.dump(a, out, default_flow_style=False) + + with open(args.leftovers_file, 'w') as out: + yaml.dump({'tools': leftover_tools}, out, default_flow_style=False) + +if __name__ == "__main__": + main() diff --git a/test.galaxyproject.org/annotation.yml b/test.galaxyproject.org/annotation.yml index e749edb5..e8f56df6 100644 --- a/test.galaxyproject.org/annotation.yml +++ b/test.galaxyproject.org/annotation.yml @@ -8,3 +8,5 @@ tools: owner: bgruening - name: busco owner: iuc +- name: maker + owner: iuc diff --git a/test.galaxyproject.org/annotation.yml.lock b/test.galaxyproject.org/annotation.yml.lock index 69710262..119c725b 100644 --- a/test.galaxyproject.org/annotation.yml.lock +++ b/test.galaxyproject.org/annotation.yml.lock @@ -6,15 +6,15 @@ tools: - name: prokka owner: crs4 revisions: - - eaee459f3d69 - d643e3b03500 + - eaee459f3d69 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: augustus owner: bgruening revisions: - - b3f5d0879dab - 28433faa6e42 + - b3f5d0879dab tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: augustus_training @@ -27,7 +27,13 @@ tools: - name: busco owner: iuc revisions: - - 1e62c28ba91d - 0d243f458b53 + - 1e62c28ba91d + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: maker + owner: iuc + revisions: + - a444254e9a57 tool_panel_section_id: annotation tool_panel_section_label: Annotation diff --git a/test.galaxyproject.org/assembly.yml.lock b/test.galaxyproject.org/assembly.yml.lock index 40a8132f..cffa8519 100644 --- a/test.galaxyproject.org/assembly.yml.lock +++ b/test.galaxyproject.org/assembly.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Assembly tools: @@ -16,6 +16,7 @@ tools: owner: iuc revisions: - 0834c823d4b9 + - 3061c8b029e5 - 59db8ea8c845 - ebb0dcdb621a tool_panel_section_id: assembly @@ -35,9 +36,10 @@ tools: - name: trinity owner: iuc revisions: + - 5b60313a6ce7 - c9cfec002f71 + - d2bc35f3d1c5 - d84caa5a98ad - - 5b60313a6ce7 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: spades @@ -50,18 +52,21 @@ tools: - name: meryl owner: iuc revisions: + - 29dabd8db6f2 - 5ae3496f9ca3 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: hifiasm owner: bgruening revisions: + - 366a11d316a7 - 9ef6920c3089 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: bionano_scaffold owner: bgruening revisions: + - 5258e18bbe23 - 96cacb31d571 tool_panel_section_id: assembly tool_panel_section_label: Assembly diff --git a/test.galaxyproject.org/bed.yml.lock b/test.galaxyproject.org/bed.yml.lock index 648f1a77..2b045725 100644 --- a/test.galaxyproject.org/bed.yml.lock +++ b/test.galaxyproject.org/bed.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: BED tools: diff --git a/test.galaxyproject.org/collection_operations.yml.lock b/test.galaxyproject.org/collection_operations.yml.lock index 2a76162d..1599fe7f 100644 --- a/test.galaxyproject.org/collection_operations.yml.lock +++ b/test.galaxyproject.org/collection_operations.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Collection Operations tools: diff --git a/test.galaxyproject.org/convert_formats.yml.lock b/test.galaxyproject.org/convert_formats.yml.lock index af261da4..f133f56b 100644 --- a/test.galaxyproject.org/convert_formats.yml.lock +++ b/test.galaxyproject.org/convert_formats.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Convert Formats tools: diff --git a/test.galaxyproject.org/data_managers.yml b/test.galaxyproject.org/data_managers.yml index 01322b86..7977c024 100644 --- a/test.galaxyproject.org/data_managers.yml +++ b/test.galaxyproject.org/data_managers.yml @@ -1,5 +1,7 @@ tool_panel_section_label: Data Managers tools: +- name: data_manager_pangolearn + owner: iuc - name: data_manager_selection_background owner: iuc - name: data_manager_build_kraken2_database diff --git a/test.galaxyproject.org/data_managers.yml.lock b/test.galaxyproject.org/data_managers.yml.lock index 651efd4a..ed30aa35 100644 --- a/test.galaxyproject.org/data_managers.yml.lock +++ b/test.galaxyproject.org/data_managers.yml.lock @@ -1,8 +1,14 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Data Managers tools: +- name: data_manager_pangolearn + owner: iuc + revisions: + - 6e24e79d3d69 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers - name: data_manager_selection_background owner: iuc revisions: diff --git a/test.galaxyproject.org/deeptools.yml.lock b/test.galaxyproject.org/deeptools.yml.lock index b3ee9723..f9a69ce2 100644 --- a/test.galaxyproject.org/deeptools.yml.lock +++ b/test.galaxyproject.org/deeptools.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: deepTools tools: diff --git a/test.galaxyproject.org/du_novo.yml.lock b/test.galaxyproject.org/du_novo.yml.lock index 3576742a..0eddb43c 100644 --- a/test.galaxyproject.org/du_novo.yml.lock +++ b/test.galaxyproject.org/du_novo.yml.lock @@ -19,6 +19,7 @@ tools: owner: nick revisions: - 7f170cb06e2e + - 464aee13e2df tool_panel_section_id: du_novo tool_panel_section_label: Du Novo - name: duplex_family_size_distribution diff --git a/test.galaxyproject.org/emboss.yml.lock b/test.galaxyproject.org/emboss.yml.lock index 04676c6d..323a0cf7 100644 --- a/test.galaxyproject.org/emboss.yml.lock +++ b/test.galaxyproject.org/emboss.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: EMBOSS tools: diff --git a/test.galaxyproject.org/evolution.yml.lock b/test.galaxyproject.org/evolution.yml.lock index 700d952e..220601d6 100644 --- a/test.galaxyproject.org/evolution.yml.lock +++ b/test.galaxyproject.org/evolution.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Evolution tools: diff --git a/test.galaxyproject.org/extract_features.yml b/test.galaxyproject.org/extract_features.yml new file mode 100644 index 00000000..69714543 --- /dev/null +++ b/test.galaxyproject.org/extract_features.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Extract Features +tools: +- name: parse_mito_blast + owner: iuc diff --git a/test.galaxyproject.org/extract_features.yml.lock b/test.galaxyproject.org/extract_features.yml.lock new file mode 100644 index 00000000..edb56292 --- /dev/null +++ b/test.galaxyproject.org/extract_features.yml.lock @@ -0,0 +1,11 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tools: +- name: parse_mito_blast + owner: iuc + revisions: + - 3c9ad4adf8d2 + - f172b1f77d6c + tool_panel_section_id: extract_features + tool_panel_section_label: Extract Features diff --git a/test.galaxyproject.org/fabio_tools.yml.lock b/test.galaxyproject.org/fabio_tools.yml.lock index f6c467a2..6979a697 100644 --- a/test.galaxyproject.org/fabio_tools.yml.lock +++ b/test.galaxyproject.org/fabio_tools.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Fabio Tools tools: diff --git a/test.galaxyproject.org/fasta_fastq.yml.lock b/test.galaxyproject.org/fasta_fastq.yml.lock index 8002c89c..23472ee7 100644 --- a/test.galaxyproject.org/fasta_fastq.yml.lock +++ b/test.galaxyproject.org/fasta_fastq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: FASTA/FASTQ tools: diff --git a/test.galaxyproject.org/fastq_quality_control.yml.lock b/test.galaxyproject.org/fastq_quality_control.yml.lock index cbaed337..cb10331b 100644 --- a/test.galaxyproject.org/fastq_quality_control.yml.lock +++ b/test.galaxyproject.org/fastq_quality_control.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: FASTQ Quality Control tools: diff --git a/test.galaxyproject.org/filter_and_sort.yml.lock b/test.galaxyproject.org/filter_and_sort.yml.lock index 22a70f5f..6965c92f 100644 --- a/test.galaxyproject.org/filter_and_sort.yml.lock +++ b/test.galaxyproject.org/filter_and_sort.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Filter and Sort tools: diff --git a/test.galaxyproject.org/gatk.yml.lock b/test.galaxyproject.org/gatk.yml.lock index cf99b7a2..5511f6f2 100644 --- a/test.galaxyproject.org/gatk.yml.lock +++ b/test.galaxyproject.org/gatk.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: GATK tools: diff --git a/test.galaxyproject.org/gemini.yml.lock b/test.galaxyproject.org/gemini.yml.lock index db7ccc4b..74d8e1e8 100644 --- a/test.galaxyproject.org/gemini.yml.lock +++ b/test.galaxyproject.org/gemini.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: GEMINI tools: diff --git a/test.galaxyproject.org/get_data.yml.lock b/test.galaxyproject.org/get_data.yml.lock index a9cc5175..17a4cfa8 100644 --- a/test.galaxyproject.org/get_data.yml.lock +++ b/test.galaxyproject.org/get_data.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Get Data tools: diff --git a/test.galaxyproject.org/graph_display_data.yml.lock b/test.galaxyproject.org/graph_display_data.yml.lock index 5266c497..4e648ede 100644 --- a/test.galaxyproject.org/graph_display_data.yml.lock +++ b/test.galaxyproject.org/graph_display_data.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Graph/Display Data tools: diff --git a/test.galaxyproject.org/hicexplorer.yml.lock b/test.galaxyproject.org/hicexplorer.yml.lock index ede80c6c..11aa49ac 100644 --- a/test.galaxyproject.org/hicexplorer.yml.lock +++ b/test.galaxyproject.org/hicexplorer.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: HiCExplorer tools: diff --git a/test.galaxyproject.org/hyphy_tools.yml.lock b/test.galaxyproject.org/hyphy_tools.yml.lock index c72b85b0..e4a713b0 100644 --- a/test.galaxyproject.org/hyphy_tools.yml.lock +++ b/test.galaxyproject.org/hyphy_tools.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: HyPhy Methods tools: diff --git a/test.galaxyproject.org/ideas.yml.lock b/test.galaxyproject.org/ideas.yml.lock index 77e69ac9..724904eb 100644 --- a/test.galaxyproject.org/ideas.yml.lock +++ b/test.galaxyproject.org/ideas.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: IDEAS tools: diff --git a/test.galaxyproject.org/join__subtract_and_group.yml.lock b/test.galaxyproject.org/join__subtract_and_group.yml.lock index 0bd6bf79..cfbfa100 100644 --- a/test.galaxyproject.org/join__subtract_and_group.yml.lock +++ b/test.galaxyproject.org/join__subtract_and_group.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Join, Subtract and Group tools: diff --git a/test.galaxyproject.org/machine_learning.yml.lock b/test.galaxyproject.org/machine_learning.yml.lock index 971d1e74..21aca19e 100644 --- a/test.galaxyproject.org/machine_learning.yml.lock +++ b/test.galaxyproject.org/machine_learning.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Machine Learning tools: diff --git a/test.galaxyproject.org/metagenomic_analysis.yml.lock b/test.galaxyproject.org/metagenomic_analysis.yml.lock index e6f28c13..f33cf365 100644 --- a/test.galaxyproject.org/metagenomic_analysis.yml.lock +++ b/test.galaxyproject.org/metagenomic_analysis.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Metagenomic Analysis tools: diff --git a/test.galaxyproject.org/metagenomic_analysis__deprecated_.yml.lock b/test.galaxyproject.org/metagenomic_analysis__deprecated_.yml.lock index 89834bcd..c8dd5650 100644 --- a/test.galaxyproject.org/metagenomic_analysis__deprecated_.yml.lock +++ b/test.galaxyproject.org/metagenomic_analysis__deprecated_.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Metagenomic Analysis (deprecated) tools: diff --git a/test.galaxyproject.org/mimodd.yml.lock b/test.galaxyproject.org/mimodd.yml.lock index 90858eba..4991ece2 100644 --- a/test.galaxyproject.org/mimodd.yml.lock +++ b/test.galaxyproject.org/mimodd.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: MiModD tools: diff --git a/test.galaxyproject.org/motifs.yml.lock b/test.galaxyproject.org/motifs.yml.lock index ebc47858..bde98c5e 100644 --- a/test.galaxyproject.org/motifs.yml.lock +++ b/test.galaxyproject.org/motifs.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Motifs tools: diff --git a/test.galaxyproject.org/multiple_alignments.yml.lock b/test.galaxyproject.org/multiple_alignments.yml.lock index 03876f8d..76ab2186 100644 --- a/test.galaxyproject.org/multiple_alignments.yml.lock +++ b/test.galaxyproject.org/multiple_alignments.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Multiple Alignments tools: diff --git a/test.galaxyproject.org/nanopore.yml.lock b/test.galaxyproject.org/nanopore.yml.lock index 5405c221..1b3eff8c 100644 --- a/test.galaxyproject.org/nanopore.yml.lock +++ b/test.galaxyproject.org/nanopore.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Nanopore tools: diff --git a/test.galaxyproject.org/ncbi_blast_.yml b/test.galaxyproject.org/ncbi_blast_.yml index b03bebe9..d1a1f6a5 100644 --- a/test.galaxyproject.org/ncbi_blast_.yml +++ b/test.galaxyproject.org/ncbi_blast_.yml @@ -2,3 +2,5 @@ tool_panel_section_label: NCBI BLAST+ tools: - name: ncbi_blast_plus owner: devteam +- name: kraken2 + owner: iuc diff --git a/test.galaxyproject.org/ncbi_blast_.yml.lock b/test.galaxyproject.org/ncbi_blast_.yml.lock index 43b8802a..a0fb1f85 100644 --- a/test.galaxyproject.org/ncbi_blast_.yml.lock +++ b/test.galaxyproject.org/ncbi_blast_.yml.lock @@ -1,11 +1,23 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: NCBI BLAST+ tools: - name: ncbi_blast_plus owner: devteam revisions: + - 0e3cf9594bb7 - 2889433c7ae1 + - 5edc472ec434 + - acf4e47b734c + - e25d3acf6e68 + tool_panel_section_id: ncbi_blast_ + tool_panel_section_label: NCBI BLAST+ +- name: kraken2 + owner: iuc + revisions: + - 328c607150ff + - 4a9da2b6c2e3 + - e674066930b2 tool_panel_section_id: ncbi_blast_ tool_panel_section_label: NCBI BLAST+ diff --git a/test.galaxyproject.org/operate_on_genomic_intervals.yml.lock b/test.galaxyproject.org/operate_on_genomic_intervals.yml.lock index ae3f4a62..4d01979d 100644 --- a/test.galaxyproject.org/operate_on_genomic_intervals.yml.lock +++ b/test.galaxyproject.org/operate_on_genomic_intervals.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Operate on Genomic Intervals tools: diff --git a/test.galaxyproject.org/picard.yml.lock b/test.galaxyproject.org/picard.yml.lock index ebb9051d..dfd7e405 100644 --- a/test.galaxyproject.org/picard.yml.lock +++ b/test.galaxyproject.org/picard.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Picard tools: diff --git a/test.galaxyproject.org/planttribes.yml.lock b/test.galaxyproject.org/planttribes.yml.lock index c4667e66..6f691e42 100644 --- a/test.galaxyproject.org/planttribes.yml.lock +++ b/test.galaxyproject.org/planttribes.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: PlantTribes tools: diff --git a/test.galaxyproject.org/protein_modeling.yml.lock b/test.galaxyproject.org/protein_modeling.yml.lock index b8ac2d35..5d4b9275 100644 --- a/test.galaxyproject.org/protein_modeling.yml.lock +++ b/test.galaxyproject.org/protein_modeling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Protein Modeling tools: diff --git a/test.galaxyproject.org/regional_variation.yml.lock b/test.galaxyproject.org/regional_variation.yml.lock index aca56dd7..520ef635 100644 --- a/test.galaxyproject.org/regional_variation.yml.lock +++ b/test.galaxyproject.org/regional_variation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Regional Variation tools: diff --git a/test.galaxyproject.org/rna_seq.yml.lock b/test.galaxyproject.org/rna_seq.yml.lock index 15df3368..528d6b5c 100644 --- a/test.galaxyproject.org/rna_seq.yml.lock +++ b/test.galaxyproject.org/rna_seq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RNA-seq tools: @@ -13,6 +13,7 @@ tools: owner: iuc revisions: - 850f3679b9b4 + - 4074fc1940e2 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: hisat2 diff --git a/test.galaxyproject.org/rseqc.yml.lock b/test.galaxyproject.org/rseqc.yml.lock index 35ccb93a..1ceafe2a 100644 --- a/test.galaxyproject.org/rseqc.yml.lock +++ b/test.galaxyproject.org/rseqc.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RSeQC tools: diff --git a/test.galaxyproject.org/sam_bam.yml.lock b/test.galaxyproject.org/sam_bam.yml.lock index e4f50af9..ead4bf41 100644 --- a/test.galaxyproject.org/sam_bam.yml.lock +++ b/test.galaxyproject.org/sam_bam.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: SAM/BAM tools: diff --git a/test.galaxyproject.org/statistics.yml.lock b/test.galaxyproject.org/statistics.yml.lock index 0cbbe849..4b4208dd 100644 --- a/test.galaxyproject.org/statistics.yml.lock +++ b/test.galaxyproject.org/statistics.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Statistics tools: diff --git a/test.galaxyproject.org/text_manipulation.yml.lock b/test.galaxyproject.org/text_manipulation.yml.lock index f53d8cd2..5aada8c8 100644 --- a/test.galaxyproject.org/text_manipulation.yml.lock +++ b/test.galaxyproject.org/text_manipulation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Text Manipulation tools: diff --git a/test.galaxyproject.org/transposon_insertion_sequencing.yml.lock b/test.galaxyproject.org/transposon_insertion_sequencing.yml.lock index 8487e26b..068030bc 100644 --- a/test.galaxyproject.org/transposon_insertion_sequencing.yml.lock +++ b/test.galaxyproject.org/transposon_insertion_sequencing.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Transposon Insertion Sequencing tools: diff --git a/test.galaxyproject.org/usegalaxy___common_tools_test.yml.lock b/test.galaxyproject.org/usegalaxy___common_tools_test.yml.lock index 8167b9cb..2f08daa9 100644 --- a/test.galaxyproject.org/usegalaxy___common_tools_test.yml.lock +++ b/test.galaxyproject.org/usegalaxy___common_tools_test.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: usegalaxy.* common tools test tools: diff --git a/test.galaxyproject.org/variant_calling.yml.lock b/test.galaxyproject.org/variant_calling.yml.lock index a3213c41..bf6d9480 100644 --- a/test.galaxyproject.org/variant_calling.yml.lock +++ b/test.galaxyproject.org/variant_calling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Variant Calling tools: diff --git a/test.galaxyproject.org/vcf_bcf.yml.lock b/test.galaxyproject.org/vcf_bcf.yml.lock index 4aae8a50..47223f0f 100644 --- a/test.galaxyproject.org/vcf_bcf.yml.lock +++ b/test.galaxyproject.org/vcf_bcf.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: VCF/BCF tools: diff --git a/usegalaxy.eu/annotation.yml b/usegalaxy.eu/annotation.yml deleted file mode 100644 index f695c71a..00000000 --- a/usegalaxy.eu/annotation.yml +++ /dev/null @@ -1,80 +0,0 @@ -tool_panel_section_label: Annotation -tools: -- name: annotatemyids - owner: iuc -- name: goseq - owner: iuc -- name: spaln - owner: iuc -- name: goslimmer - owner: iuc -- name: goenrichment - owner: iuc -- name: chipseeker - owner: rnateam -- name: fgsea - owner: iuc -- name: exonerate - owner: iuc -- name: jcvi_gff_stats - owner: iuc -- name: abricate - owner: iuc -- name: prokka - owner: crs4 -- name: hammock - owner: hammock -- name: kobas - owner: iuc -- name: tmhmm_and_signalp - owner: peterjc -- name: picrust_metagenome_contributions - owner: iuc -- name: picrust_format_tree_and_trait_table - owner: iuc -- name: picrust_compare_biom - owner: iuc -- name: picrust_predict_metagenomes - owner: iuc -- name: picrust_categorize - owner: iuc -- name: antismash - owner: bgruening -- name: augustus - owner: bgruening -- name: roary - owner: iuc -- name: sortmerna - owner: rnateam -- name: trna_prediction - owner: bgruening -- name: transtermhp - owner: iuc -- name: segmentation_fold - owner: yhoogstrate -- name: gubbins - owner: iuc -- name: probmetab - owner: mmonsoor -- name: lcmsmatching - owner: prog -- name: nucleosome_prediction - owner: bgruening -- name: miranda - owner: tgac -- name: dotknot - owner: bgruening -- name: blast2go - owner: peterjc -- name: hmmer3 - owner: iuc -- name: find_subsequences - owner: bgruening -- name: gotohscan - owner: rnateam -- name: interproscan5 - owner: bgruening -- name: glimmer3 - owner: bgruening -- name: dgidb_annotator - owner: devteam diff --git a/usegalaxy.eu/annotation.yml.lock b/usegalaxy.eu/annotation.yml.lock deleted file mode 100644 index 39f26284..00000000 --- a/usegalaxy.eu/annotation.yml.lock +++ /dev/null @@ -1,201 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: annotatemyids - owner: iuc - revisions: - - 38eedf3cc3c9 - tool_panel_section_label: Annotation -- name: goseq - owner: iuc - revisions: - - bbcf5f7f2af2 - tool_panel_section_label: Annotation -- name: spaln - owner: iuc - revisions: - - 95ea8d97abb4 - tool_panel_section_label: Annotation -- name: goslimmer - owner: iuc - revisions: - - 294de027cb5d - tool_panel_section_label: Annotation -- name: goenrichment - owner: iuc - revisions: - - 5ace5c7d1a86 - tool_panel_section_label: Annotation -- name: chipseeker - owner: rnateam - revisions: - - 4c2dbe4dbb4e - tool_panel_section_label: Annotation -- name: fgsea - owner: iuc - revisions: - - 9bb7943b5263 - tool_panel_section_label: Annotation -- name: exonerate - owner: iuc - revisions: - - f48ed38dfddf - tool_panel_section_label: Annotation -- name: jcvi_gff_stats - owner: iuc - revisions: - - 8cffbd184762 - tool_panel_section_label: Annotation -- name: abricate - owner: iuc - revisions: - - 78c75f134c16 - tool_panel_section_label: Annotation -- name: prokka - owner: crs4 - revisions: - - eaee459f3d69 - tool_panel_section_label: Annotation -- name: hammock - owner: hammock - revisions: - - 4db310b7e37c - tool_panel_section_label: Annotation -- name: kobas - owner: iuc - revisions: - - 83b998fa34ea - tool_panel_section_label: Annotation -- name: tmhmm_and_signalp - owner: peterjc - revisions: - - a19b3ded8f33 - tool_panel_section_label: Annotation -- name: picrust_metagenome_contributions - owner: iuc - revisions: - - bc71c2b53097 - tool_panel_section_label: Annotation -- name: picrust_format_tree_and_trait_table - owner: iuc - revisions: - - 61c60e3c8768 - tool_panel_section_label: Annotation -- name: picrust_compare_biom - owner: iuc - revisions: - - 9c0daedfbb0f - tool_panel_section_label: Annotation -- name: picrust_predict_metagenomes - owner: iuc - revisions: - - d2c35bdb60bd - tool_panel_section_label: Annotation -- name: picrust_categorize - owner: iuc - revisions: - - 86694fa8b64c - tool_panel_section_label: Annotation -- name: antismash - owner: bgruening - revisions: - - 3f0077c88c16 - tool_panel_section_label: Annotation -- name: augustus - owner: bgruening - revisions: - - 4de31938431b - tool_panel_section_label: Annotation -- name: roary - owner: iuc - revisions: - - f1ccc8a6eb05 - tool_panel_section_label: Annotation -- name: sortmerna - owner: rnateam - revisions: - - 65c38d020fea - tool_panel_section_label: Annotation -- name: trna_prediction - owner: bgruening - revisions: - - 358f58401cd6 - tool_panel_section_label: Annotation -- name: transtermhp - owner: iuc - revisions: - - 1a1ec22a7e28 - tool_panel_section_label: Annotation -- name: segmentation_fold - owner: yhoogstrate - revisions: - - 09e921a25c68 - - 4d16cf9414cf - tool_panel_section_label: Annotation -- name: gubbins - owner: iuc - revisions: - - 637ec5d5368c - tool_panel_section_label: Annotation -- name: probmetab - owner: mmonsoor - revisions: - - 3a9914b37f2f - tool_panel_section_label: Annotation -- name: lcmsmatching - owner: prog - revisions: - - 253d531a0193 - tool_panel_section_label: Annotation -- name: nucleosome_prediction - owner: bgruening - revisions: - - 2c42bb973ac3 - tool_panel_section_label: Annotation -- name: miranda - owner: tgac - revisions: - - bf6976462251 - tool_panel_section_label: Annotation -- name: dotknot - owner: bgruening - revisions: - - 42d20ff5da1b - tool_panel_section_label: Annotation -- name: blast2go - owner: peterjc - revisions: - - e23b621eb7bb - tool_panel_section_label: Annotation -- name: hmmer3 - owner: iuc - revisions: - - b5066aa77fea - tool_panel_section_label: Annotation -- name: find_subsequences - owner: bgruening - revisions: - - d882a0a75759 - tool_panel_section_label: Annotation -- name: gotohscan - owner: rnateam - revisions: - - 6845ddcd5588 - tool_panel_section_label: Annotation -- name: interproscan5 - owner: bgruening - revisions: - - e32f2ea6a139 - tool_panel_section_label: Annotation -- name: glimmer3 - owner: bgruening - revisions: - - b1ad88bbc5fa - tool_panel_section_label: Annotation -- name: dgidb_annotator - owner: devteam - revisions: - - 792f3cb0eff4 - - c5bb987015c5 - tool_panel_section_label: Annotation diff --git a/usegalaxy.eu/apollo.yml b/usegalaxy.eu/apollo.yml deleted file mode 100644 index 73f3d4ce..00000000 --- a/usegalaxy.eu/apollo.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: Apollo -tools: -- name: apollo_iframe - owner: gga -- name: apollo_feat_from_gff3 - owner: gga -- name: apollo_create_or_update - owner: gga -- name: apollo_export - owner: gga -- name: apollo_delete_organism - owner: gga -- name: apollo_fetch_jbrowse - owner: gga -- name: apollo_list_organism - owner: gga diff --git a/usegalaxy.eu/apollo.yml.lock b/usegalaxy.eu/apollo.yml.lock deleted file mode 100644 index f0ec1568..00000000 --- a/usegalaxy.eu/apollo.yml.lock +++ /dev/null @@ -1,39 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: apollo_iframe - owner: gga - revisions: - - a10003dc6c85 - tool_panel_section_label: Apollo -- name: apollo_feat_from_gff3 - owner: gga - revisions: - - 7c4a3e737e08 - tool_panel_section_label: Apollo -- name: apollo_create_or_update - owner: gga - revisions: - - aee984715db1 - tool_panel_section_label: Apollo -- name: apollo_export - owner: gga - revisions: - - 5559e41721c3 - tool_panel_section_label: Apollo -- name: apollo_delete_organism - owner: gga - revisions: - - a5de2095bd01 - tool_panel_section_label: Apollo -- name: apollo_fetch_jbrowse - owner: gga - revisions: - - 9968eec7430e - tool_panel_section_label: Apollo -- name: apollo_list_organism - owner: gga - revisions: - - b69804a685e2 - tool_panel_section_label: Apollo diff --git a/usegalaxy.eu/assembly.yml b/usegalaxy.eu/assembly.yml deleted file mode 100644 index 103af1f6..00000000 --- a/usegalaxy.eu/assembly.yml +++ /dev/null @@ -1,46 +0,0 @@ -tool_panel_section_label: Assembly -tools: -- name: flye - owner: bgruening -- name: racon - owner: bgruening -- name: spades - owner: nml -- name: quast - owner: iuc -- name: shovill - owner: iuc -- name: velvetoptimiser - owner: simon-gladman -- name: idba_ud - owner: iuc -- name: unicycler - owner: iuc -- name: megahit - owner: iuc -- name: pilon - owner: iuc -- name: wtdbg - owner: bgruening -- name: canu - owner: bgruening -- name: nanopolish_eventalign - owner: bgruening -- name: metaspades - owner: nml -- name: disco - owner: iuc -- name: rnaspades - owner: iuc -- name: mira_assembler - owner: peterjc -- name: edena - owner: crs4 -- name: sopra - owner: crs4 -- name: ssake - owner: crs4 -- name: crispr_recognition_tool - owner: bgruening -- name: minced - owner: bgruening diff --git a/usegalaxy.eu/assembly.yml.lock b/usegalaxy.eu/assembly.yml.lock deleted file mode 100644 index 005d4584..00000000 --- a/usegalaxy.eu/assembly.yml.lock +++ /dev/null @@ -1,114 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: flye - owner: bgruening - revisions: - - 1ce9b1d72ec3 - tool_panel_section_label: Assembly -- name: racon - owner: bgruening - revisions: - - aa39b19ca11e - tool_panel_section_label: Assembly -- name: spades - owner: nml - revisions: - - b8d633fbf5f5 - tool_panel_section_label: Assembly -- name: quast - owner: iuc - revisions: - - 81df4950d65b - tool_panel_section_label: Assembly -- name: shovill - owner: iuc - revisions: - - 865119fcb694 - tool_panel_section_label: Assembly -- name: velvetoptimiser - owner: simon-gladman - revisions: - - 37d88f41c810 - tool_panel_section_label: Assembly -- name: idba_ud - owner: iuc - revisions: - - fdaf2375d405 - tool_panel_section_label: Assembly -- name: unicycler - owner: iuc - revisions: - - 2db911a4efc5 - tool_panel_section_label: Assembly -- name: megahit - owner: iuc - revisions: - - 98242353faa4 - tool_panel_section_label: Assembly -- name: pilon - owner: iuc - revisions: - - 11e5408fd238 - tool_panel_section_label: Assembly -- name: wtdbg - owner: bgruening - revisions: - - 6a060928f7ff - tool_panel_section_label: Assembly -- name: canu - owner: bgruening - revisions: - - 58346ef3116b - tool_panel_section_label: Assembly -- name: nanopolish_eventalign - owner: bgruening - revisions: - - c8c5caecfacc - tool_panel_section_label: Assembly -- name: metaspades - owner: nml - revisions: - - 05c394313b1c - tool_panel_section_label: Assembly -- name: disco - owner: iuc - revisions: - - 6de3e77073ad - tool_panel_section_label: Assembly -- name: rnaspades - owner: iuc - revisions: - - 9e58ff014088 - tool_panel_section_label: Assembly -- name: mira_assembler - owner: peterjc - revisions: - - 63ebe9726219 - tool_panel_section_label: Assembly -- name: edena - owner: crs4 - revisions: - - b8c6a38530eb - tool_panel_section_label: Assembly -- name: sopra - owner: crs4 - revisions: - - 87ffe493b6c1 - tool_panel_section_label: Assembly -- name: ssake - owner: crs4 - revisions: - - f20db7280f89 - tool_panel_section_label: Assembly -- name: crispr_recognition_tool - owner: bgruening - revisions: - - db0f5c1cb227 - tool_panel_section_label: Assembly -- name: minced - owner: bgruening - revisions: - - e8cbdbc4de58 - tool_panel_section_label: Assembly diff --git a/usegalaxy.eu/chemicaltoolbox.yml b/usegalaxy.eu/chemicaltoolbox.yml deleted file mode 100644 index 4d16aab2..00000000 --- a/usegalaxy.eu/chemicaltoolbox.yml +++ /dev/null @@ -1,90 +0,0 @@ -tool_panel_section_label: ChemicalToolBox -tools: -- name: openbabel_filter - owner: bgruening -- name: openbabel_remsmall - owner: bgruening -- name: openbabel_obgrep - owner: bgruening -- name: openbabel_addh - owner: bgruening -- name: openbabel_remduplicates - owner: bgruening -- name: openbabel_svg_depiction - owner: bgruening -- name: openbabel_multi_obgrep - owner: bgruening -- name: openbabel_genprop - owner: bgruening -- name: openbabel_subsearch - owner: bgruening -- name: openbabel_remove_protonation_state - owner: bgruening -- name: openbabel_spectrophore_search - owner: bgruening -- name: md_converter - owner: chemteam -- name: bio3d_pca - owner: chemteam -- name: bio3d_rmsd - owner: chemteam -- name: bio3d_rmsf - owner: chemteam -- name: mdanalysis_distance - owner: chemteam -- name: mdanalysis_dihedral - owner: chemteam -- name: mdanalysis_rdf - owner: chemteam -- name: mdanalysis_angle - owner: chemteam -- name: packmol - owner: chemteam -- name: gmx_nvt - owner: chemteam -- name: gmx_md - owner: chemteam -- name: gmx_solvate - owner: chemteam -- name: gmx_em - owner: chemteam -- name: gmx_setup - owner: chemteam -- name: gmx_npt - owner: chemteam -- name: openbabel - owner: bgruening -- name: osra - owner: bgruening -- name: openbabel_remions - owner: bgruening -- name: openbabel_compound_convert - owner: bgruening -- name: openbabel_change_title - owner: bgruening -- name: chemfp - owner: bgruening -- name: natural_product_likeness - owner: bgruening -- name: simsearch - owner: bgruening -- name: confab - owner: bgruening -- name: ctb_machine_learning - owner: bgruening -- name: silicos_it - owner: bgruening -- name: opsin - owner: bgruening -- name: rdkit - owner: bgruening -- name: chemical_data_sources - owner: bgruening -- name: openmg - owner: bgruening -- name: autodock_vina - owner: bgruening -- name: autodock_vina_prepare_ligand - owner: bgruening -- name: autodock_vina_prepare_receptor - owner: bgruening diff --git a/usegalaxy.eu/chemicaltoolbox.yml.lock b/usegalaxy.eu/chemicaltoolbox.yml.lock deleted file mode 100644 index 184aeb43..00000000 --- a/usegalaxy.eu/chemicaltoolbox.yml.lock +++ /dev/null @@ -1,225 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: openbabel_filter - owner: bgruening - revisions: - - 69e02cf88856 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_remsmall - owner: bgruening - revisions: - - 11952f619e90 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_obgrep - owner: bgruening - revisions: - - 50dc8ca09a50 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_addh - owner: bgruening - revisions: - - bfb8555f0003 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_remduplicates - owner: bgruening - revisions: - - d751e92477ea - tool_panel_section_label: ChemicalToolBox -- name: openbabel_svg_depiction - owner: bgruening - revisions: - - ed50b83b02e9 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_multi_obgrep - owner: bgruening - revisions: - - 09640954740c - tool_panel_section_label: ChemicalToolBox -- name: openbabel_genprop - owner: bgruening - revisions: - - ebe0654a8b85 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_subsearch - owner: bgruening - revisions: - - 9a83f24376b0 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_remove_protonation_state - owner: bgruening - revisions: - - 44488fa95d1d - tool_panel_section_label: ChemicalToolBox -- name: openbabel_spectrophore_search - owner: bgruening - revisions: - - 0b9ee280c439 - tool_panel_section_label: ChemicalToolBox -- name: md_converter - owner: chemteam - revisions: - - acce5039ece7 - tool_panel_section_label: ChemicalToolBox -- name: bio3d_pca - owner: chemteam - revisions: - - f56fb2762abb - tool_panel_section_label: ChemicalToolBox -- name: bio3d_rmsd - owner: chemteam - revisions: - - 75fd897bd85d - tool_panel_section_label: ChemicalToolBox -- name: bio3d_rmsf - owner: chemteam - revisions: - - e838317708a6 - tool_panel_section_label: ChemicalToolBox -- name: mdanalysis_distance - owner: chemteam - revisions: - - c33b972fe040 - tool_panel_section_label: ChemicalToolBox -- name: mdanalysis_dihedral - owner: chemteam - revisions: - - f95d4348ed7c - tool_panel_section_label: ChemicalToolBox -- name: mdanalysis_rdf - owner: chemteam - revisions: - - 9bb57bd1fdc8 - tool_panel_section_label: ChemicalToolBox -- name: mdanalysis_angle - owner: chemteam - revisions: - - fc7293c6cb6a - tool_panel_section_label: ChemicalToolBox -- name: packmol - owner: chemteam - revisions: - - 0b8a0ce446f5 - tool_panel_section_label: ChemicalToolBox -- name: gmx_nvt - owner: chemteam - revisions: - - f425c1453662 - tool_panel_section_label: ChemicalToolBox -- name: gmx_md - owner: chemteam - revisions: - - d97433b7d482 - tool_panel_section_label: ChemicalToolBox -- name: gmx_solvate - owner: chemteam - revisions: - - 77aaf9a68166 - tool_panel_section_label: ChemicalToolBox -- name: gmx_em - owner: chemteam - revisions: - - 6d9a9ab96195 - tool_panel_section_label: ChemicalToolBox -- name: gmx_setup - owner: chemteam - revisions: - - acc9922f3eab - tool_panel_section_label: ChemicalToolBox -- name: gmx_npt - owner: chemteam - revisions: - - 93e39b0321c7 - tool_panel_section_label: ChemicalToolBox -- name: openbabel - owner: bgruening - revisions: - - b52872a1755a - tool_panel_section_label: ChemicalToolBox -- name: osra - owner: bgruening - revisions: - - aeb1f7daa7c2 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_remions - owner: bgruening - revisions: - - abceed0106cd - tool_panel_section_label: ChemicalToolBox -- name: openbabel_compound_convert - owner: bgruening - revisions: - - 37f6668ce540 - tool_panel_section_label: ChemicalToolBox -- name: openbabel_change_title - owner: bgruening - revisions: - - 3bf4dcc945f9 - tool_panel_section_label: ChemicalToolBox -- name: chemfp - owner: bgruening - revisions: - - e3a7d6cc87af - tool_panel_section_label: ChemicalToolBox -- name: natural_product_likeness - owner: bgruening - revisions: - - 41e31a198b34 - tool_panel_section_label: ChemicalToolBox -- name: simsearch - owner: bgruening - revisions: - - 0892f7ced10c - tool_panel_section_label: ChemicalToolBox -- name: confab - owner: bgruening - revisions: - - 4c4e812a67a2 - tool_panel_section_label: ChemicalToolBox -- name: ctb_machine_learning - owner: bgruening - revisions: - - fe542273784f - tool_panel_section_label: ChemicalToolBox -- name: silicos_it - owner: bgruening - revisions: - - 5f1d98674a21 - tool_panel_section_label: ChemicalToolBox -- name: opsin - owner: bgruening - revisions: - - cda22c799d0a - tool_panel_section_label: ChemicalToolBox -- name: rdkit - owner: bgruening - revisions: - - 6bb56f3a8de0 - tool_panel_section_label: ChemicalToolBox -- name: chemical_data_sources - owner: bgruening - revisions: - - 7c1f9962ac07 - - c2055dd1927b - tool_panel_section_label: ChemicalToolBox -- name: openmg - owner: bgruening - revisions: - - 8d2b075966d6 - tool_panel_section_label: ChemicalToolBox -- name: autodock_vina - owner: bgruening - revisions: - - 65ffed035ca8 - tool_panel_section_label: ChemicalToolBox -- name: autodock_vina_prepare_ligand - owner: bgruening - revisions: - - 965badb456d4 - tool_panel_section_label: ChemicalToolBox -- name: autodock_vina_prepare_receptor - owner: bgruening - revisions: - - d15e5a2a7558 - tool_panel_section_label: ChemicalToolBox diff --git a/usegalaxy.eu/collection_operations.yml b/usegalaxy.eu/collection_operations.yml deleted file mode 100644 index f39dbdbe..00000000 --- a/usegalaxy.eu/collection_operations.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Collection Operations -tools: -- name: collapse_collections - owner: nml -- name: collection_column_join - owner: iuc diff --git a/usegalaxy.eu/collection_operations.yml.lock b/usegalaxy.eu/collection_operations.yml.lock deleted file mode 100644 index 376f4840..00000000 --- a/usegalaxy.eu/collection_operations.yml.lock +++ /dev/null @@ -1,14 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: collapse_collections - owner: nml - revisions: - - 25136a2b0cfe - tool_panel_section_label: Collection Operations -- name: collection_column_join - owner: iuc - revisions: - - 58228a4d58fe - tool_panel_section_label: Collection Operations diff --git a/usegalaxy.eu/convert_formats.yml b/usegalaxy.eu/convert_formats.yml deleted file mode 100644 index d7254bde..00000000 --- a/usegalaxy.eu/convert_formats.yml +++ /dev/null @@ -1,46 +0,0 @@ -tool_panel_section_label: Convert Formats -tools: -- name: tabular_to_fasta - owner: devteam -- name: fasta_to_tabular - owner: devteam -- name: tabular_to_fastq - owner: devteam -- name: fastqtofasta - owner: devteam -- name: fastq_to_tabular - owner: devteam -- name: graphicsmagick_image_montage - owner: bgruening -- name: graphicsmagick_image_convert - owner: bgruening -- name: mz_to_sqlite - owner: galaxyp -- name: bed_to_protein_map - owner: galaxyp -- name: gffcompare_to_bed - owner: galaxyp -- name: thermo_raw_file_converter - owner: galaxyp -- name: gtftobed12 - owner: iuc -- name: resize_coordinate_window - owner: iuc -- name: ucsc_twobittofa - owner: iuc -- name: idpquery - owner: galaxyp -- name: gffread - owner: devteam -- name: bam_to_scidx - owner: iuc -- name: msconvert_nix - owner: galaxyp -- name: map_peptides_to_bed - owner: galaxyp -- name: msconvert - owner: galaxyp -- name: idconvert - owner: galaxyp -- name: bigwig_to_bedgraph - owner: bgruening diff --git a/usegalaxy.eu/convert_formats.yml.lock b/usegalaxy.eu/convert_formats.yml.lock deleted file mode 100644 index 616a1f6c..00000000 --- a/usegalaxy.eu/convert_formats.yml.lock +++ /dev/null @@ -1,114 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: tabular_to_fasta - owner: devteam - revisions: - - 0b4e36026794 - tool_panel_section_label: Convert Formats -- name: fasta_to_tabular - owner: devteam - revisions: - - 7e801ab2b70e - tool_panel_section_label: Convert Formats -- name: tabular_to_fastq - owner: devteam - revisions: - - 92034dcbb40a - tool_panel_section_label: Convert Formats -- name: fastqtofasta - owner: devteam - revisions: - - 723b5b38d88a - tool_panel_section_label: Convert Formats -- name: fastq_to_tabular - owner: devteam - revisions: - - 7da7ddea4425 - tool_panel_section_label: Convert Formats -- name: graphicsmagick_image_montage - owner: bgruening - revisions: - - 7e2ee5f43778 - tool_panel_section_label: Convert Formats -- name: graphicsmagick_image_convert - owner: bgruening - revisions: - - 627e8b38f24f - tool_panel_section_label: Convert Formats -- name: mz_to_sqlite - owner: galaxyp - revisions: - - e34bdac5b157 - tool_panel_section_label: Convert Formats -- name: bed_to_protein_map - owner: galaxyp - revisions: - - 024ed7b0ad93 - tool_panel_section_label: Convert Formats -- name: gffcompare_to_bed - owner: galaxyp - revisions: - - 7e572e148175 - tool_panel_section_label: Convert Formats -- name: thermo_raw_file_converter - owner: galaxyp - revisions: - - 15d2a50acaeb - tool_panel_section_label: Convert Formats -- name: gtftobed12 - owner: iuc - revisions: - - 75a14cc16d4d - tool_panel_section_label: Convert Formats -- name: resize_coordinate_window - owner: iuc - revisions: - - 9ba78e8985dc - tool_panel_section_label: Convert Formats -- name: ucsc_twobittofa - owner: iuc - revisions: - - 356dc923f8d3 - tool_panel_section_label: Convert Formats -- name: idpquery - owner: galaxyp - revisions: - - 42dc8e9e58d8 - tool_panel_section_label: Convert Formats -- name: gffread - owner: devteam - revisions: - - 0232f19d300f - tool_panel_section_label: Convert Formats -- name: bam_to_scidx - owner: iuc - revisions: - - 408520e1ae1a - tool_panel_section_label: Convert Formats -- name: msconvert_nix - owner: galaxyp - revisions: - - c9b96a178758 - tool_panel_section_label: Convert Formats -- name: map_peptides_to_bed - owner: galaxyp - revisions: - - 78b8213e122d - tool_panel_section_label: Convert Formats -- name: msconvert - owner: galaxyp - revisions: - - dd4ba10d0c45 - tool_panel_section_label: Convert Formats -- name: idconvert - owner: galaxyp - revisions: - - 9e6e840d6b52 - tool_panel_section_label: Convert Formats -- name: bigwig_to_bedgraph - owner: bgruening - revisions: - - 3799012ce2ff - tool_panel_section_label: Convert Formats diff --git a/usegalaxy.eu/custom.yml b/usegalaxy.eu/custom.yml deleted file mode 100644 index 038a3696..00000000 --- a/usegalaxy.eu/custom.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Test Tools -tools: -- name: hifive - owner: sauria diff --git a/usegalaxy.eu/custom.yml.lock b/usegalaxy.eu/custom.yml.lock deleted file mode 100644 index 1e54956b..00000000 --- a/usegalaxy.eu/custom.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: hifive - owner: sauria - revisions: - - 20dfaec1678c - tool_panel_section_label: Test Tools diff --git a/usegalaxy.eu/deeptools.yml b/usegalaxy.eu/deeptools.yml deleted file mode 100644 index eefef94f..00000000 --- a/usegalaxy.eu/deeptools.yml +++ /dev/null @@ -1,44 +0,0 @@ -tool_panel_section_label: deepTools -tools: -- name: deeptools_plot_profile - owner: bgruening -- name: deeptools_plot_pca - owner: bgruening -- name: deeptools_alignmentsieve - owner: bgruening -- name: deeptools_plot_enrichment - owner: bgruening -- name: deeptools_estimatereadfiltering - owner: bgruening -- name: deeptools_compute_matrix_operations - owner: bgruening -- name: deeptools_bam_compare - owner: bgruening -- name: deeptools_bam_coverage - owner: bgruening -- name: deeptools_bam_pe_fragmentsize - owner: bgruening -- name: deeptools_bigwig_compare - owner: bgruening -- name: deeptools_plot_heatmap - owner: bgruening -- name: deeptools_correct_gc_bias - owner: bgruening -- name: deeptools_multi_bam_summary - owner: bgruening -- name: deeptools_compute_matrix - owner: bgruening -- name: deeptools_compute_gc_bias - owner: bgruening -- name: deeptools_multi_bigwig_summary - owner: bgruening -- name: deeptools_plot_correlation - owner: bgruening -- name: deeptools_plot_coverage - owner: bgruening -- name: deeptools_plot_fingerprint - owner: bgruening -- name: hicup_deduplicator - owner: bgruening -- name: bowtie2 - owner: devteam diff --git a/usegalaxy.eu/deeptools.yml.lock b/usegalaxy.eu/deeptools.yml.lock deleted file mode 100644 index 6eb7ddd2..00000000 --- a/usegalaxy.eu/deeptools.yml.lock +++ /dev/null @@ -1,109 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: deeptools_plot_profile - owner: bgruening - revisions: - - 0cd2331b6e4f - tool_panel_section_label: deepTools -- name: deeptools_plot_pca - owner: bgruening - revisions: - - 93ce2662f917 - tool_panel_section_label: deepTools -- name: deeptools_alignmentsieve - owner: bgruening - revisions: - - ea8efdcf151f - tool_panel_section_label: deepTools -- name: deeptools_plot_enrichment - owner: bgruening - revisions: - - 36de8f366d51 - tool_panel_section_label: deepTools -- name: deeptools_estimatereadfiltering - owner: bgruening - revisions: - - 080733c7865a - tool_panel_section_label: deepTools -- name: deeptools_compute_matrix_operations - owner: bgruening - revisions: - - d8c2a68643ce - tool_panel_section_label: deepTools -- name: deeptools_bam_compare - owner: bgruening - revisions: - - 439e75416e1a - tool_panel_section_label: deepTools -- name: deeptools_bam_coverage - owner: bgruening - revisions: - - 3033c3fba046 - tool_panel_section_label: deepTools -- name: deeptools_bam_pe_fragmentsize - owner: bgruening - revisions: - - f011488450e6 - tool_panel_section_label: deepTools -- name: deeptools_bigwig_compare - owner: bgruening - revisions: - - a3c9520f611a - tool_panel_section_label: deepTools -- name: deeptools_plot_heatmap - owner: bgruening - revisions: - - 010e58e9d822 - tool_panel_section_label: deepTools -- name: deeptools_correct_gc_bias - owner: bgruening - revisions: - - 9e60bf557373 - tool_panel_section_label: deepTools -- name: deeptools_multi_bam_summary - owner: bgruening - revisions: - - 6dfe9740ffc5 - tool_panel_section_label: deepTools -- name: deeptools_compute_matrix - owner: bgruening - revisions: - - fb9cf9c97ec4 - tool_panel_section_label: deepTools -- name: deeptools_compute_gc_bias - owner: bgruening - revisions: - - f0fd1cdbe506 - tool_panel_section_label: deepTools -- name: deeptools_multi_bigwig_summary - owner: bgruening - revisions: - - a5bb0a28f2e6 - tool_panel_section_label: deepTools -- name: deeptools_plot_correlation - owner: bgruening - revisions: - - 4e8b35fd2173 - tool_panel_section_label: deepTools -- name: deeptools_plot_coverage - owner: bgruening - revisions: - - d884552cd194 - tool_panel_section_label: deepTools -- name: deeptools_plot_fingerprint - owner: bgruening - revisions: - - a064962bb6e2 - tool_panel_section_label: deepTools -- name: hicup_deduplicator - owner: bgruening - revisions: - - c7bed3fe0e23 - tool_panel_section_label: deepTools -- name: bowtie2 - owner: devteam - revisions: - - a9d4f71dbfb0 - tool_panel_section_label: deepTools diff --git a/usegalaxy.eu/emboss_tools.yml b/usegalaxy.eu/emboss_tools.yml deleted file mode 100644 index cc6c7e93..00000000 --- a/usegalaxy.eu/emboss_tools.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: EMBOSS Tools -tools: -- name: emboss_5 - owner: devteam diff --git a/usegalaxy.eu/emboss_tools.yml.lock b/usegalaxy.eu/emboss_tools.yml.lock deleted file mode 100644 index fd2dbe6f..00000000 --- a/usegalaxy.eu/emboss_tools.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: emboss_5 - owner: devteam - revisions: - - 832c20329690 - - ce22ceec214a - - dc492eb6a4fc - tool_panel_section_label: EMBOSS Tools diff --git a/usegalaxy.eu/epigenetics.yml.lock b/usegalaxy.eu/epigenetics.yml.lock deleted file mode 100644 index 55371548..00000000 --- a/usegalaxy.eu/epigenetics.yml.lock +++ /dev/null @@ -1,69 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: vcf_filter - owner: devteam - revisions: - - da1a6f33b504 - tool_panel_section_label: Epigenetics -- name: pileometh - owner: bgruening - revisions: - - 15df15127c18 - tool_panel_section_label: Epigenetics -- name: nanopolish_methylation - owner: bgruening - revisions: - - 709490665bad - tool_panel_section_label: Epigenetics -- name: hicup_truncater - owner: bgruening - revisions: - - 17f80a8600ac - tool_panel_section_label: Epigenetics -- name: hicup_hicup - owner: bgruening - revisions: - - bd1594d55a38 - tool_panel_section_label: Epigenetics -- name: hicup_filter - owner: bgruening - revisions: - - a7bbbf32da62 - tool_panel_section_label: Epigenetics -- name: hicup_digester - owner: bgruening - revisions: - - a2f3a4129052 - tool_panel_section_label: Epigenetics -- name: hicup_deduplicator - owner: bgruening - revisions: - - 46e5b4782715 - tool_panel_section_label: Epigenetics -- name: epicseg - owner: rnateam - revisions: - - 6260e42c7d49 - tool_panel_section_label: Epigenetics -- name: bwameth - owner: iuc - revisions: - - 95219305823a - tool_panel_section_label: Epigenetics -- name: hicup_mapper - owner: bgruening - revisions: - - f396b479c2f2 - tool_panel_section_label: Epigenetics -- name: metilene - owner: rnateam - revisions: - - cd253831a014 - tool_panel_section_label: Epigenetics -- name: rnbeads - owner: pavlo-lutsik - revisions: - - 6b0981ab063e - tool_panel_section_label: Epigenetics diff --git a/usegalaxy.eu/evolution.yml b/usegalaxy.eu/evolution.yml deleted file mode 100644 index 92c97767..00000000 --- a/usegalaxy.eu/evolution.yml +++ /dev/null @@ -1,10 +0,0 @@ -tool_panel_section_label: Evolution -tools: -- name: mutate_snp_codon - owner: devteam -- name: iqtree - owner: iuc -- name: structure - owner: iuc -- name: codeml - owner: iuc diff --git a/usegalaxy.eu/evolution.yml.lock b/usegalaxy.eu/evolution.yml.lock deleted file mode 100644 index 5336914f..00000000 --- a/usegalaxy.eu/evolution.yml.lock +++ /dev/null @@ -1,24 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: mutate_snp_codon - owner: devteam - revisions: - - 8f0af7251167 - tool_panel_section_label: Evolution -- name: iqtree - owner: iuc - revisions: - - d1c340a5664b - tool_panel_section_label: Evolution -- name: structure - owner: iuc - revisions: - - 64e681a1cad5 - tool_panel_section_label: Evolution -- name: codeml - owner: iuc - revisions: - - ba71e26d5bdc - tool_panel_section_label: Evolution diff --git a/usegalaxy.eu/extract_features.yml b/usegalaxy.eu/extract_features.yml deleted file mode 100644 index 8b442de2..00000000 --- a/usegalaxy.eu/extract_features.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Extract Features -tools: -- name: length_and_gc_content - owner: iuc -- name: fraggenescan - owner: iuc diff --git a/usegalaxy.eu/extract_features.yml.lock b/usegalaxy.eu/extract_features.yml.lock deleted file mode 100644 index a513e5df..00000000 --- a/usegalaxy.eu/extract_features.yml.lock +++ /dev/null @@ -1,14 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: length_and_gc_content - owner: iuc - revisions: - - f088370d2a3c - tool_panel_section_label: Extract Features -- name: fraggenescan - owner: iuc - revisions: - - 1f0a3e4497d4 - tool_panel_section_label: Extract Features diff --git a/usegalaxy.eu/fastafastq_manipulation.yml b/usegalaxy.eu/fastafastq_manipulation.yml deleted file mode 100644 index d9daaf03..00000000 --- a/usegalaxy.eu/fastafastq_manipulation.yml +++ /dev/null @@ -1,168 +0,0 @@ -tool_panel_section_label: FASTA/FASTQ manipulation -tools: -- name: fastq_to_fasta - owner: devteam -- name: fastx_nucleotides_distribution - owner: devteam -- name: fastp - owner: iuc -- name: short_reads_trim_seq - owner: devteam -- name: fasta_compute_length - owner: devteam -- name: fasta_concatenate_by_species - owner: devteam -- name: fasta_filter_by_length - owner: devteam -- name: fastq_trimmer - owner: devteam -- name: fastq_trimmer_by_quality - owner: devteam -- name: fastq_combiner - owner: devteam -- name: fastq_filter - owner: devteam -- name: fastq_groomer - owner: devteam -- name: fastq_manipulation - owner: devteam -- name: fastq_masker_by_quality - owner: devteam -- name: fastq_paired_end_deinterlacer - owner: devteam -- name: fastq_paired_end_interlacer - owner: devteam -- name: fastq_paired_end_joiner - owner: devteam -- name: fastq_paired_end_splitter - owner: devteam -- name: fastx_renamer - owner: devteam -- name: fastx_reverse_complement - owner: devteam -- name: fastx_trimmer - owner: devteam -- name: fastq_quality_converter - owner: devteam -- name: fastq_quality_filter - owner: devteam -- name: fasta_formatter - owner: devteam -- name: fasta_nucleotide_changer - owner: devteam -- name: cutadapt - owner: lparsons -- name: fastx_collapser - owner: devteam -- name: seqtk - owner: iuc -- name: fasta_stats - owner: iuc -- name: porechop - owner: iuc -- name: filtlong - owner: iuc -- name: fastx_clipper - owner: devteam -- name: fastq_quality_boxplot - owner: devteam -- name: fastx_quality_statistics - owner: devteam -- name: fastqc - owner: devteam -- name: fastx_barcode_splitter - owner: devteam -- name: fastx_artifacts_filter - owner: devteam -- name: umi_tools_count - owner: iuc -- name: umi_tools_extract - owner: iuc -- name: bctools_extract_crosslinked_nucleotides - owner: iuc -- name: ucsc_fasplit - owner: iuc -- name: atactk_trim_adapters - owner: rnateam -- name: bctools_convert_to_binary_barcode - owner: iuc -- name: bctools_extract_barcodes - owner: iuc -- name: bctools_extract_alignment_ends - owner: iuc -- name: bctools_merge_pcr_duplicates - owner: iuc -- name: bctools_remove_spurious_events - owner: iuc -- name: bctools_remove_tail - owner: iuc -- name: flash - owner: iuc -- name: umi_tools_whitelist - owner: iuc -- name: je_clip - owner: gbcs-embl-heidelberg -- name: je_demultiplex - owner: gbcs-embl-heidelberg -- name: je_markdupes - owner: gbcs-embl-heidelberg -- name: je_demultiplex_illu - owner: gbcs-embl-heidelberg -- name: umi_tools_dedup - owner: iuc -- name: umi_tools_group - owner: iuc -- name: poretools_times - owner: iuc -- name: poretools_nucdist - owner: iuc -- name: poretools_qualdist - owner: iuc -- name: poretools_extract - owner: iuc -- name: poretools_tabular - owner: iuc -- name: poretools_stats - owner: iuc -- name: poretools_squiggle - owner: iuc -- name: poretools_occupancy - owner: iuc -- name: poretools_hist - owner: iuc -- name: poretools_yield_plot - owner: iuc -- name: poretools_qualpos - owner: iuc -- name: poretools_winner - owner: iuc -- name: poretools_events - owner: iuc -- name: tabular_to_fastq - owner: devteam -- name: fastq_to_tabular - owner: devteam -- name: fastq_stats - owner: devteam -- name: fastqtofasta - owner: devteam -- name: fasta_merge_files_and_filter_unique_sequences - owner: galaxyp -- name: align_back_trans - owner: peterjc -- name: seq_filter_by_mapping - owner: peterjc -- name: trim_galore - owner: bgruening -- name: sickle - owner: iuc -- name: pear - owner: iuc -- name: trimmomatic - owner: pjbriggs -- name: lighter - owner: bgruening -- name: fastq_join - owner: lparsons -- name: splitfasta - owner: rnateam diff --git a/usegalaxy.eu/fastafastq_manipulation.yml.lock b/usegalaxy.eu/fastafastq_manipulation.yml.lock deleted file mode 100644 index f18521a5..00000000 --- a/usegalaxy.eu/fastafastq_manipulation.yml.lock +++ /dev/null @@ -1,421 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: fastq_to_fasta - owner: devteam - revisions: - - 02a5f43cd5d1 - - 186b8d913e6c - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_nucleotides_distribution - owner: devteam - revisions: - - 18a51655db17 - - 21796f46e0ba - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastp - owner: iuc - revisions: - - 6c2351178f8d - tool_panel_section_label: FASTA/FASTQ manipulation -- name: short_reads_trim_seq - owner: devteam - revisions: - - 25e6fe525306 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fasta_compute_length - owner: devteam - revisions: - - de2db1bdfbf8 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fasta_concatenate_by_species - owner: devteam - revisions: - - 717aee069681 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fasta_filter_by_length - owner: devteam - revisions: - - 2fd6033d0e9c - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_trimmer - owner: devteam - revisions: - - 2d0d13b0b0f1 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_trimmer_by_quality - owner: devteam - revisions: - - c64d534a763c - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_combiner - owner: devteam - revisions: - - 56389130cb63 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_filter - owner: devteam - revisions: - - 06934412f56d - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_groomer - owner: devteam - revisions: - - 71e5fa25b8a2 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_manipulation - owner: devteam - revisions: - - 4ac14b275aca - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_masker_by_quality - owner: devteam - revisions: - - eb592e9ec47a - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_paired_end_deinterlacer - owner: devteam - revisions: - - b7ce72b00e62 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_paired_end_interlacer - owner: devteam - revisions: - - ef49268ee579 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_paired_end_joiner - owner: devteam - revisions: - - 822cc1e6274e - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_paired_end_splitter - owner: devteam - revisions: - - 9bbe5b7ffa12 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_renamer - owner: devteam - revisions: - - d8a3d31554d7 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_reverse_complement - owner: devteam - revisions: - - 0c2907307ba4 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_trimmer - owner: devteam - revisions: - - b98f3fa516a3 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_quality_converter - owner: devteam - revisions: - - 54053ea6c77e - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_quality_filter - owner: devteam - revisions: - - 7b4468117008 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fasta_formatter - owner: devteam - revisions: - - 859422bcb689 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fasta_nucleotide_changer - owner: devteam - revisions: - - 091ca73f5804 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: cutadapt - owner: lparsons - revisions: - - 49370cb85f0f - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_collapser - owner: devteam - revisions: - - 7ce1891db6f5 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: seqtk - owner: iuc - revisions: - - a09586d5149a - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fasta_stats - owner: iuc - revisions: - - 9c620a950d3a - tool_panel_section_label: FASTA/FASTQ manipulation -- name: porechop - owner: iuc - revisions: - - 93d623d9979c - tool_panel_section_label: FASTA/FASTQ manipulation -- name: filtlong - owner: iuc - revisions: - - 8880fb74ef56 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_clipper - owner: devteam - revisions: - - 736b8f6ee456 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_quality_boxplot - owner: devteam - revisions: - - 3987db70a4b0 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_quality_statistics - owner: devteam - revisions: - - 59003d0543cd - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastqc - owner: devteam - revisions: - - c15237684a01 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_barcode_splitter - owner: devteam - revisions: - - 015dc921d814 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastx_artifacts_filter - owner: devteam - revisions: - - dd3737e40dce - tool_panel_section_label: FASTA/FASTQ manipulation -- name: umi_tools_count - owner: iuc - revisions: - - b557acca0b56 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: umi_tools_extract - owner: iuc - revisions: - - 99aea37a7ff7 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: bctools_extract_crosslinked_nucleotides - owner: iuc - revisions: - - 66d1f96c5600 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: ucsc_fasplit - owner: iuc - revisions: - - 71f649c23021 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: atactk_trim_adapters - owner: rnateam - revisions: - - 9839a3fe72f7 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: bctools_convert_to_binary_barcode - owner: iuc - revisions: - - 695b3aa43711 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: bctools_extract_barcodes - owner: iuc - revisions: - - c30fc94e6611 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: bctools_extract_alignment_ends - owner: iuc - revisions: - - 8076141a76a7 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: bctools_merge_pcr_duplicates - owner: iuc - revisions: - - 2cbc4dd55cd8 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: bctools_remove_spurious_events - owner: iuc - revisions: - - 3175047fb607 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: bctools_remove_tail - owner: iuc - revisions: - - f7c115a05f50 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: flash - owner: iuc - revisions: - - dce033fd3c80 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: umi_tools_whitelist - owner: iuc - revisions: - - a211847807c4 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: je_clip - owner: gbcs-embl-heidelberg - revisions: - - fcc1a953b3e0 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: je_demultiplex - owner: gbcs-embl-heidelberg - revisions: - - 47c0d9f76232 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: je_markdupes - owner: gbcs-embl-heidelberg - revisions: - - a79f67128fc3 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: je_demultiplex_illu - owner: gbcs-embl-heidelberg - revisions: - - d556679c88d6 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: umi_tools_dedup - owner: iuc - revisions: - - fda15c620969 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: umi_tools_group - owner: iuc - revisions: - - 10c037f6d0d1 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_times - owner: iuc - revisions: - - e5072f0d3772 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_nucdist - owner: iuc - revisions: - - 3ae7ccba16cf - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_qualdist - owner: iuc - revisions: - - 44111014e7c1 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_extract - owner: iuc - revisions: - - 7593f94691fb - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_tabular - owner: iuc - revisions: - - 7f0b324de883 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_stats - owner: iuc - revisions: - - ae4c8446ce30 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_squiggle - owner: iuc - revisions: - - ce8af9373061 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_occupancy - owner: iuc - revisions: - - 336791b5665f - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_hist - owner: iuc - revisions: - - 47936349f3e9 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_yield_plot - owner: iuc - revisions: - - 64a83664b814 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_qualpos - owner: iuc - revisions: - - 2e22ebec211a - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_winner - owner: iuc - revisions: - - 9d8f41103cc6 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: poretools_events - owner: iuc - revisions: - - 1d835c691480 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: tabular_to_fastq - owner: devteam - revisions: - - b8cdc0507586 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_to_tabular - owner: devteam - revisions: - - ccf4e1d1fcbe - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_stats - owner: devteam - revisions: - - e2cf940128d5 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastqtofasta - owner: devteam - revisions: - - 4844c1810c16 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fasta_merge_files_and_filter_unique_sequences - owner: galaxyp - revisions: - - 650d553c1fda - tool_panel_section_label: FASTA/FASTQ manipulation -- name: align_back_trans - owner: peterjc - revisions: - - b27388e5a0bb - tool_panel_section_label: FASTA/FASTQ manipulation -- name: seq_filter_by_mapping - owner: peterjc - revisions: - - 481b0a925e66 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: trim_galore - owner: bgruening - revisions: - - 949f01671246 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: sickle - owner: iuc - revisions: - - 3905ccd5c631 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: pear - owner: iuc - revisions: - - 240f611a46f3 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: trimmomatic - owner: pjbriggs - revisions: - - 14d05f2d511d - tool_panel_section_label: FASTA/FASTQ manipulation -- name: lighter - owner: bgruening - revisions: - - b0cfd92907eb - tool_panel_section_label: FASTA/FASTQ manipulation -- name: fastq_join - owner: lparsons - revisions: - - b007d9642911 - tool_panel_section_label: FASTA/FASTQ manipulation -- name: splitfasta - owner: rnateam - revisions: - - ae4d5733272f - tool_panel_section_label: FASTA/FASTQ manipulation diff --git a/usegalaxy.eu/filter_and_sort.yml b/usegalaxy.eu/filter_and_sort.yml deleted file mode 100644 index dd812833..00000000 --- a/usegalaxy.eu/filter_and_sort.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: Filter and Sort -tools: -- name: gffcompare - owner: iuc -- name: filter_by_fasta_ids - owner: galaxyp -- name: xpath - owner: iuc -- name: sample_seqs - owner: peterjc -- name: seq_filter_by_id - owner: peterjc -- name: sqlite_to_tabular - owner: jjohnson -- name: column_arrange_by_header - owner: bgruening -- name: find_in_reference - owner: jjohnson -- name: query_tabular - owner: jjohnson diff --git a/usegalaxy.eu/filter_and_sort.yml.lock b/usegalaxy.eu/filter_and_sort.yml.lock deleted file mode 100644 index 1cee025f..00000000 --- a/usegalaxy.eu/filter_and_sort.yml.lock +++ /dev/null @@ -1,49 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: gffcompare - owner: iuc - revisions: - - c80cdc2eac6d - tool_panel_section_label: Filter and Sort -- name: filter_by_fasta_ids - owner: galaxyp - revisions: - - 1bd985f14938 - tool_panel_section_label: Filter and Sort -- name: xpath - owner: iuc - revisions: - - b1dbdbf2be18 - tool_panel_section_label: Filter and Sort -- name: sample_seqs - owner: peterjc - revisions: - - 7c40a1fbc82e - tool_panel_section_label: Filter and Sort -- name: seq_filter_by_id - owner: peterjc - revisions: - - 141612f8c3e3 - tool_panel_section_label: Filter and Sort -- name: sqlite_to_tabular - owner: jjohnson - revisions: - - 123b9ca5e26a - tool_panel_section_label: Filter and Sort -- name: column_arrange_by_header - owner: bgruening - revisions: - - f18f67056946 - tool_panel_section_label: Filter and Sort -- name: find_in_reference - owner: jjohnson - revisions: - - c4fd2ea4f988 - tool_panel_section_label: Filter and Sort -- name: query_tabular - owner: jjohnson - revisions: - - 49ca06d66762 - tool_panel_section_label: Filter and Sort diff --git a/usegalaxy.eu/gatk_tools.yml b/usegalaxy.eu/gatk_tools.yml deleted file mode 100644 index e074c4ad..00000000 --- a/usegalaxy.eu/gatk_tools.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: GATK Tools -tools: -- name: count_covariates - owner: devteam -- name: gatk2 - owner: iuc diff --git a/usegalaxy.eu/gatk_tools.yml.lock b/usegalaxy.eu/gatk_tools.yml.lock deleted file mode 100644 index b32d6d08..00000000 --- a/usegalaxy.eu/gatk_tools.yml.lock +++ /dev/null @@ -1,14 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: count_covariates - owner: devteam - revisions: - - 14e304b70425 - tool_panel_section_label: GATK Tools -- name: gatk2 - owner: iuc - revisions: - - 84584664264c - tool_panel_section_label: GATK Tools diff --git a/usegalaxy.eu/gemini_tools.yml b/usegalaxy.eu/gemini_tools.yml deleted file mode 100644 index da03f99a..00000000 --- a/usegalaxy.eu/gemini_tools.yml +++ /dev/null @@ -1,38 +0,0 @@ -tool_panel_section_label: Gemini Tools -tools: -- name: gemini_annotate - owner: iuc -- name: gemini_inheritance - owner: iuc -- name: gemini_interactions - owner: iuc -- name: gemini_qc - owner: iuc -- name: gemini_set_somatic - owner: iuc -- name: gemini_roh - owner: iuc -- name: gemini_load - owner: iuc -- name: gemini_fusions - owner: iuc -- name: gemini_query - owner: iuc -- name: gemini_lof_sieve - owner: iuc -- name: gemini_actionable_mutations - owner: iuc -- name: gemini_pathways - owner: iuc -- name: gemini_amend - owner: iuc -- name: gemini_stats - owner: iuc -- name: gemini_gene_wise - owner: iuc -- name: gemini_burden - owner: iuc -- name: gemini_windower - owner: iuc -- name: gemini_db_info - owner: iuc diff --git a/usegalaxy.eu/gemini_tools.yml.lock b/usegalaxy.eu/gemini_tools.yml.lock deleted file mode 100644 index 577082be..00000000 --- a/usegalaxy.eu/gemini_tools.yml.lock +++ /dev/null @@ -1,94 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: gemini_annotate - owner: iuc - revisions: - - 0c8f7322f8fc - tool_panel_section_label: Gemini Tools -- name: gemini_inheritance - owner: iuc - revisions: - - 3123ce7acd0e - tool_panel_section_label: Gemini Tools -- name: gemini_interactions - owner: iuc - revisions: - - 7028ca3cac1c - tool_panel_section_label: Gemini Tools -- name: gemini_qc - owner: iuc - revisions: - - 8414eecc3828 - tool_panel_section_label: Gemini Tools -- name: gemini_set_somatic - owner: iuc - revisions: - - '991049484627' - tool_panel_section_label: Gemini Tools -- name: gemini_roh - owner: iuc - revisions: - - d65ca2fa673b - tool_panel_section_label: Gemini Tools -- name: gemini_load - owner: iuc - revisions: - - b5b53c27baca - tool_panel_section_label: Gemini Tools -- name: gemini_fusions - owner: iuc - revisions: - - 6e3d2bd01a96 - tool_panel_section_label: Gemini Tools -- name: gemini_query - owner: iuc - revisions: - - cd00221d67cb - tool_panel_section_label: Gemini Tools -- name: gemini_lof_sieve - owner: iuc - revisions: - - dda378a72430 - tool_panel_section_label: Gemini Tools -- name: gemini_actionable_mutations - owner: iuc - revisions: - - 643a9ad97f08 - tool_panel_section_label: Gemini Tools -- name: gemini_pathways - owner: iuc - revisions: - - c63b7eefb07a - tool_panel_section_label: Gemini Tools -- name: gemini_amend - owner: iuc - revisions: - - bff8fad3fb69 - tool_panel_section_label: Gemini Tools -- name: gemini_stats - owner: iuc - revisions: - - 86d4303cc3ca - tool_panel_section_label: Gemini Tools -- name: gemini_gene_wise - owner: iuc - revisions: - - 4b26f6c99227 - tool_panel_section_label: Gemini Tools -- name: gemini_burden - owner: iuc - revisions: - - 699ce2631e79 - tool_panel_section_label: Gemini Tools -- name: gemini_windower - owner: iuc - revisions: - - 3b5b1ebc8423 - tool_panel_section_label: Gemini Tools -- name: gemini_db_info - owner: iuc - revisions: - - bc8b01d1b496 - tool_panel_section_label: Gemini Tools diff --git a/usegalaxy.eu/genome_diversity.yml b/usegalaxy.eu/genome_diversity.yml deleted file mode 100644 index 799d84ee..00000000 --- a/usegalaxy.eu/genome_diversity.yml +++ /dev/null @@ -1,6 +0,0 @@ -tool_panel_section_label: Genome Diversity -tools: -- name: fasttree - owner: iuc -- name: genome_diversity - owner: miller-lab diff --git a/usegalaxy.eu/genome_diversity.yml.lock b/usegalaxy.eu/genome_diversity.yml.lock deleted file mode 100644 index 5823a583..00000000 --- a/usegalaxy.eu/genome_diversity.yml.lock +++ /dev/null @@ -1,14 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: fasttree - owner: iuc - revisions: - - c7e73acfa3eb - tool_panel_section_label: Genome Diversity -- name: genome_diversity - owner: miller-lab - revisions: - - e56023008e36 - tool_panel_section_label: Genome Diversity diff --git a/usegalaxy.eu/genome_editing.yml b/usegalaxy.eu/genome_editing.yml deleted file mode 100644 index ef38d7bc..00000000 --- a/usegalaxy.eu/genome_editing.yml +++ /dev/null @@ -1,12 +0,0 @@ -tool_panel_section_label: Genome editing -tools: -- name: mageck_test - owner: iuc -- name: mageck_mle - owner: iuc -- name: mageck_gsea - owner: iuc -- name: mageck_count - owner: iuc -- name: mageck_pathway - owner: iuc diff --git a/usegalaxy.eu/genome_editing.yml.lock b/usegalaxy.eu/genome_editing.yml.lock deleted file mode 100644 index 8cc59fbc..00000000 --- a/usegalaxy.eu/genome_editing.yml.lock +++ /dev/null @@ -1,29 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: mageck_test - owner: iuc - revisions: - - 688a8eccea71 - tool_panel_section_label: Genome editing -- name: mageck_mle - owner: iuc - revisions: - - b36c85e37a48 - tool_panel_section_label: Genome editing -- name: mageck_gsea - owner: iuc - revisions: - - d46e36492bff - tool_panel_section_label: Genome editing -- name: mageck_count - owner: iuc - revisions: - - 3edbd1ff5602 - tool_panel_section_label: Genome editing -- name: mageck_pathway - owner: iuc - revisions: - - 9744e1124d0f - tool_panel_section_label: Genome editing diff --git a/usegalaxy.eu/get_data.yml b/usegalaxy.eu/get_data.yml deleted file mode 100644 index 32c91664..00000000 --- a/usegalaxy.eu/get_data.yml +++ /dev/null @@ -1,50 +0,0 @@ -tool_panel_section_label: Get Data -tools: -- name: ncbi_eutils_esearch - owner: iuc -- name: ncbi_eutils_egquery - owner: iuc -- name: ncbi_eutils_ecitmatch - owner: iuc -- name: ncbi_eutils_epost - owner: iuc -- name: ncbi_eutils_elink - owner: iuc -- name: ncbi_eutils_einfo - owner: iuc -- name: ncbi_eutils_esummary - owner: iuc -- name: ncbi_eutils_efetch - owner: iuc -- name: sra_tools - owner: iuc -- name: uniprot_rest_interface - owner: bgruening -- name: ensembl_get_sequences - owner: earlhaminst -- name: ensembl_get_genetree - owner: earlhaminst -- name: ensembl_get_feature_info - owner: earlhaminst -- name: enasearch_search_data - owner: iuc -- name: enasearch_retrieve_data - owner: iuc -- name: enasearch_retrieve_taxons - owner: iuc -- name: enasearch_retrieve_analysis_report - owner: iuc -- name: enasearch_retrieve_run_report - owner: iuc -- name: ebi_search_rest_results - owner: iuc -- name: unipept - owner: galaxyp -- name: dbbuilder - owner: galaxyp -- name: uniprotxml_downloader - owner: galaxyp -- name: ebi_metagenomics_run_downloader - owner: iuc -- name: ega_download_streamer - owner: yhoogstrate diff --git a/usegalaxy.eu/get_data.yml.lock b/usegalaxy.eu/get_data.yml.lock deleted file mode 100644 index 358a4e5d..00000000 --- a/usegalaxy.eu/get_data.yml.lock +++ /dev/null @@ -1,125 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: ncbi_eutils_esearch - owner: iuc - revisions: - - 30150bd36c9a - tool_panel_section_label: Get Data -- name: ncbi_eutils_egquery - owner: iuc - revisions: - - 28f69754ddc5 - tool_panel_section_label: Get Data -- name: ncbi_eutils_ecitmatch - owner: iuc - revisions: - - 732a52c18758 - tool_panel_section_label: Get Data -- name: ncbi_eutils_epost - owner: iuc - revisions: - - 196b8dd07896 - tool_panel_section_label: Get Data -- name: ncbi_eutils_elink - owner: iuc - revisions: - - 2791c731fc65 - tool_panel_section_label: Get Data -- name: ncbi_eutils_einfo - owner: iuc - revisions: - - 5b1dc5936af2 - tool_panel_section_label: Get Data -- name: ncbi_eutils_esummary - owner: iuc - revisions: - - c8d4ea6376a7 - tool_panel_section_label: Get Data -- name: ncbi_eutils_efetch - owner: iuc - revisions: - - 0fc65a60436f - tool_panel_section_label: Get Data -- name: sra_tools - owner: iuc - revisions: - - 1790dcf3c32d - - c38286ea7047 - tool_panel_section_label: Get Data -- name: uniprot_rest_interface - owner: bgruening - revisions: - - 054483e27a35 - tool_panel_section_label: Get Data -- name: ensembl_get_sequences - owner: earlhaminst - revisions: - - 3b686142e9c2 - tool_panel_section_label: Get Data -- name: ensembl_get_genetree - owner: earlhaminst - revisions: - - 0602dcf02768 - tool_panel_section_label: Get Data -- name: ensembl_get_feature_info - owner: earlhaminst - revisions: - - 234d7babf34b - tool_panel_section_label: Get Data -- name: enasearch_search_data - owner: iuc - revisions: - - 6e692d5a5599 - tool_panel_section_label: Get Data -- name: enasearch_retrieve_data - owner: iuc - revisions: - - 0719cfc3ebcb - tool_panel_section_label: Get Data -- name: enasearch_retrieve_taxons - owner: iuc - revisions: - - 8881ac3eebd7 - tool_panel_section_label: Get Data -- name: enasearch_retrieve_analysis_report - owner: iuc - revisions: - - a5f787bfe69e - tool_panel_section_label: Get Data -- name: enasearch_retrieve_run_report - owner: iuc - revisions: - - ccc0e55c9e16 - tool_panel_section_label: Get Data -- name: ebi_search_rest_results - owner: iuc - revisions: - - 42d5e40fcd0b - tool_panel_section_label: Get Data -- name: unipept - owner: galaxyp - revisions: - - 34758ab8aaa4 - tool_panel_section_label: Get Data -- name: dbbuilder - owner: galaxyp - revisions: - - a85fbebe8b2f - tool_panel_section_label: Get Data -- name: uniprotxml_downloader - owner: galaxyp - revisions: - - e1abc9a35c64 - tool_panel_section_label: Get Data -- name: ebi_metagenomics_run_downloader - owner: iuc - revisions: - - e2e9fae080ad - tool_panel_section_label: Get Data -- name: ega_download_streamer - owner: yhoogstrate - revisions: - - 3e2cccf08053 - tool_panel_section_label: Get Data diff --git a/usegalaxy.eu/graphclust.yml b/usegalaxy.eu/graphclust.yml deleted file mode 100644 index 153edef8..00000000 --- a/usegalaxy.eu/graphclust.yml +++ /dev/null @@ -1,28 +0,0 @@ -tool_panel_section_label: GraphClust -tools: -- name: structure_to_gspan - owner: rnateam -- name: graphclust_preprocessing - owner: rnateam -- name: graphclust_prepocessing_for_mlocarna - owner: rnateam -- name: graphclust_nspdk - owner: rnateam -- name: graphclust_mlocarna - owner: rnateam -- name: graphclust_fasta_to_gspan - owner: rnateam -- name: graphclust_postprocessing - owner: rnateam -- name: graphclust_cmfinder - owner: rnateam -- name: graphclust_align_cluster - owner: rnateam -- name: graphclust_aggregate_alignments - owner: rnateam -- name: graphclust_postprocessing_no_align - owner: rnateam -- name: graphclust_motif_finder_plot - owner: rnateam -- name: infernal - owner: bgruening diff --git a/usegalaxy.eu/graphclust.yml.lock b/usegalaxy.eu/graphclust.yml.lock deleted file mode 100644 index 93986e46..00000000 --- a/usegalaxy.eu/graphclust.yml.lock +++ /dev/null @@ -1,70 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: structure_to_gspan - owner: rnateam - revisions: - - d34ab3aa1724 - tool_panel_section_label: GraphClust -- name: graphclust_preprocessing - owner: rnateam - revisions: - - 2a5defc09381 - tool_panel_section_label: GraphClust -- name: graphclust_prepocessing_for_mlocarna - owner: rnateam - revisions: - - 5c92a3f7b59c - tool_panel_section_label: GraphClust -- name: graphclust_nspdk - owner: rnateam - revisions: - - 90da74fd1c5c - tool_panel_section_label: GraphClust -- name: graphclust_mlocarna - owner: rnateam - revisions: - - c45eef4517d9 - tool_panel_section_label: GraphClust -- name: graphclust_fasta_to_gspan - owner: rnateam - revisions: - - d2784e70dd19 - tool_panel_section_label: GraphClust -- name: graphclust_postprocessing - owner: rnateam - revisions: - - f93c868203cc - tool_panel_section_label: GraphClust -- name: graphclust_cmfinder - owner: rnateam - revisions: - - 5a1dcc77b0ce - tool_panel_section_label: GraphClust -- name: graphclust_align_cluster - owner: rnateam - revisions: - - 953353eacec2 - tool_panel_section_label: GraphClust -- name: graphclust_aggregate_alignments - owner: rnateam - revisions: - - 8778478a754f - tool_panel_section_label: GraphClust -- name: graphclust_postprocessing_no_align - owner: rnateam - revisions: - - 0a48b2db75e7 - tool_panel_section_label: GraphClust -- name: graphclust_motif_finder_plot - owner: rnateam - revisions: - - f00fb88794dc - tool_panel_section_label: GraphClust -- name: infernal - owner: bgruening - revisions: - - 55bb96edfc07 - - c47a7c52ac4f - tool_panel_section_label: GraphClust diff --git a/usegalaxy.eu/graphdisplay_data.yml b/usegalaxy.eu/graphdisplay_data.yml deleted file mode 100644 index 66373425..00000000 --- a/usegalaxy.eu/graphdisplay_data.yml +++ /dev/null @@ -1,64 +0,0 @@ -tool_panel_section_label: Graph/Display Data -tools: -- name: jbrowse - owner: iuc -- name: ucsc_custom_track - owner: devteam -- name: scatterplot - owner: devteam -- name: histogram - owner: devteam -- name: gmaj - owner: devteam -- name: xy_plot - owner: devteam -- name: volcanoplot - owner: iuc -- name: plotly_regression_performance_plots - owner: bgruening -- name: newick_utils - owner: iuc -- name: plotly_ml_performance_plots - owner: bgruening -- name: nanoplot - owner: iuc -- name: plotly_parallel_coordinates_plot - owner: bgruening -- name: bandage - owner: iuc -- name: intervene - owner: iuc -- name: pygenometracks - owner: iuc -- name: ggplot2_histogram - owner: iuc -- name: ggplot2_point - owner: iuc -- name: ggplot2_heatmap2 - owner: iuc -- name: ggplot2_violin - owner: iuc -- name: ggplot2_heatmap - owner: iuc -- name: ggplot2_pca - owner: iuc -- name: fasta_nucleotide_color_plot - owner: iuc -- name: graphlan - owner: iuc -- name: graphlan_annotate - owner: iuc -- name: export2graphlan - owner: iuc -- name: circos - owner: iuc -- name: tsne - owner: iuc -- name: krona_text - owner: saskia-hiltemann -- name: venn_list - owner: peterjc -- name: mummer - owner: peterjc -- name: karyotype_plot - owner: guru-ananda diff --git a/usegalaxy.eu/graphdisplay_data.yml.lock b/usegalaxy.eu/graphdisplay_data.yml.lock deleted file mode 100644 index def35abd..00000000 --- a/usegalaxy.eu/graphdisplay_data.yml.lock +++ /dev/null @@ -1,160 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: jbrowse - owner: iuc - revisions: - - 1cfc579079a6 - tool_panel_section_label: Graph/Display Data -- name: ucsc_custom_track - owner: devteam - revisions: - - 760f588e8a26 - tool_panel_section_label: Graph/Display Data -- name: scatterplot - owner: devteam - revisions: - - efda9a4a50e7 - tool_panel_section_label: Graph/Display Data -- name: histogram - owner: devteam - revisions: - - cdb9e89e2970 - tool_panel_section_label: Graph/Display Data -- name: gmaj - owner: devteam - revisions: - - 2cd5ee197ec7 - tool_panel_section_label: Graph/Display Data -- name: xy_plot - owner: devteam - revisions: - - 319fa5a9fc1b - tool_panel_section_label: Graph/Display Data -- name: volcanoplot - owner: iuc - revisions: - - d1d39c72b755 - tool_panel_section_label: Graph/Display Data -- name: plotly_regression_performance_plots - owner: bgruening - revisions: - - 389227fa1864 - tool_panel_section_label: Graph/Display Data -- name: newick_utils - owner: iuc - revisions: - - fe4235285ee8 - tool_panel_section_label: Graph/Display Data -- name: plotly_ml_performance_plots - owner: bgruening - revisions: - - 4fac53da862f - tool_panel_section_label: Graph/Display Data -- name: nanoplot - owner: iuc - revisions: - - db1eeffba23e - tool_panel_section_label: Graph/Display Data -- name: plotly_parallel_coordinates_plot - owner: bgruening - revisions: - - 7b2455348edf - tool_panel_section_label: Graph/Display Data -- name: bandage - owner: iuc - revisions: - - 067592b6b312 - tool_panel_section_label: Graph/Display Data -- name: intervene - owner: iuc - revisions: - - f5fa293605ca - tool_panel_section_label: Graph/Display Data -- name: pygenometracks - owner: iuc - revisions: - - 0ea86f6bf2a1 - tool_panel_section_label: Graph/Display Data -- name: ggplot2_histogram - owner: iuc - revisions: - - f52035800250 - tool_panel_section_label: Graph/Display Data -- name: ggplot2_point - owner: iuc - revisions: - - 9a482995958c - tool_panel_section_label: Graph/Display Data -- name: ggplot2_heatmap2 - owner: iuc - revisions: - - 4955e9bb96d1 - tool_panel_section_label: Graph/Display Data -- name: ggplot2_violin - owner: iuc - revisions: - - 43778344b955 - tool_panel_section_label: Graph/Display Data -- name: ggplot2_heatmap - owner: iuc - revisions: - - f44dc95928aa - tool_panel_section_label: Graph/Display Data -- name: ggplot2_pca - owner: iuc - revisions: - - c21099566418 - tool_panel_section_label: Graph/Display Data -- name: fasta_nucleotide_color_plot - owner: iuc - revisions: - - 980917b09eb8 - - e4b5401adcec - tool_panel_section_label: Graph/Display Data -- name: graphlan - owner: iuc - revisions: - - 8f62f666dcb6 - tool_panel_section_label: Graph/Display Data -- name: graphlan_annotate - owner: iuc - revisions: - - 5d6f8f0bef7c - tool_panel_section_label: Graph/Display Data -- name: export2graphlan - owner: iuc - revisions: - - ed1becc01910 - tool_panel_section_label: Graph/Display Data -- name: circos - owner: iuc - revisions: - - ef5f8bbf7730 - tool_panel_section_label: Graph/Display Data -- name: tsne - owner: iuc - revisions: - - 53cfe6f313b3 - tool_panel_section_label: Graph/Display Data -- name: krona_text - owner: saskia-hiltemann - revisions: - - b14f1444e464 - tool_panel_section_label: Graph/Display Data -- name: venn_list - owner: peterjc - revisions: - - 20d347feb882 - tool_panel_section_label: Graph/Display Data -- name: mummer - owner: peterjc - revisions: - - d9f3d4779507 - tool_panel_section_label: Graph/Display Data -- name: karyotype_plot - owner: guru-ananda - revisions: - - d810aa84ee6a - tool_panel_section_label: Graph/Display Data diff --git a/usegalaxy.eu/hicexplorer.yml b/usegalaxy.eu/hicexplorer.yml deleted file mode 100644 index 5820f238..00000000 --- a/usegalaxy.eu/hicexplorer.yml +++ /dev/null @@ -1,30 +0,0 @@ -tool_panel_section_label: HiCExplorer -tools: -- name: hicexplorer_hicfindtads - owner: bgruening -- name: hicexplorer_hicplottads - owner: bgruening -- name: hicexplorer_hicmergematrixbins - owner: bgruening -- name: hicexplorer_hicplotmatrix - owner: bgruening -- name: hicexplorer_hicbuildmatrix - owner: bgruening -- name: hicexplorer_hicplotviewpoint - owner: bgruening -- name: hicexplorer_hictransform - owner: bgruening -- name: hicexplorer_hiccorrelate - owner: bgruening -- name: hicexplorer_hiccomparematrices - owner: bgruening -- name: hicexplorer_hicaggregatecontacts - owner: bgruening -- name: hicexplorer_hicsummatrices - owner: bgruening -- name: hicexplorer_hicpca - owner: bgruening -- name: hicexplorer_hicplotdistvscounts - owner: bgruening -- name: hicexplorer_hiccorrectmatrix - owner: bgruening diff --git a/usegalaxy.eu/hicexplorer.yml.lock b/usegalaxy.eu/hicexplorer.yml.lock deleted file mode 100644 index 948a4bbf..00000000 --- a/usegalaxy.eu/hicexplorer.yml.lock +++ /dev/null @@ -1,74 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: hicexplorer_hicfindtads - owner: bgruening - revisions: - - 78e22ca9f2ce - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicplottads - owner: bgruening - revisions: - - a67942d17a91 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicmergematrixbins - owner: bgruening - revisions: - - 90645548f8cc - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicplotmatrix - owner: bgruening - revisions: - - c2521cba1c32 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicbuildmatrix - owner: bgruening - revisions: - - 4ceaee0043a5 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicplotviewpoint - owner: bgruening - revisions: - - 67bd57e960a3 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hictransform - owner: bgruening - revisions: - - 09ae55eb26fa - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hiccorrelate - owner: bgruening - revisions: - - 8a5b13451a9e - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hiccomparematrices - owner: bgruening - revisions: - - b6c95ff7c3c3 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicaggregatecontacts - owner: bgruening - revisions: - - a48457358aa8 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicsummatrices - owner: bgruening - revisions: - - 6d1526527417 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicpca - owner: bgruening - revisions: - - ebb9b94138c1 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hicplotdistvscounts - owner: bgruening - revisions: - - d7a84a789c83 - tool_panel_section_label: HiCExplorer -- name: hicexplorer_hiccorrectmatrix - owner: bgruening - revisions: - - 92fc291ceb1a - tool_panel_section_label: HiCExplorer diff --git a/usegalaxy.eu/join_subtract_and_group.yml b/usegalaxy.eu/join_subtract_and_group.yml deleted file mode 100644 index b41d4da5..00000000 --- a/usegalaxy.eu/join_subtract_and_group.yml +++ /dev/null @@ -1,10 +0,0 @@ -tool_panel_section_label: Join, Subtract and Group -tools: -- name: subtract - owner: devteam -- name: datamash_ops - owner: iuc -- name: datamash_reverse - owner: iuc -- name: datamash_transpose - owner: iuc diff --git a/usegalaxy.eu/join_subtract_and_group.yml.lock b/usegalaxy.eu/join_subtract_and_group.yml.lock deleted file mode 100644 index 35643152..00000000 --- a/usegalaxy.eu/join_subtract_and_group.yml.lock +++ /dev/null @@ -1,25 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: subtract - owner: devteam - revisions: - - 7a2a604ae9c8 - tool_panel_section_label: Join, Subtract and Group -- name: datamash_ops - owner: iuc - revisions: - - 2f3c6f2dcf39 - - 562f3c677828 - tool_panel_section_label: Join, Subtract and Group -- name: datamash_reverse - owner: iuc - revisions: - - 0f1724dd59d2 - tool_panel_section_label: Join, Subtract and Group -- name: datamash_transpose - owner: iuc - revisions: - - 22c2a1ac7ae3 - tool_panel_section_label: Join, Subtract and Group diff --git a/usegalaxy.eu/mapping.yml b/usegalaxy.eu/mapping.yml deleted file mode 100644 index 87ac851f..00000000 --- a/usegalaxy.eu/mapping.yml +++ /dev/null @@ -1,36 +0,0 @@ -tool_panel_section_label: Mapping -tools: -- name: hisat2 - owner: iuc -- name: megablast_xml_parser - owner: devteam -- name: megablast_wrapper - owner: devteam -- name: bowtie2 - owner: devteam -- name: lastz_paired_reads - owner: devteam -- name: lastz - owner: devteam -- name: bowtie_wrappers - owner: devteam -- name: bismark - owner: bgruening -- name: graphmap_overlap - owner: bgruening -- name: graphmap_align - owner: bgruening -- name: minimap2 - owner: iuc -- name: rgrnastar - owner: iuc -- name: bwa - owner: devteam -- name: star_fusion - owner: iuc -- name: tophat2 - owner: devteam -- name: bowtie_color_wrappers - owner: devteam -- name: bwa_mem - owner: crs4 diff --git a/usegalaxy.eu/mapping.yml.lock b/usegalaxy.eu/mapping.yml.lock deleted file mode 100644 index ba0c53a5..00000000 --- a/usegalaxy.eu/mapping.yml.lock +++ /dev/null @@ -1,91 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: hisat2 - owner: iuc - revisions: - - 3fb01a8c902d - tool_panel_section_label: Mapping -- name: megablast_xml_parser - owner: devteam - revisions: - - 03ca082aeb2e - tool_panel_section_label: Mapping -- name: megablast_wrapper - owner: devteam - revisions: - - fb2e0e1dac89 - tool_panel_section_label: Mapping -- name: bowtie2 - owner: devteam - revisions: - - c3dd1aeb7d07 - tool_panel_section_label: Mapping -- name: lastz_paired_reads - owner: devteam - revisions: - - ecc974513241 - tool_panel_section_label: Mapping -- name: lastz - owner: devteam - revisions: - - e7f19d6a9af8 - tool_panel_section_label: Mapping -- name: bowtie_wrappers - owner: devteam - revisions: - - b46e7d48076a - tool_panel_section_label: Mapping -- name: bismark - owner: bgruening - revisions: - - 9bfe38410155 - - 9d02cd7883ad - tool_panel_section_label: Mapping -- name: graphmap_overlap - owner: bgruening - revisions: - - d0a712cf0518 - tool_panel_section_label: Mapping -- name: graphmap_align - owner: bgruening - revisions: - - 190175f4e143 - tool_panel_section_label: Mapping -- name: minimap2 - owner: iuc - revisions: - - 17e61517c166 - tool_panel_section_label: Mapping -- name: rgrnastar - owner: iuc - revisions: - - d5659efd66aa - tool_panel_section_label: Mapping -- name: bwa - owner: devteam - revisions: - - 8d2a528a9513 - - dfd8b7f78c37 - tool_panel_section_label: Mapping -- name: star_fusion - owner: iuc - revisions: - - 0b44456754e2 - tool_panel_section_label: Mapping -- name: tophat2 - owner: devteam - revisions: - - 16c4255042be - tool_panel_section_label: Mapping -- name: bowtie_color_wrappers - owner: devteam - revisions: - - a3825c73805c - tool_panel_section_label: Mapping -- name: bwa_mem - owner: crs4 - revisions: - - ebb02ba5987c - tool_panel_section_label: Mapping diff --git a/usegalaxy.eu/metabolomics.yml b/usegalaxy.eu/metabolomics.yml deleted file mode 100644 index eeec43ed..00000000 --- a/usegalaxy.eu/metabolomics.yml +++ /dev/null @@ -1,60 +0,0 @@ -tool_panel_section_label: Metabolomics -tools: -- name: lipidmaps_textsearch - owner: fgiacomoni -- name: w4mcorcov - owner: eschen42 -- name: w4mclassfilter - owner: eschen42 -- name: w4mjoinpn - owner: eschen42 -- name: normalization - owner: marie-tremblay-metatoul -- name: xcms_xcmsset - owner: lecorguille -- name: xcms_group - owner: lecorguille -- name: xcms_retcor - owner: lecorguille -- name: xcms_fillpeaks - owner: lecorguille -- name: xcms_merge - owner: lecorguille -- name: generic_filter - owner: melpetera -- name: xcms_summary - owner: lecorguille -- name: qualitymetrics - owner: ethevenot -- name: metams_rungc - owner: yguitton -- name: withinvariation - owner: yguitton -- name: checkformat - owner: ethevenot -- name: batchcorrection - owner: melpetera -- name: golm_ws_lib_search - owner: fgiacomoni -- name: lcmsmatching - owner: prog -- name: massbank_ws_searchspectrum - owner: fgiacomoni -- name: hmdb_ms_search - owner: fgiacomoni -- name: probmetab - owner: mmonsoor -- name: camera_annotate - owner: lecorguille -- name: camera_combinexsannos - owner: mmonsoor -- name: profia - owner: ethevenot -- name: nmr_bucketing - owner: marie-tremblay-metatoul -- name: nmr_normalization - owner: marie-tremblay-metatoul -- name: nmr_preprocessing - owner: marie-tremblay-metatoul -- name: nmr_alignment - owner: marie-tremblay-metatoul diff --git a/usegalaxy.eu/metabolomics.yml.lock b/usegalaxy.eu/metabolomics.yml.lock deleted file mode 100644 index 53950819..00000000 --- a/usegalaxy.eu/metabolomics.yml.lock +++ /dev/null @@ -1,150 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: lipidmaps_textsearch - owner: fgiacomoni - revisions: - - f4e6b77c46e3 - tool_panel_section_label: Metabolomics -- name: w4mcorcov - owner: eschen42 - revisions: - - 2ae2d26e3270 - tool_panel_section_label: Metabolomics -- name: w4mclassfilter - owner: eschen42 - revisions: - - 9f5c0e23c205 - tool_panel_section_label: Metabolomics -- name: w4mjoinpn - owner: eschen42 - revisions: - - dcfaffec48c8 - tool_panel_section_label: Metabolomics -- name: normalization - owner: marie-tremblay-metatoul - revisions: - - f9554d5bb47e - tool_panel_section_label: Metabolomics -- name: xcms_xcmsset - owner: lecorguille - revisions: - - 363cce459fff - tool_panel_section_label: Metabolomics -- name: xcms_group - owner: lecorguille - revisions: - - 13558e8a4778 - tool_panel_section_label: Metabolomics -- name: xcms_retcor - owner: lecorguille - revisions: - - e4e0254a3c0a - tool_panel_section_label: Metabolomics -- name: xcms_fillpeaks - owner: lecorguille - revisions: - - dcb9041cb9ea - tool_panel_section_label: Metabolomics -- name: xcms_merge - owner: lecorguille - revisions: - - 3a5204f14fff - tool_panel_section_label: Metabolomics -- name: generic_filter - owner: melpetera - revisions: - - 12cf1eed21f4 - tool_panel_section_label: Metabolomics -- name: xcms_summary - owner: lecorguille - revisions: - - 4c757d1ba7b4 - tool_panel_section_label: Metabolomics -- name: qualitymetrics - owner: ethevenot - revisions: - - 596320b84315 - tool_panel_section_label: Metabolomics -- name: metams_rungc - owner: yguitton - revisions: - - c75532b75ba1 - tool_panel_section_label: Metabolomics -- name: withinvariation - owner: yguitton - revisions: - - 5086ad0c0992 - tool_panel_section_label: Metabolomics -- name: checkformat - owner: ethevenot - revisions: - - e7c5811ec12f - tool_panel_section_label: Metabolomics -- name: batchcorrection - owner: melpetera - revisions: - - 73892ef177e3 - tool_panel_section_label: Metabolomics -- name: golm_ws_lib_search - owner: fgiacomoni - revisions: - - 11779b6402bc - tool_panel_section_label: Metabolomics -- name: lcmsmatching - owner: prog - revisions: - - fb9c0409d85c - tool_panel_section_label: Metabolomics -- name: massbank_ws_searchspectrum - owner: fgiacomoni - revisions: - - 023c380900ef - tool_panel_section_label: Metabolomics -- name: hmdb_ms_search - owner: fgiacomoni - revisions: - - 97788e4bf3fc - tool_panel_section_label: Metabolomics -- name: probmetab - owner: mmonsoor - revisions: - - 52b222a626b0 - tool_panel_section_label: Metabolomics -- name: camera_annotate - owner: lecorguille - revisions: - - 6139bfcc95cb - tool_panel_section_label: Metabolomics -- name: camera_combinexsannos - owner: mmonsoor - revisions: - - 479a83f62863 - tool_panel_section_label: Metabolomics -- name: profia - owner: ethevenot - revisions: - - de9d1270a9ae - tool_panel_section_label: Metabolomics -- name: nmr_bucketing - owner: marie-tremblay-metatoul - revisions: - - 4d5c06b46c2f - tool_panel_section_label: Metabolomics -- name: nmr_normalization - owner: marie-tremblay-metatoul - revisions: - - fc66c35dcd4f - tool_panel_section_label: Metabolomics -- name: nmr_preprocessing - owner: marie-tremblay-metatoul - revisions: - - 68e2d63bece0 - - cbea5e9fd0b4 - tool_panel_section_label: Metabolomics -- name: nmr_alignment - owner: marie-tremblay-metatoul - revisions: - - 265ee538e120 - tool_panel_section_label: Metabolomics diff --git a/usegalaxy.eu/metagenomic_analyses.yml b/usegalaxy.eu/metagenomic_analyses.yml deleted file mode 100644 index 4f95a501..00000000 --- a/usegalaxy.eu/metagenomic_analyses.yml +++ /dev/null @@ -1,92 +0,0 @@ -tool_panel_section_label: Metagenomic analyses -tools: -- name: t2t_report - owner: devteam -- name: t2ps - owner: devteam -- name: poisson2test - owner: devteam -- name: lca_wrapper - owner: devteam -- name: gi2taxonomy - owner: devteam -- name: find_diag_hits - owner: devteam -- name: plasflow - owner: iuc -- name: khmer_abundance_distribution_single - owner: iuc -- name: khmer_normalize_by_median - owner: iuc -- name: khmer_partition - owner: iuc -- name: khmer_count_median - owner: iuc -- name: khmer_abundance_distribution - owner: iuc -- name: khmer_extract_partitions - owner: iuc -- name: khmer_filter_below_abundance_cutoff - owner: iuc -- name: khmer_filter_abundance - owner: iuc -- name: vsearch - owner: iuc -- name: vegan_rarefaction - owner: iuc -- name: vegan_fisher_alpha - owner: iuc -- name: vegan_diversity - owner: iuc -- name: compare_humann2_output - owner: bebatut -- name: group_humann2_uniref_abundances_to_go - owner: bebatut -- name: combine_metaphlan2_humann2 - owner: bebatut -- name: format_metaphlan2_output - owner: bebatut -- name: valet - owner: iuc -- name: humann2_split_stratified_table - owner: iuc -- name: humann2_renorm_table - owner: iuc -- name: humann2_genefamilies_genus_level - owner: iuc -- name: humann2_rna_dna_norm - owner: iuc -- name: humann2_regroup_table - owner: iuc -- name: humann2_barplot - owner: iuc -- name: humann2 - owner: iuc -- name: humann2_split_table - owner: iuc -- name: humann2_strain_profiler - owner: iuc -- name: humann2_rename_table - owner: iuc -- name: humann2_reduce_table - owner: iuc -- name: humann2_unpack_pathways - owner: iuc -- name: humann2_join_tables - owner: iuc -- name: humann2_associate - owner: iuc -- name: bio_hansel - owner: iuc -- name: nonpareil - owner: iuc -- name: metaphlan2 - owner: iuc -- name: metaphlan2krona - owner: iuc -- name: merge_metaphlan_tables - owner: iuc -- name: metaphlan_hclust_heatmap - owner: iuc -- name: metagenomeseq_normalization - owner: iuc diff --git a/usegalaxy.eu/metagenomic_analyses.yml.lock b/usegalaxy.eu/metagenomic_analyses.yml.lock deleted file mode 100644 index f0a30637..00000000 --- a/usegalaxy.eu/metagenomic_analyses.yml.lock +++ /dev/null @@ -1,229 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: t2t_report - owner: devteam - revisions: - - 592acb9505fc - tool_panel_section_label: Metagenomic analyses -- name: t2ps - owner: devteam - revisions: - - 4d9910e996f7 - tool_panel_section_label: Metagenomic analyses -- name: poisson2test - owner: devteam - revisions: - - 5ff18ec88181 - tool_panel_section_label: Metagenomic analyses -- name: lca_wrapper - owner: devteam - revisions: - - 33e8ed5a4601 - tool_panel_section_label: Metagenomic analyses -- name: gi2taxonomy - owner: devteam - revisions: - - 7b1b03c4465d - tool_panel_section_label: Metagenomic analyses -- name: find_diag_hits - owner: devteam - revisions: - - acf51ff24c7d - tool_panel_section_label: Metagenomic analyses -- name: plasflow - owner: iuc - revisions: - - bda6012394f7 - tool_panel_section_label: Metagenomic analyses -- name: khmer_abundance_distribution_single - owner: iuc - revisions: - - 792d520ba676 - tool_panel_section_label: Metagenomic analyses -- name: khmer_normalize_by_median - owner: iuc - revisions: - - f0290a079720 - tool_panel_section_label: Metagenomic analyses -- name: khmer_partition - owner: iuc - revisions: - - c393687bd857 - tool_panel_section_label: Metagenomic analyses -- name: khmer_count_median - owner: iuc - revisions: - - 5efc5f21d0c1 - tool_panel_section_label: Metagenomic analyses -- name: khmer_abundance_distribution - owner: iuc - revisions: - - a02efb62565b - tool_panel_section_label: Metagenomic analyses -- name: khmer_extract_partitions - owner: iuc - revisions: - - 7d8138b4a593 - tool_panel_section_label: Metagenomic analyses -- name: khmer_filter_below_abundance_cutoff - owner: iuc - revisions: - - d9cc87dfec6e - tool_panel_section_label: Metagenomic analyses -- name: khmer_filter_abundance - owner: iuc - revisions: - - a4970dfc331c - tool_panel_section_label: Metagenomic analyses -- name: vsearch - owner: iuc - revisions: - - b3c7199d8786 - tool_panel_section_label: Metagenomic analyses -- name: vegan_rarefaction - owner: iuc - revisions: - - b0d5976540e3 - tool_panel_section_label: Metagenomic analyses -- name: vegan_fisher_alpha - owner: iuc - revisions: - - f9966e11885b - tool_panel_section_label: Metagenomic analyses -- name: vegan_diversity - owner: iuc - revisions: - - a2c047a2c380 - tool_panel_section_label: Metagenomic analyses -- name: compare_humann2_output - owner: bebatut - revisions: - - c1aca37cb1fc - tool_panel_section_label: Metagenomic analyses -- name: group_humann2_uniref_abundances_to_go - owner: bebatut - revisions: - - cad28d7b49d2 - tool_panel_section_label: Metagenomic analyses -- name: combine_metaphlan2_humann2 - owner: bebatut - revisions: - - 31394a0c0242 - tool_panel_section_label: Metagenomic analyses -- name: format_metaphlan2_output - owner: bebatut - revisions: - - 2bfa9b200600 - tool_panel_section_label: Metagenomic analyses -- name: valet - owner: iuc - revisions: - - 56236acaad45 - tool_panel_section_label: Metagenomic analyses -- name: humann2_split_stratified_table - owner: iuc - revisions: - - b58d3f965a49 - tool_panel_section_label: Metagenomic analyses -- name: humann2_renorm_table - owner: iuc - revisions: - - dbf0e8eeeeed - tool_panel_section_label: Metagenomic analyses -- name: humann2_genefamilies_genus_level - owner: iuc - revisions: - - c7ac7103023d - tool_panel_section_label: Metagenomic analyses -- name: humann2_rna_dna_norm - owner: iuc - revisions: - - c8ef30c8451d - tool_panel_section_label: Metagenomic analyses -- name: humann2_regroup_table - owner: iuc - revisions: - - 1d141730ec69 - tool_panel_section_label: Metagenomic analyses -- name: humann2_barplot - owner: iuc - revisions: - - efd98a5e8255 - tool_panel_section_label: Metagenomic analyses -- name: humann2 - owner: iuc - revisions: - - 1d6d855c10d8 - tool_panel_section_label: Metagenomic analyses -- name: humann2_split_table - owner: iuc - revisions: - - ace84aac38ce - tool_panel_section_label: Metagenomic analyses -- name: humann2_strain_profiler - owner: iuc - revisions: - - eb13789029de - tool_panel_section_label: Metagenomic analyses -- name: humann2_rename_table - owner: iuc - revisions: - - b6d4c448782f - tool_panel_section_label: Metagenomic analyses -- name: humann2_reduce_table - owner: iuc - revisions: - - d020ce7b0e4c - tool_panel_section_label: Metagenomic analyses -- name: humann2_unpack_pathways - owner: iuc - revisions: - - d2e4fee96dd1 - tool_panel_section_label: Metagenomic analyses -- name: humann2_join_tables - owner: iuc - revisions: - - 9ada8e95bdd0 - tool_panel_section_label: Metagenomic analyses -- name: humann2_associate - owner: iuc - revisions: - - b6f52c19973d - tool_panel_section_label: Metagenomic analyses -- name: bio_hansel - owner: iuc - revisions: - - e3698ac146d7 - tool_panel_section_label: Metagenomic analyses -- name: nonpareil - owner: iuc - revisions: - - 280386b252a5 - tool_panel_section_label: Metagenomic analyses -- name: metaphlan2 - owner: iuc - revisions: - - 8c82c4d90cc6 - tool_panel_section_label: Metagenomic analyses -- name: metaphlan2krona - owner: iuc - revisions: - - fdbd63e92b01 - tool_panel_section_label: Metagenomic analyses -- name: merge_metaphlan_tables - owner: iuc - revisions: - - 3b469e230e82 - tool_panel_section_label: Metagenomic analyses -- name: metaphlan_hclust_heatmap - owner: iuc - revisions: - - f7353110d18c - tool_panel_section_label: Metagenomic analyses -- name: metagenomeseq_normalization - owner: iuc - revisions: - - d16f7cc26516 - tool_panel_section_label: Metagenomic analyses diff --git a/usegalaxy.eu/mimodd.yml b/usegalaxy.eu/mimodd.yml deleted file mode 100644 index 50da3c14..00000000 --- a/usegalaxy.eu/mimodd.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: MiModD -tools: -- name: mimodd_main - owner: wolma diff --git a/usegalaxy.eu/mimodd.yml.lock b/usegalaxy.eu/mimodd.yml.lock deleted file mode 100644 index a856024b..00000000 --- a/usegalaxy.eu/mimodd.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: mimodd_main - owner: wolma - revisions: - - f0f2795de2c7 - tool_panel_section_label: MiModD diff --git a/usegalaxy.eu/mothur.yml b/usegalaxy.eu/mothur.yml deleted file mode 100644 index de684384..00000000 --- a/usegalaxy.eu/mothur.yml +++ /dev/null @@ -1,264 +0,0 @@ -tool_panel_section_label: Mothur -tools: -- name: mothur_chimera_vsearch - owner: iuc -- name: mothur_clearcut - owner: iuc -- name: mothur_chimera_pintail - owner: iuc -- name: mothur_cooccurrence - owner: iuc -- name: mothur_split_abund - owner: iuc -- name: mothur_get_otus - owner: iuc -- name: mothur_chimera_slayer - owner: iuc -- name: mothur_filter_shared - owner: iuc -- name: mothur_mimarks_attributes - owner: iuc -- name: mothur_summary_single - owner: iuc -- name: mothur_pre_cluster - owner: iuc -- name: mothur_sub_sample - owner: iuc -- name: mothur_get_oturep - owner: iuc -- name: mothur_get_lineage - owner: iuc -- name: mothur_chop_seqs - owner: iuc -- name: mothur_sffinfo - owner: iuc -- name: mothur_remove_otulabels - owner: iuc -- name: mothur_remove_otus - owner: iuc -- name: mothur_lefse - owner: iuc -- name: mothur_rarefaction_single - owner: iuc -- name: mothur_get_sabund - owner: iuc -- name: mothur_get_label - owner: iuc -- name: mothur_unifrac_unweighted - owner: iuc -- name: mothur_cluster - owner: iuc -- name: mothur_indicator - owner: iuc -- name: mothur_get_dists - owner: iuc -- name: mothur_remove_rare - owner: iuc -- name: mothur_consensus_seqs - owner: iuc -- name: mothur_libshuff - owner: iuc -- name: mothur_chimera_check - owner: iuc -- name: mothur_make_sra - owner: iuc -- name: mothur_chimera_bellerophon - owner: iuc -- name: mothur_make_group - owner: iuc -- name: mothur_count_groups - owner: iuc -- name: mothur_seq_error - owner: iuc -- name: mothur_nmds - owner: iuc -- name: mothur_dist_shared - owner: iuc -- name: mothur_align_seqs - owner: iuc -- name: mothur_merge_groups - owner: iuc -- name: mothur_align_check - owner: iuc -- name: mothur_metastats - owner: iuc -- name: mothur_otu_association - owner: iuc -- name: mothur_get_communitytype - owner: iuc -- name: mothur_list_otulabels - owner: iuc -- name: mothur_get_otulabels - owner: iuc -- name: mothur_count_seqs - owner: iuc -- name: mothur_make_contigs - owner: iuc -- name: mothur_get_relabund - owner: iuc -- name: mothur_sens_spec - owner: iuc -- name: mothur_fastq_info - owner: iuc -- name: mothur_chimera_ccode - owner: iuc -- name: mothur_create_database - owner: iuc -- name: mothur_deunique_seqs - owner: iuc -- name: mothur_deunique_tree - owner: iuc -- name: mothur_merge_taxsummary - owner: iuc -- name: mothur_summary_seqs - owner: iuc -- name: mothur_corr_axes - owner: iuc -- name: mothur_degap_seqs - owner: iuc -- name: mothur_get_sharedseqs - owner: iuc -- name: mothur_biom_info - owner: iuc -- name: mothur_pairwise_seqs - owner: iuc -- name: mothur_merge_count - owner: iuc -- name: mothur_unifrac_weighted - owner: iuc -- name: mothur_pcr_seqs - owner: iuc -- name: mothur_make_lookup - owner: iuc -- name: mothur_get_group - owner: iuc -- name: mothur_normalize_shared - owner: iuc -- name: mothur_taxonomy_to_krona - owner: iuc -- name: mothur_remove_groups - owner: iuc -- name: mothur_chimera_perseus - owner: iuc -- name: mothur_split_groups - owner: iuc -- name: mothur_classify_tree - owner: iuc -- name: mothur_pca - owner: iuc -- name: mothur_mantel - owner: iuc -- name: mothur_summary_qual - owner: iuc -- name: mothur_pcoa - owner: iuc -- name: mothur_rarefaction_shared - owner: iuc -- name: mothur_venn - owner: iuc -- name: mothur_summary_shared - owner: iuc -- name: mothur_bin_seqs - owner: iuc -- name: mothur_get_otulist - owner: iuc -- name: mothur_get_coremicrobiome - owner: iuc -- name: mothur_classify_otu - owner: iuc -- name: mothur_screen_seqs - owner: iuc -- name: mothur_shhh_seqs - owner: iuc -- name: mothur_cluster_split - owner: iuc -- name: mothur_sort_seqs - owner: iuc -- name: mothur_parsimony - owner: iuc -- name: mothur_make_biom - owner: iuc -- name: mothur_get_mimarkspackage - owner: iuc -- name: mothur_remove_dists - owner: iuc -- name: mothur_cluster_fragments - owner: iuc -- name: mothur_anosim - owner: iuc -- name: mothur_collect_shared - owner: iuc -- name: mothur_reverse_seqs - owner: iuc -- name: mothur_make_lefse - owner: iuc -- name: mothur_chimera_uchime - owner: iuc -- name: mothur_collect_single - owner: iuc -- name: mothur_cluster_classic - owner: iuc -- name: mothur_classify_seqs - owner: iuc -- name: mothur_make_shared - owner: iuc -- name: mothur_filter_seqs - owner: iuc -- name: mothur_merge_sfffiles - owner: iuc -- name: mothur_amova - owner: iuc -- name: mothur_get_seqs - owner: iuc -- name: mothur_merge_files - owner: iuc -- name: mothur_phylotype - owner: iuc -- name: mothur_make_design - owner: iuc -- name: mothur_otu_hierarchy - owner: iuc -- name: mothur_unique_seqs - owner: iuc -- name: mothur_trim_flows - owner: iuc -- name: mothur_primer_design - owner: iuc -- name: mothur_rename_seqs - owner: iuc -- name: mothur_shhh_flows - owner: iuc -- name: mothur_get_groups - owner: iuc -- name: mothur_homova - owner: iuc -- name: mothur_phylo_diversity - owner: iuc -- name: mothur_list_seqs - owner: iuc -- name: mothur_remove_lineage - owner: iuc -- name: mothur_tree_shared - owner: iuc -- name: mothur_heatmap_sim - owner: iuc -- name: mothur_summary_tax - owner: iuc -- name: mothur_get_rabund - owner: iuc -- name: mothur_parse_list - owner: iuc -- name: mothur_heatmap_bin - owner: iuc -- name: mothur_dist_seqs - owner: iuc -- name: mothur_classify_rf - owner: iuc -- name: mothur_trim_seqs - owner: iuc -- name: mothur_remove_seqs - owner: iuc -- name: mothur_make_fastq - owner: iuc -- name: mothur_hcluster - owner: iuc diff --git a/usegalaxy.eu/mothur.yml.lock b/usegalaxy.eu/mothur.yml.lock deleted file mode 100644 index ae54d82c..00000000 --- a/usegalaxy.eu/mothur.yml.lock +++ /dev/null @@ -1,659 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: mothur_chimera_vsearch - owner: iuc - revisions: - - 1f9f30aed284 - tool_panel_section_label: Mothur -- name: mothur_clearcut - owner: iuc - revisions: - - 7e5184c75727 - tool_panel_section_label: Mothur -- name: mothur_chimera_pintail - owner: iuc - revisions: - - a98f92e8923d - tool_panel_section_label: Mothur -- name: mothur_cooccurrence - owner: iuc - revisions: - - 5076b26f99d0 - tool_panel_section_label: Mothur -- name: mothur_split_abund - owner: iuc - revisions: - - 3a364dd93195 - tool_panel_section_label: Mothur -- name: mothur_get_otus - owner: iuc - revisions: - - 971ab18e74d7 - tool_panel_section_label: Mothur -- name: mothur_chimera_slayer - owner: iuc - revisions: - - cc983edb4db0 - tool_panel_section_label: Mothur -- name: mothur_filter_shared - owner: iuc - revisions: - - 38bb70251d7a - tool_panel_section_label: Mothur -- name: mothur_mimarks_attributes - owner: iuc - revisions: - - 7986e1c4bc23 - tool_panel_section_label: Mothur -- name: mothur_summary_single - owner: iuc - revisions: - - de4801f05e5e - tool_panel_section_label: Mothur -- name: mothur_pre_cluster - owner: iuc - revisions: - - baba9fff9dba - tool_panel_section_label: Mothur -- name: mothur_sub_sample - owner: iuc - revisions: - - 88d66f3b47e0 - tool_panel_section_label: Mothur -- name: mothur_get_oturep - owner: iuc - revisions: - - '782220733828' - tool_panel_section_label: Mothur -- name: mothur_get_lineage - owner: iuc - revisions: - - d1abc038d4bd - tool_panel_section_label: Mothur -- name: mothur_chop_seqs - owner: iuc - revisions: - - 3eeb1a2b2ae4 - tool_panel_section_label: Mothur -- name: mothur_sffinfo - owner: iuc - revisions: - - 13d1e5e44a91 - tool_panel_section_label: Mothur -- name: mothur_remove_otulabels - owner: iuc - revisions: - - 2cbf56d15f4b - tool_panel_section_label: Mothur -- name: mothur_remove_otus - owner: iuc - revisions: - - 530698de365d - tool_panel_section_label: Mothur -- name: mothur_lefse - owner: iuc - revisions: - - c98e47f7b233 - tool_panel_section_label: Mothur -- name: mothur_rarefaction_single - owner: iuc - revisions: - - 5c2157147393 - tool_panel_section_label: Mothur -- name: mothur_get_sabund - owner: iuc - revisions: - - 0bc1dc0c6aad - tool_panel_section_label: Mothur -- name: mothur_get_label - owner: iuc - revisions: - - 78e5065b27bd - tool_panel_section_label: Mothur -- name: mothur_unifrac_unweighted - owner: iuc - revisions: - - 46ba42ec466b - tool_panel_section_label: Mothur -- name: mothur_cluster - owner: iuc - 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Ontology manipulation -- name: onto_tk_get_relationship_id_vs_relationship_name - owner: iuc - revisions: - - e3e11b9e7750 - tool_panel_section_label: OBO Ontology manipulation diff --git a/usegalaxy.eu/operate_on_genomic_intervals.yml b/usegalaxy.eu/operate_on_genomic_intervals.yml deleted file mode 100644 index bbbae116..00000000 --- a/usegalaxy.eu/operate_on_genomic_intervals.yml +++ /dev/null @@ -1,20 +0,0 @@ -tool_panel_section_label: Operate on Genomic Intervals -tools: -- name: basecoverage - owner: devteam -- name: complement - owner: devteam -- name: cluster - owner: devteam -- name: bedtools - owner: iuc -- name: annotation_profiler - owner: devteam -- name: translate_bed - owner: galaxyp -- name: concat - owner: devteam -- name: translate_bed_sequences - owner: jjohnson -- name: filter_bed_on_splice_junctions - owner: jjohnson diff --git a/usegalaxy.eu/operate_on_genomic_intervals.yml.lock b/usegalaxy.eu/operate_on_genomic_intervals.yml.lock deleted file mode 100644 index 119bb3cf..00000000 --- a/usegalaxy.eu/operate_on_genomic_intervals.yml.lock +++ /dev/null @@ -1,54 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: basecoverage - owner: devteam - revisions: - - 2cedec3759e4 - tool_panel_section_label: Operate on Genomic Intervals -- name: complement - owner: devteam - revisions: - - 38c8bb402872 - tool_panel_section_label: Operate on Genomic Intervals -- name: cluster - owner: devteam - revisions: - - 05696474ee89 - tool_panel_section_label: Operate on Genomic Intervals -- name: bedtools - owner: iuc - revisions: - - 4f7a5ccd2ae9 - - 6283d16e40ed - - a33db97b220c - - b3c147390100 - - b8348686a0b9 - - bd7721ad15aa - tool_panel_section_label: Operate on Genomic Intervals -- name: annotation_profiler - owner: devteam - revisions: - - 3b33da018e74 - tool_panel_section_label: Operate on Genomic Intervals -- name: translate_bed - owner: galaxyp - revisions: - - 038ecf54cbec - tool_panel_section_label: Operate on Genomic Intervals -- name: concat - owner: devteam - revisions: - - 32e1c8dac438 - tool_panel_section_label: Operate on Genomic Intervals -- name: translate_bed_sequences - owner: jjohnson - revisions: - - d328db400280 - tool_panel_section_label: Operate on Genomic Intervals -- name: filter_bed_on_splice_junctions - owner: jjohnson - revisions: - - 915e5c5e02e6 - tool_panel_section_label: Operate on Genomic Intervals diff --git a/usegalaxy.eu/other_tools.yml b/usegalaxy.eu/other_tools.yml deleted file mode 100644 index 4241479e..00000000 --- a/usegalaxy.eu/other_tools.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Other Tools -tools: -- name: extract_genomic_dna - owner: iuc diff --git a/usegalaxy.eu/other_tools.yml.lock b/usegalaxy.eu/other_tools.yml.lock deleted file mode 100644 index a02fbd83..00000000 --- a/usegalaxy.eu/other_tools.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: extract_genomic_dna - owner: iuc - revisions: - - e400dcbc60d0 - tool_panel_section_label: Other Tools diff --git a/usegalaxy.eu/peak_calling.yml b/usegalaxy.eu/peak_calling.yml deleted file mode 100644 index 78802b96..00000000 --- a/usegalaxy.eu/peak_calling.yml +++ /dev/null @@ -1,22 +0,0 @@ -tool_panel_section_label: Peak Calling -tools: -- name: macs - owner: devteam -- name: sicer - owner: devteam -- name: ccat - owner: devteam -- name: peakachu - owner: rnateam -- name: zerone - owner: iuc -- name: diffbind - owner: bgruening -- name: pureclip - owner: iuc -- name: macs2 - owner: iuc -- name: jamm - owner: messersc -- name: piranha - owner: rnateam diff --git a/usegalaxy.eu/peak_calling.yml.lock b/usegalaxy.eu/peak_calling.yml.lock deleted file mode 100644 index ca42965c..00000000 --- a/usegalaxy.eu/peak_calling.yml.lock +++ /dev/null @@ -1,56 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: macs - owner: devteam - revisions: - - f6319b0b4391 - tool_panel_section_label: Peak Calling -- name: sicer - owner: devteam - revisions: - - 74c9214cc8e6 - tool_panel_section_label: Peak Calling -- name: ccat - owner: devteam - revisions: - - 201d8e7dfc43 - tool_panel_section_label: Peak Calling -- name: peakachu - owner: rnateam - revisions: - - 49a5a2e86c84 - tool_panel_section_label: Peak Calling -- name: zerone - owner: iuc - revisions: - - 75962a01d8ab - tool_panel_section_label: Peak Calling -- name: diffbind - owner: bgruening - revisions: - - c97a786e8fb5 - tool_panel_section_label: Peak Calling -- name: pureclip - owner: iuc - revisions: - - eb000bccef28 - tool_panel_section_label: Peak Calling -- name: macs2 - owner: iuc - revisions: - - 01cded2297b7 - - c33686854b19 - - f5d67c722d67 - tool_panel_section_label: Peak Calling -- name: jamm - owner: messersc - revisions: - - 243f75d0ed6e - tool_panel_section_label: Peak Calling -- name: piranha - owner: rnateam - revisions: - - f7f366ede872 - tool_panel_section_label: Peak Calling diff --git a/usegalaxy.eu/phenotype_association.yml b/usegalaxy.eu/phenotype_association.yml deleted file mode 100644 index 912a5d40..00000000 --- a/usegalaxy.eu/phenotype_association.yml +++ /dev/null @@ -1,14 +0,0 @@ -tool_panel_section_label: Phenotype Association -tools: -- name: vcf2pgsnp - owner: devteam -- name: snpfreq - owner: devteam -- name: hgv_fundo - owner: devteam -- name: hgv_hilbertvis - owner: devteam -- name: divide_pg_snp - owner: devteam -- name: ctd_batch - owner: devteam diff --git a/usegalaxy.eu/phenotype_association.yml.lock b/usegalaxy.eu/phenotype_association.yml.lock deleted file mode 100644 index 3d5376ce..00000000 --- a/usegalaxy.eu/phenotype_association.yml.lock +++ /dev/null @@ -1,34 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: vcf2pgsnp - owner: devteam - revisions: - - 5fca46616675 - tool_panel_section_label: Phenotype Association -- name: snpfreq - owner: devteam - revisions: - - 5c3ac057608b - tool_panel_section_label: Phenotype Association -- name: hgv_fundo - owner: devteam - revisions: - - ca3fcd18dc3e - tool_panel_section_label: Phenotype Association -- name: hgv_hilbertvis - owner: devteam - revisions: - - e1a9ad05dced - tool_panel_section_label: Phenotype Association -- name: divide_pg_snp - owner: devteam - revisions: - - f74fdfc17143 - tool_panel_section_label: Phenotype Association -- name: ctd_batch - owner: devteam - revisions: - - 4a32700dcaa2 - tool_panel_section_label: Phenotype Association diff --git a/usegalaxy.eu/phylogenetics.yml b/usegalaxy.eu/phylogenetics.yml deleted file mode 100644 index 5b894901..00000000 --- a/usegalaxy.eu/phylogenetics.yml +++ /dev/null @@ -1,18 +0,0 @@ -tool_panel_section_label: Phylogenetics -tools: -- name: ete - owner: earlhaminst -- name: treebest_best - owner: earlhaminst -- name: gstf_preparation - owner: earlhaminst -- name: gafa - owner: earlhaminst -- name: t_coffee - owner: earlhaminst -- name: hcluster_sg_parser - owner: earlhaminst -- name: hcluster_sg - owner: earlhaminst -- name: blast_parser - owner: earlhaminst diff --git a/usegalaxy.eu/phylogenetics.yml.lock b/usegalaxy.eu/phylogenetics.yml.lock deleted file mode 100644 index 837d2d2d..00000000 --- a/usegalaxy.eu/phylogenetics.yml.lock +++ /dev/null @@ -1,46 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: ete - owner: earlhaminst - revisions: - - 276e3ee68c37 - - 6a5282f71f82 - tool_panel_section_label: Phylogenetics -- name: treebest_best - owner: earlhaminst - revisions: - - 4f9e5110914b - - b78b529f66db - tool_panel_section_label: Phylogenetics -- name: gstf_preparation - owner: earlhaminst - revisions: - - 92f3966d5bc3 - tool_panel_section_label: Phylogenetics -- name: gafa - owner: earlhaminst - revisions: - - b9f1bcf5ee59 - tool_panel_section_label: Phylogenetics -- name: t_coffee - owner: earlhaminst - revisions: - - df6527887a18 - tool_panel_section_label: Phylogenetics -- name: hcluster_sg_parser - owner: earlhaminst - revisions: - - f9e418125021 - tool_panel_section_label: Phylogenetics -- name: hcluster_sg - owner: earlhaminst - revisions: - - 1d2de27d7a9c - tool_panel_section_label: Phylogenetics -- name: blast_parser - owner: earlhaminst - revisions: - - 363f3480622d - tool_panel_section_label: Phylogenetics diff --git a/usegalaxy.eu/picard.yml b/usegalaxy.eu/picard.yml deleted file mode 100644 index 44fb2253..00000000 --- a/usegalaxy.eu/picard.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Picard -tools: -- name: picard - owner: devteam diff --git a/usegalaxy.eu/picard.yml.lock b/usegalaxy.eu/picard.yml.lock deleted file mode 100644 index a84a9d05..00000000 --- a/usegalaxy.eu/picard.yml.lock +++ /dev/null @@ -1,10 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: picard - owner: devteam - revisions: - - 2a17c789e0a5 - - ab1f60c26526 - tool_panel_section_label: Picard diff --git a/usegalaxy.eu/proteomics.yml b/usegalaxy.eu/proteomics.yml deleted file mode 100644 index b5d25666..00000000 --- a/usegalaxy.eu/proteomics.yml +++ /dev/null @@ -1,396 +0,0 @@ -tool_panel_section_label: Proteomics -tools: -- name: pep_pointer - owner: galaxyp -- name: custom_pro_db - owner: galaxyp -- name: megahit_contig2fastg - owner: iuc -- name: query_tabular - owner: iuc -- name: maldi_quant_peak_detection - owner: galaxyp -- name: cardinal_mz_images - owner: galaxyp -- name: cardinal_filtering - owner: galaxyp -- name: maldi_quant_preprocessing - owner: galaxyp -- name: cardinal_spectra_plots - owner: galaxyp -- name: cardinal_segmentations - owner: galaxyp -- name: cardinal_quality_report - owner: galaxyp -- name: cardinal_preprocessing - owner: galaxyp -- name: cardinal_data_exporter - owner: galaxyp -- name: cardinal_combine - owner: galaxyp -- name: cardinal_classification - owner: galaxyp -- name: percolator - owner: galaxyp -- name: lfq_protein_quant - owner: galaxyp -- name: quantp - owner: galaxyp -- name: msi_preprocessing - owner: galaxyp -- name: peptideshaker - owner: galaxyp -- name: msi_spectra_plot - owner: galaxyp -- name: msi_qualitycontrol - owner: galaxyp -- name: msi_filtering - owner: galaxyp -- name: msi_ion_images - owner: galaxyp -- name: mass_spectrometry_imaging_segmentations - owner: galaxyp -- name: msi_combine - owner: galaxyp -- name: reactome_pathwaymatcher - owner: galaxyp -- name: msi_classification - owner: galaxyp -- name: msgfplus - owner: galaxyp -- name: eggnog_mapper - owner: galaxyp -- name: protease_prediction - owner: bgruening -- name: sqlite_to_tabular - owner: iuc -- name: protein_properties - owner: bgruening -- name: filter_tabular - owner: iuc -- name: proteomics_moff - owner: galaxyp -- name: openms_idposteriorerrorprobability - owner: galaxyp -- name: openms_targetedfileconverter - owner: galaxyp -- name: openms_idscoreswitcher - owner: galaxyp -- name: openms_ticcalculator - owner: galaxyp -- name: openms_spectrafilternlargest - owner: galaxyp -- name: openms_spectrafilterwindowmower - owner: galaxyp -- name: openms_qcimporter - owner: galaxyp -- name: openms_openswathrewritetofeaturexml - owner: galaxyp -- name: openms_rtmodel - owner: galaxyp -- name: openms_ptmodel - owner: galaxyp -- name: openms_proteinresolver - owner: galaxyp -- name: openms_proteininference - owner: galaxyp -- name: openms_xmlvalidator - owner: galaxyp -- name: openms_spectrafilterparentpeakmower - owner: galaxyp -- name: openms_peakpickerwavelet - owner: galaxyp -- name: openms_spectrafilterthresholdmower - owner: galaxyp -- name: openms_openswathmzmlfilecacher - owner: galaxyp -- name: openms_precursormasscorrector - owner: galaxyp -- name: openms_spectrastsearchadapter - 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owner: galaxyp -- name: openms_lowmempeakpickerhires_randomaccess - owner: galaxyp -- name: openms_idfileconverter - owner: galaxyp -- name: openms_noisefiltergaussian - owner: galaxyp -- name: openms_idextractor - owner: galaxyp -- name: openms_mascotadapter - owner: galaxyp -- name: openms_iddecoyprobability - owner: galaxyp -- name: openms_peakpickeriterative - owner: galaxyp -- name: openms_openswathdiaprescoring - owner: galaxyp -- name: openms_idconflictresolver - owner: galaxyp -- name: openms_precursorionselector - owner: galaxyp -- name: openms_fuzzydiff - owner: galaxyp -- name: openms_rnpxlsearch - owner: galaxyp -- name: openms_filefilter - owner: galaxyp -- name: openms_seedlistgenerator - owner: galaxyp -- name: openms_fileconverter - owner: galaxyp -- name: openms_mapnormalizer - owner: galaxyp -- name: openms_peptideindexer - owner: galaxyp -- name: openms_featurelinkerunlabeled - owner: galaxyp -- name: openms_rnpxl - owner: galaxyp -- name: 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- owner: galaxyp -- name: openms_openswathanalyzer - owner: galaxyp -- name: openms_compnovocid - owner: galaxyp -- name: openms_qcexporter - owner: galaxyp -- name: openms_spectramerger - owner: galaxyp -- name: openms_sequencecoveragecalculator - owner: galaxyp -- name: openms_metabolitespectralmatcher - owner: galaxyp -- name: openms_ffeval - owner: galaxyp -- name: openms_featurefindercentroided - owner: galaxyp -- name: openms_eicextractor - owner: galaxyp -- name: openms_qcembedder - owner: galaxyp -- name: flashlfq - owner: galaxyp -- name: idpqonvert - owner: galaxyp -- name: idpquery - owner: galaxyp -- name: idpassemble - owner: galaxyp -- name: myrimatch - owner: galaxyp -- name: query_tabular - owner: jjohnson -- name: openms_masstraceextractor - owner: galaxyp -- name: openms_idrtcalibration - owner: galaxyp -- name: openms_topperc - owner: galaxyp -- name: openms_openswathchromatogramextractor - owner: galaxyp -- name: hardklor - owner: galaxyp -- name: protease_prediction - owner: bgruening -- name: decoyfasta - owner: galaxyp -- name: morpheus - owner: galaxyp diff --git a/usegalaxy.eu/proteomics.yml.lock b/usegalaxy.eu/proteomics.yml.lock deleted file mode 100644 index 6af40b3b..00000000 --- a/usegalaxy.eu/proteomics.yml.lock +++ /dev/null @@ -1,991 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: pep_pointer - owner: galaxyp - revisions: - - 073a2965e3b2 - tool_panel_section_label: Proteomics -- name: custom_pro_db - owner: galaxyp - revisions: - - a3a66063d460 - tool_panel_section_label: Proteomics -- name: megahit_contig2fastg - owner: iuc - revisions: - - ed22349139ee - tool_panel_section_label: Proteomics -- name: query_tabular - owner: iuc - revisions: - - 33d61c89fb8d - tool_panel_section_label: Proteomics -- name: maldi_quant_peak_detection - owner: galaxyp - revisions: - - 17c54820f3be - tool_panel_section_label: Proteomics -- name: 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false -tools: -- name: qiime_collapse_samples - owner: iuc - revisions: - - 242462fc608b - tool_panel_section_label: Qiime -- name: qiime_make_otu_table - owner: iuc - revisions: - - e00b6983b175 - tool_panel_section_label: Qiime -- name: qiime_pick_open_reference_otus - owner: iuc - revisions: - - 41482ca21d31 - tool_panel_section_label: Qiime -- name: qiime_pick_closed_reference_otus - owner: iuc - revisions: - - 935abbf93f99 - tool_panel_section_label: Qiime -- name: qiime_count_seqs - owner: iuc - revisions: - - bb0c29df7392 - tool_panel_section_label: Qiime -- name: qiime_extract_barcodes - owner: iuc - revisions: - - c7eeac78cb64 - tool_panel_section_label: Qiime -- name: count_seqs - owner: iuc - revisions: - - bafc9bf1d0fc - tool_panel_section_label: Qiime -- name: qiime_make_emperor - owner: iuc - revisions: - - d1ae914eac40 - tool_panel_section_label: Qiime -- name: qiime_make_otu_heatmap - owner: iuc - revisions: - - bd379bfdaa41 - tool_panel_section_label: Qiime -- name: qiime_pick_rep_set - owner: iuc - revisions: - - 05feaea4b7fb - tool_panel_section_label: Qiime -- name: qiime_multiple_join_paired_ends - owner: iuc - revisions: - - 64a2a08844af - tool_panel_section_label: Qiime -- name: qiime_align_seqs - owner: iuc - revisions: - - 98614f0549e3 - tool_panel_section_label: Qiime -- name: qiime_alpha_rarefaction - owner: iuc - revisions: - - 0a097fc6e5a6 - tool_panel_section_label: Qiime -- name: pick_open_reference_otus - owner: iuc - revisions: - - b1ffac561861 - tool_panel_section_label: Qiime -- name: pick_closed_reference_otus - owner: iuc - revisions: - - 768fb40ad1e8 - tool_panel_section_label: Qiime -- name: qiime_core_diversity - owner: iuc - revisions: - - 486570c88d1b - tool_panel_section_label: Qiime -- name: qiime_alpha_diversity - owner: iuc - revisions: - - ffe438e1fc67 - tool_panel_section_label: Qiime -- name: qiime_split_libraries_fastq - owner: iuc - revisions: - - 10ea852bc26d - tool_panel_section_label: Qiime -- name: qiime_filter_otus_from_otu_table - owner: iuc - revisions: - - 18590df9277d - tool_panel_section_label: Qiime -- name: qiime_jackknifed_beta_diversity - owner: iuc - revisions: - - 4d94cce068bc - tool_panel_section_label: Qiime -- name: qiime_filter_taxa_from_otu_table - owner: iuc - revisions: - - 595a89cb5520 - tool_panel_section_label: Qiime -- name: qiime_pick_otus - owner: iuc - revisions: - - dcdaee7d89ae - tool_panel_section_label: Qiime -- name: qiime_compare_categories - owner: iuc - revisions: - - 21abe2afb7cf - tool_panel_section_label: Qiime -- name: qiime_plot_taxa_summary - owner: iuc - revisions: - - 6c229f22e9b6 - tool_panel_section_label: Qiime -- name: qiime_upgma_cluster - owner: iuc - revisions: - - 9f73c09cef36 - tool_panel_section_label: Qiime -- name: qiime_filter_fasta - owner: iuc - revisions: - - 87656f8deb6a - tool_panel_section_label: Qiime -- name: qiime_filter_alignment - owner: iuc - revisions: - - ffcb719ff53c - tool_panel_section_label: Qiime -- name: qiime_assign_taxonomy - owner: iuc - revisions: - - b4170e1a3b85 - tool_panel_section_label: Qiime -- name: qiime_make_phylogeny - owner: iuc - revisions: - - b3ad44e46414 - tool_panel_section_label: Qiime -- name: qiime_summarize_taxa - owner: iuc - revisions: - - 3e627f047a3f - tool_panel_section_label: Qiime -- name: qiime_beta_diversity - owner: iuc - revisions: - - 206c7eb264db - tool_panel_section_label: Qiime -- name: qiime_split_libraries - owner: iuc - revisions: - - c3a29137864b - tool_panel_section_label: Qiime -- name: qiime_filter_samples_from_otu_table - owner: iuc - revisions: - - 74880d08445c - tool_panel_section_label: Qiime -- name: qiime_summarize_taxa_through_plots - owner: iuc - revisions: - - 1ad2475bceba - tool_panel_section_label: Qiime -- name: qiime_multiple_split_libraries_fastq - owner: iuc - revisions: - - 11fd38f7b5ee - tool_panel_section_label: Qiime -- name: qiime_beta_diversity_through_plots - owner: iuc - revisions: - - a892c4d384de - tool_panel_section_label: Qiime -- name: qiime_validate_mapping_file - owner: iuc - revisions: - - a0d2430136e6 - tool_panel_section_label: Qiime diff --git a/usegalaxy.eu/quality_control.yml b/usegalaxy.eu/quality_control.yml deleted file mode 100644 index 78e46951..00000000 --- a/usegalaxy.eu/quality_control.yml +++ /dev/null @@ -1,18 +0,0 @@ -tool_panel_section_label: Quality Control -tools: -- name: short_reads_figure_score - owner: devteam -- name: fastq_stats - owner: devteam -- name: fastqc - owner: devteam -- name: fastx_quality_statistics - owner: devteam -- name: fastq_quality_boxplot - owner: devteam -- name: multiqc - owner: iuc -- name: mqc - owner: rnateam -- name: trimmomatic - owner: pjbriggs diff --git a/usegalaxy.eu/quality_control.yml.lock b/usegalaxy.eu/quality_control.yml.lock deleted file mode 100644 index f57f54bd..00000000 --- a/usegalaxy.eu/quality_control.yml.lock +++ /dev/null @@ -1,44 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: short_reads_figure_score - owner: devteam - revisions: - - b52b9c7aabd9 - tool_panel_section_label: Quality Control -- name: fastq_stats - owner: devteam - revisions: - - daaf552153fe - tool_panel_section_label: Quality Control -- name: fastqc - owner: devteam - revisions: - - ff9530579d1f - tool_panel_section_label: Quality Control -- name: fastx_quality_statistics - owner: devteam - revisions: - - 7306ec78632a - tool_panel_section_label: Quality Control -- name: fastq_quality_boxplot - owner: devteam - revisions: - - f95284aa2946 - tool_panel_section_label: Quality Control -- name: multiqc - owner: iuc - revisions: - - 161f4383df15 - tool_panel_section_label: Quality Control -- name: mqc - owner: rnateam - revisions: - - 523dd2a71270 - tool_panel_section_label: Quality Control -- name: trimmomatic - owner: pjbriggs - revisions: - - dfa082f84068 - tool_panel_section_label: Quality Control diff --git a/usegalaxy.eu/rad_seq.yml b/usegalaxy.eu/rad_seq.yml deleted file mode 100644 index b3257ba6..00000000 --- a/usegalaxy.eu/rad_seq.yml +++ /dev/null @@ -1,24 +0,0 @@ -tool_panel_section_label: RAD-seq -tools: -- name: stacks_populations - owner: iuc -- name: stacks_pstacks - owner: iuc -- name: stacks_rxstacks - owner: iuc -- name: stacks_cstacks - owner: iuc -- name: stacks_refmap - owner: iuc -- name: stacks_procrad - owner: iuc -- name: stacks_assembleperead - owner: iuc -- name: stacks_ustacks - owner: iuc -- name: stacks_denovomap - owner: iuc -- name: stacks_genotypes - owner: iuc -- name: stacks_sstacks - owner: iuc diff --git a/usegalaxy.eu/rad_seq.yml.lock b/usegalaxy.eu/rad_seq.yml.lock deleted file mode 100644 index 0dce1a1d..00000000 --- a/usegalaxy.eu/rad_seq.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: stacks_populations - owner: iuc - revisions: - - 45db1ba16163 - tool_panel_section_label: RAD-seq -- name: stacks_pstacks - owner: iuc - revisions: - - 7ebc7d229deb - tool_panel_section_label: RAD-seq -- name: stacks_rxstacks - owner: iuc - revisions: - - 2360d8cf42f7 - tool_panel_section_label: RAD-seq -- name: stacks_cstacks - owner: iuc - revisions: - - ff1f282d731e - tool_panel_section_label: RAD-seq -- name: stacks_refmap - owner: iuc - revisions: - - 4ee074ca88fb - tool_panel_section_label: RAD-seq -- name: stacks_procrad - owner: iuc - revisions: - - 57910d476be9 - tool_panel_section_label: RAD-seq -- name: stacks_assembleperead - owner: iuc - revisions: - - b08cd32d03ad - tool_panel_section_label: RAD-seq -- name: stacks_ustacks - owner: iuc - revisions: - - e5c97f09fe06 - tool_panel_section_label: RAD-seq -- name: stacks_denovomap - owner: iuc - revisions: - - 2b1dd7ab69f7 - tool_panel_section_label: RAD-seq -- name: stacks_genotypes - owner: iuc - revisions: - - 5af94af9ec8f - tool_panel_section_label: RAD-seq -- name: stacks_sstacks - owner: iuc - revisions: - - 95e37a28704b - tool_panel_section_label: RAD-seq diff --git a/usegalaxy.eu/regional_variation.yml b/usegalaxy.eu/regional_variation.yml deleted file mode 100644 index 68b338ce..00000000 --- a/usegalaxy.eu/regional_variation.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: Regional Variation -tools: -- name: indels_3way - owner: devteam -- name: draw_stacked_barplots - owner: devteam -- name: delete_overlapping_indels - owner: devteam -- name: compute_motifs_frequency - owner: devteam -- name: compute_motif_frequencies_for_all_motifs - owner: devteam -- name: categorize_elements_satisfying_criteria - owner: devteam -- name: featurecounter - owner: devteam diff --git a/usegalaxy.eu/regional_variation.yml.lock b/usegalaxy.eu/regional_variation.yml.lock deleted file mode 100644 index 9189ec45..00000000 --- a/usegalaxy.eu/regional_variation.yml.lock +++ /dev/null @@ -1,39 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: indels_3way - owner: devteam - revisions: - - 5ad24b81dd10 - tool_panel_section_label: Regional Variation -- name: draw_stacked_barplots - owner: devteam - revisions: - - e997b710e38a - tool_panel_section_label: Regional Variation -- name: delete_overlapping_indels - owner: devteam - revisions: - - f16000dc644b - tool_panel_section_label: Regional Variation -- name: compute_motifs_frequency - owner: devteam - revisions: - - 1f8ee7f9701b - tool_panel_section_label: Regional Variation -- name: compute_motif_frequencies_for_all_motifs - owner: devteam - revisions: - - 5319efa51514 - tool_panel_section_label: Regional Variation -- name: categorize_elements_satisfying_criteria - owner: devteam - revisions: - - 586c1f0e1515 - tool_panel_section_label: Regional Variation -- name: featurecounter - owner: devteam - revisions: - - ac6218e2b686 - tool_panel_section_label: Regional Variation diff --git a/usegalaxy.eu/rna_analysis.yml b/usegalaxy.eu/rna_analysis.yml deleted file mode 100644 index b362c90d..00000000 --- a/usegalaxy.eu/rna_analysis.yml +++ /dev/null @@ -1,240 +0,0 @@ -tool_panel_section_label: RNA Analysis -tools: -- name: cofold - owner: rnateam -- name: rnaz_cluster - owner: bgruening -- name: mea - owner: rnateam -- name: dr_disco - owner: erasmus-medical-center -- name: cmcv - owner: rnateam -- name: deseq2 - owner: iuc -- name: rnaz_randomize_aln - owner: bgruening -- name: rnaz_select_seqs - owner: bgruening -- name: rnaz_window - owner: bgruening -- name: rnaz_annotate - owner: bgruening -- name: egsea - owner: iuc -- name: dexseq - owner: iuc -- name: filter_transcripts_via_tracking - owner: devteam -- name: express - owner: devteam -- name: cuffmerge - owner: devteam -- name: cufflinks - owner: devteam -- name: cuffdiff - owner: devteam -- name: cuffcompare - owner: devteam -- name: crosscontamination_barcode_filter - owner: iuc -- name: deg_annotate - owner: iuc -- name: slamdunk - owner: iuc -- name: scpipe - owner: iuc -- name: featurecounts - owner: iuc -- name: limma_voom - owner: iuc -- name: edger - owner: iuc -- name: locarna_multiple - owner: rnateam -- name: cmv - owner: rnateam -- name: ribotaper - owner: rnateam -- name: pipmir - owner: rnateam -- name: nastiseq - owner: rnateam -- name: flaimapper - owner: yhoogstrate -- name: targetfinder - owner: rnateam -- name: aresite2 - owner: rnateam -- name: fuma - owner: yhoogstrate -- name: rnalien - owner: rnateam -- name: kallisto_quant - owner: iuc -- name: raceid_trajectory - owner: iuc -- name: raceid_clustering - owner: iuc -- name: raceid_inspecttrajectory - owner: iuc -- name: raceid_filtnormconf - owner: iuc -- name: raceid_inspectclusters - owner: iuc -- name: blockclust - owner: rnateam -- name: trinity_analyze_diff_expr - owner: iuc -- name: trinity_gene_to_trans_map - owner: iuc -- name: trinity_samples_qccheck - owner: iuc -- name: describe_samples - owner: iuc -- name: trinity_define_clusters_by_cutting_tree - owner: iuc -- name: trinity_run_de_analysis - owner: iuc -- name: trinity_filter_low_expr_transcripts - owner: iuc -- name: trinity_contig_exn50_statistic - owner: iuc -- name: trinity_abundance_estimates_to_matrix - owner: iuc -- name: trinity_align_and_estimate_abundance - owner: iuc -- name: trinity_super_transcripts - owner: iuc -- name: trinity - owner: iuc -- name: ruvseq - owner: iuc -- name: rseqc - owner: nilesh -- name: seurat - owner: iuc -- name: salmon - owner: bgruening -- name: heinz - owner: iuc -- name: migmap - owner: iuc -- name: stringtie - owner: iuc -- name: sshmm - owner: rnateam -- name: pizzly - owner: iuc -- name: rcas - owner: rnateam -- name: feelnc - owner: iuc -- name: graphprot_predict_profile - owner: rnateam -- name: rnacode - owner: rnateam -- name: intarna - owner: rnateam -- name: kallisto_pseudo - owner: iuc -- name: rnaz - owner: bgruening -- name: rnashapes - owner: rnateam -- name: htseq_count - owner: lparsons -- name: viennarna_rnafold - owner: rnateam -- name: idr - owner: iuc -- name: viennarna_rnacofold - owner: rnateam -- name: viennarna_rnaalifold - owner: rnateam -- name: segemehl - owner: rnateam -- name: masigpro - owner: iuc -- name: cuffnorm - owner: devteam -- name: cuffquant - owner: devteam -- name: cummerbund - owner: devteam -- name: transdecoder - owner: iuc -- name: sailfish - owner: bgruening -- name: viennarna_rnaeval - owner: rnateam -- name: viennarna_rnaplex - owner: rnateam -- name: viennarna_rna2dfold - owner: rnateam -- name: viennarna_rnapaln - owner: rnateam -- name: viennarna_rnaplot - owner: rnateam -- name: viennarna_rnasnoop - owner: rnateam -- name: viennarna_kinfold - owner: rnateam -- name: viennarna_rnaaliduplex - owner: rnateam -- name: viennarna_rnaduplex - owner: rnateam -- name: viennarna_rnadistance - owner: rnateam -- name: viennarna_rnadpdist - owner: rnateam -- name: viennarna_rnalfold - owner: rnateam -- name: viennarna_rnapkplex - owner: rnateam -- name: viennarna_rnaup - owner: rnateam -- name: viennarna_rnalalifold - owner: rnateam -- name: viennarna_rnainverse - owner: rnateam -- name: viennarna_rnaheat - owner: rnateam -- name: viennarna_rnasubopt - owner: rnateam -- name: infernal - owner: bgruening -- name: remurna - owner: rnateam -- name: rnasnp - owner: rnateam -- name: mlocarna - owner: rnateam -- name: paralyzer - owner: rnateam -- name: circexplorer - owner: bgruening -- name: rnacommender - owner: rnateam -- name: tophat_fusion_post - owner: devteam -- name: blockbuster - owner: rnateam -- name: kinwalker - owner: rnateam -- name: antarna - owner: rnateam -- name: rnabob - owner: rnateam -- name: structurefold - owner: tyty -- name: cummerbund_to_tabular - owner: devteam -- name: mirdeep2_mapper - owner: rnateam -- name: mirdeep2_quantifier - owner: rnateam -- name: mirdeep2 - owner: rnateam -- name: rsem - owner: jjohnson diff --git a/usegalaxy.eu/rna_analysis.yml.lock b/usegalaxy.eu/rna_analysis.yml.lock deleted file mode 100644 index 71f60674..00000000 --- a/usegalaxy.eu/rna_analysis.yml.lock +++ /dev/null @@ -1,604 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: cofold - owner: rnateam - revisions: - - 6fed0bc99753 - tool_panel_section_label: RNA Analysis -- name: rnaz_cluster - owner: bgruening - revisions: - - d21d8e70e802 - tool_panel_section_label: RNA Analysis -- name: mea - owner: rnateam - revisions: - - 9ebd60531aa6 - tool_panel_section_label: RNA Analysis -- name: dr_disco - owner: erasmus-medical-center - revisions: - - 3743fd602fa9 - tool_panel_section_label: RNA Analysis -- name: cmcv - owner: rnateam - revisions: - - 8405fa59c2b2 - tool_panel_section_label: RNA Analysis -- name: deseq2 - owner: iuc - revisions: - - a6fc9228e1a0 - tool_panel_section_label: RNA Analysis -- name: rnaz_randomize_aln - owner: bgruening - revisions: - - 5d006d19f70a - tool_panel_section_label: RNA Analysis -- name: rnaz_select_seqs - owner: bgruening - revisions: - - 273a961d332f - tool_panel_section_label: RNA Analysis -- name: rnaz_window - owner: bgruening - revisions: - - fdfe3dcf8fc4 - tool_panel_section_label: RNA Analysis -- name: rnaz_annotate - owner: bgruening - revisions: - - e123d5c6f489 - tool_panel_section_label: RNA Analysis -- name: egsea - owner: iuc - revisions: - - ba2111ae6eb4 - tool_panel_section_label: RNA Analysis -- name: dexseq - owner: iuc - revisions: - - 251393b72616 - - 278b189248cd - tool_panel_section_label: RNA Analysis -- name: filter_transcripts_via_tracking - owner: devteam - revisions: - - 45f89dcf0b4c - tool_panel_section_label: RNA Analysis -- name: express - owner: devteam - revisions: - - 7b0708761d05 - tool_panel_section_label: RNA Analysis -- name: cuffmerge - owner: devteam - revisions: - - cf747d1bd79a - tool_panel_section_label: RNA Analysis -- name: cufflinks - owner: devteam - revisions: - - e04dbae2abe0 - tool_panel_section_label: RNA Analysis -- name: cuffdiff - owner: devteam - revisions: - - d3ae7d9c2202 - tool_panel_section_label: RNA Analysis -- name: cuffcompare - owner: devteam - revisions: - - e66b9b5b8580 - tool_panel_section_label: RNA Analysis -- name: crosscontamination_barcode_filter - owner: iuc - revisions: - - 582b7bd4ae4c - tool_panel_section_label: RNA Analysis -- name: deg_annotate - owner: iuc - revisions: - - e98d4ab5b5bc - tool_panel_section_label: RNA Analysis -- name: slamdunk - owner: iuc - revisions: - - 24657d5edede - - 57bf9a0d49a5 - tool_panel_section_label: RNA Analysis -- name: scpipe - owner: iuc - revisions: - - 5c4bca9dd4a2 - tool_panel_section_label: RNA Analysis -- name: featurecounts - owner: iuc - revisions: - - af814359d244 - tool_panel_section_label: RNA Analysis -- name: limma_voom - owner: iuc - revisions: - - 41573afd6871 - tool_panel_section_label: RNA Analysis -- name: edger - owner: iuc - revisions: - - 4730985c816f - tool_panel_section_label: RNA Analysis -- name: locarna_multiple - owner: rnateam - revisions: - - 94b0468f0db8 - tool_panel_section_label: RNA Analysis -- name: cmv - owner: rnateam - revisions: - - 6e36667f1729 - tool_panel_section_label: RNA Analysis -- name: ribotaper - owner: rnateam - revisions: - - 9dda0cc9ff98 - tool_panel_section_label: RNA Analysis -- name: pipmir - owner: rnateam - revisions: - - 16209195224c - tool_panel_section_label: RNA Analysis -- name: nastiseq - owner: rnateam - revisions: - - 0a0bba8e1823 - tool_panel_section_label: RNA Analysis -- name: flaimapper - owner: yhoogstrate - revisions: - - 0addbdbc1344 - tool_panel_section_label: RNA Analysis -- name: targetfinder - owner: rnateam - revisions: - - 773fdd1a02ea - tool_panel_section_label: RNA Analysis -- name: aresite2 - owner: rnateam - revisions: - - a3ce813ed604 - tool_panel_section_label: RNA Analysis -- name: fuma - owner: yhoogstrate - revisions: - - b21145d59d9c - tool_panel_section_label: RNA Analysis -- name: rnalien - owner: rnateam - 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a/usegalaxy.eu/sam_tools.yml.lock b/usegalaxy.eu/sam_tools.yml.lock deleted file mode 100644 index 7e921f78..00000000 --- a/usegalaxy.eu/sam_tools.yml.lock +++ /dev/null @@ -1,150 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: pileup_parser - owner: devteam - revisions: - - 85bedbea8a12 - tool_panel_section_label: SAM Tools -- name: sam2interval - owner: devteam - revisions: - - 8c737b8ddc45 - tool_panel_section_label: SAM Tools -- name: sam_bitwise_flag_filter - owner: devteam - revisions: - - 0b2424a404d9 - tool_panel_section_label: SAM Tools -- name: sam_merge - owner: devteam - revisions: - - 1977f1637890 - tool_panel_section_label: SAM Tools -- name: sam_pileup - owner: devteam - revisions: - - 890d97772e2a - tool_panel_section_label: SAM Tools -- name: sam_to_bam - owner: devteam - revisions: - - f7a0d41036c7 - tool_panel_section_label: SAM Tools -- name: samtools_flagstat - owner: devteam - 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bgruening -- name: sklearn_searchcv - owner: bgruening -- name: sklearn_sample_generator - owner: bgruening -- name: sklearn_svm_classifier - owner: bgruening -- name: nn_classifier - owner: bgruening -- name: svm_classifier - owner: bgruening -- name: anova - owner: lecorguille -- name: multivariate - owner: ethevenot -- name: univariate - owner: ethevenot -- name: iwtomics_plotwithscale - owner: iuc -- name: iwtomics_testandplot - owner: iuc -- name: iwtomics_loadandplot - owner: iuc -- name: seq_composition - owner: peterjc -- name: biosigner - owner: ethevenot -- name: transformation - owner: ethevenot -- name: heatmap - owner: ethevenot -- name: numeric_clustering - owner: bgruening diff --git a/usegalaxy.eu/statistics.yml.lock b/usegalaxy.eu/statistics.yml.lock deleted file mode 100644 index 1c0a21ee..00000000 --- a/usegalaxy.eu/statistics.yml.lock +++ /dev/null @@ -1,214 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true 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a/usegalaxy.eu/text_manipulation.yml b/usegalaxy.eu/text_manipulation.yml deleted file mode 100644 index 719f65f2..00000000 --- a/usegalaxy.eu/text_manipulation.yml +++ /dev/null @@ -1,56 +0,0 @@ -tool_panel_section_label: Text Manipulation -tools: -- name: dna_filtering - owner: devteam -- name: join_files_on_column_fuzzy - owner: bgruening -- name: column_maker - owner: devteam -- name: replace_chromosome_names - owner: earlhaminst -- name: text_processing - owner: bgruening -- name: jq - owner: iuc -- name: reshape2_cast - owner: iuc -- name: reshape2_melt - owner: iuc -- name: prinseq - owner: iuc -- name: gff3_rebase - owner: iuc -- name: column_remove_by_header - owner: iuc -- name: column_order_header_sort - owner: iuc -- name: replace_column_by_key_value_file - owner: bgruening -- name: add_input_name_as_column - owner: mvdbeek -- name: split_file_on_column - owner: bgruening -- name: coverage - owner: devteam -- name: regex_replace - owner: kellrott -- name: tables_arithmetic_operations - owner: devteam -- name: merge - owner: devteam -- name: intersect - owner: devteam -- name: flanking_features - owner: devteam -- name: join - owner: devteam -- name: get_flanks - owner: devteam -- name: subtract_query - owner: devteam -- name: merge_cols - owner: devteam -- name: unique - owner: bgruening -- name: add_value - owner: devteam diff --git a/usegalaxy.eu/text_manipulation.yml.lock b/usegalaxy.eu/text_manipulation.yml.lock deleted file mode 100644 index 8f4738d8..00000000 --- a/usegalaxy.eu/text_manipulation.yml.lock +++ /dev/null @@ -1,143 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: dna_filtering - owner: devteam - revisions: - - 549d2cb4c6f2 - tool_panel_section_label: Text Manipulation -- name: join_files_on_column_fuzzy - owner: bgruening - revisions: - - 22ec3c1a20cd - tool_panel_section_label: Text Manipulation -- name: column_maker - owner: devteam - revisions: - - 464b9305180e - tool_panel_section_label: Text Manipulation -- name: replace_chromosome_names - owner: earlhaminst - revisions: - - 6c0373cc070f - tool_panel_section_label: Text Manipulation -- name: text_processing - owner: bgruening - revisions: - - 20344ce0c811 - - 616efa22d193 - - 74a8bef53a00 - - a6f147a050a2 - - e39fceb6ab85 - tool_panel_section_label: Text Manipulation -- name: jq - owner: iuc - revisions: - - 5ff75eb1a893 - tool_panel_section_label: Text Manipulation -- name: reshape2_cast - owner: iuc - revisions: - - d3b66a3a08ca - tool_panel_section_label: Text Manipulation -- name: reshape2_melt - owner: iuc - revisions: - - 317ed0ee8bf2 - tool_panel_section_label: Text Manipulation -- name: prinseq - owner: iuc - revisions: - - 02befcb391f5 - tool_panel_section_label: Text Manipulation -- name: gff3_rebase - owner: iuc - revisions: - - 238981ed43b7 - tool_panel_section_label: Text Manipulation -- name: column_remove_by_header - owner: iuc - revisions: - - 372967836e98 - tool_panel_section_label: Text Manipulation -- name: column_order_header_sort - owner: iuc - revisions: - - 6ae9724caf4d - tool_panel_section_label: Text Manipulation -- name: replace_column_by_key_value_file - owner: bgruening - revisions: - - cc18bac5afdb - tool_panel_section_label: Text Manipulation -- name: add_input_name_as_column - owner: mvdbeek - revisions: - - b31219f26a8f - tool_panel_section_label: Text Manipulation -- name: split_file_on_column - owner: bgruening - revisions: - - 90b52d8d6f2c - tool_panel_section_label: Text Manipulation -- name: coverage - owner: devteam - revisions: - - bc9c66c1e9c9 - tool_panel_section_label: Text Manipulation -- name: regex_replace - owner: kellrott - revisions: - - 9a77d5fca67c - tool_panel_section_label: Text Manipulation -- name: tables_arithmetic_operations - owner: devteam - revisions: - - 2e9f3b6ebfbc - tool_panel_section_label: Text Manipulation -- name: merge - owner: devteam - revisions: - - 0926c81f382c - tool_panel_section_label: Text Manipulation -- name: intersect - owner: devteam - revisions: - - 8ddabc73af92 - tool_panel_section_label: Text Manipulation -- name: flanking_features - owner: devteam - revisions: - - 8307665c4b6c - tool_panel_section_label: Text Manipulation -- name: join - owner: devteam - revisions: - - ffbd1de29c28 - tool_panel_section_label: Text Manipulation -- name: get_flanks - owner: devteam - revisions: - - 4cd116158aef - tool_panel_section_label: Text Manipulation -- name: subtract_query - owner: devteam - revisions: - - 960d5d114184 - tool_panel_section_label: Text Manipulation -- name: merge_cols - owner: devteam - revisions: - - f2aac0c5c60d - tool_panel_section_label: Text Manipulation -- name: unique - owner: bgruening - revisions: - - 7ce75adb93be - tool_panel_section_label: Text Manipulation -- name: add_value - owner: devteam - revisions: - - 745871c0b055 - tool_panel_section_label: Text Manipulation diff --git a/usegalaxy.eu/variant_calling.yml b/usegalaxy.eu/variant_calling.yml deleted file mode 100644 index ea82ad0d..00000000 --- a/usegalaxy.eu/variant_calling.yml +++ /dev/null @@ -1,112 +0,0 @@ -tool_panel_section_label: Variant Calling -tools: -- name: snippy - owner: iuc -- name: bcftools_consensus - owner: iuc -- name: varscan_somatic - owner: iuc -- name: vcffilter - owner: devteam -- name: varscan_mpileup - owner: iuc -- name: varscan_copynumber - owner: iuc -- name: bcftools_cnv - owner: iuc -- name: bcftools_csq - owner: iuc -- name: snpsift - owner: iuc -- name: bcftools_norm - owner: iuc -- name: vcfselectsamples - owner: devteam -- name: snpeff - owner: iuc -- name: vcfannotategenotypes - owner: devteam -- name: vcfflatten - owner: devteam -- name: vcfcommonsamples - owner: devteam -- name: vcfannotate - owner: devteam -- name: vcfvcfintersect - owner: devteam -- name: vcfbreakcreatemulti - owner: devteam -- name: vcfallelicprimitives - owner: devteam -- name: vcfgeno2haplo - owner: devteam -- name: vcffixup - owner: devteam -- name: vcfgenotypes - owner: devteam -- name: vcfbedintersect - owner: devteam -- name: vcfrandomsample - owner: devteam -- name: vcfhethom - owner: devteam -- name: vcfsort - owner: devteam -- name: vcfprimers - owner: devteam -- name: vcfcombine - owner: devteam -- name: vcfleftalign - owner: devteam -- name: vcf2tsv - owner: devteam -- name: vcfaddinfo - owner: devteam -- name: vcfcheck - owner: devteam -- name: varscan_version_2 - owner: devteam -- name: nanopolish_variants - owner: bgruening -- name: bcftools - owner: iuc -- name: freebayes - owner: devteam -- name: vcfdistance - owner: iuc -- name: naive_variant_caller - owner: blankenberg -- name: ococo - owner: iuc -- name: bcftools_call - owner: iuc -- name: snpsift_genesets - owner: iuc -- name: snpsift_dbnsfp - owner: iuc -- name: snpsift_dbnsfp_generic - owner: iuc -- name: vcfdistance - owner: devteam -- name: allele_counts - owner: nick -- name: vcftools_merge - owner: devteam -- name: vcftools_isec - owner: devteam -- name: vt_variant_tools - owner: iuc -- name: bamleftalign - owner: devteam -- name: snpeff_cds_report - owner: jjohnson -- name: snpeff_to_peptides - owner: jjohnson -- name: vcftools_compare - owner: devteam -- name: vcftools_annotate - owner: devteam -- name: vcftools_slice - owner: devteam -- name: vcftools_subset - owner: devteam diff --git a/usegalaxy.eu/variant_calling.yml.lock b/usegalaxy.eu/variant_calling.yml.lock deleted file mode 100644 index 8eadff43..00000000 --- a/usegalaxy.eu/variant_calling.yml.lock +++ /dev/null @@ -1,287 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: snippy - owner: iuc - revisions: - - 82f2b6f20fa2 - - c9a8ef2aa380 - tool_panel_section_label: Variant Calling -- name: bcftools_consensus - owner: iuc - revisions: - - 1829900b5dcd - tool_panel_section_label: Variant Calling -- name: varscan_somatic - owner: iuc - revisions: - - 2657ab48e16a - tool_panel_section_label: Variant Calling -- name: vcffilter - owner: devteam - revisions: - - de885f4afb7f - tool_panel_section_label: Variant Calling -- name: varscan_mpileup - owner: iuc - revisions: - - db517af07461 - tool_panel_section_label: Variant Calling -- name: varscan_copynumber - owner: iuc - revisions: - - 807448b77107 - tool_panel_section_label: Variant Calling -- name: bcftools_cnv - owner: iuc - revisions: - - 8408bffd5616 - tool_panel_section_label: Variant Calling -- name: bcftools_csq - owner: iuc - revisions: - - 7cbf3c66d4ad - tool_panel_section_label: Variant Calling -- name: snpsift - owner: iuc - revisions: - - 09d6806c609e - - 2b3e65a4252f - - b04635ebfab0 - tool_panel_section_label: Variant Calling -- name: bcftools_norm - owner: iuc - revisions: - - a404f786a94c - tool_panel_section_label: Variant Calling -- name: vcfselectsamples - owner: devteam - revisions: - - 958b6484a7f1 - tool_panel_section_label: Variant Calling -- name: snpeff - owner: iuc - revisions: - - 85ca751407c3 - - 8f92c2b26e6d - - c9ecd2a96ecf - - dd3622f501f3 - - e8adfc4c0a6b - tool_panel_section_label: Variant Calling -- name: vcfannotategenotypes - owner: devteam - revisions: - - 70bc6ced57f7 - tool_panel_section_label: Variant Calling -- name: vcfflatten - owner: devteam - revisions: - - b24e368ae7b1 - tool_panel_section_label: Variant Calling -- name: vcfcommonsamples - owner: devteam - revisions: - - 254f285dbaaa - tool_panel_section_label: Variant Calling -- name: vcfannotate - owner: devteam - revisions: - - 6faa2c4c71d2 - tool_panel_section_label: Variant Calling -- name: vcfvcfintersect - owner: devteam - revisions: - - 6f6bf10618d7 - tool_panel_section_label: Variant Calling -- name: vcfbreakcreatemulti - owner: devteam - revisions: - - 690b1d846263 - tool_panel_section_label: Variant Calling -- name: vcfallelicprimitives - owner: devteam - revisions: - - a8a4f94aa321 - tool_panel_section_label: Variant Calling -- name: vcfgeno2haplo - owner: devteam - revisions: - - b890055e07bd - tool_panel_section_label: Variant Calling -- name: vcffixup - owner: devteam - revisions: - - fc5a64fdd5b2 - tool_panel_section_label: Variant Calling -- name: vcfgenotypes - owner: devteam - revisions: - - f5653ed90dfd - tool_panel_section_label: Variant Calling -- name: vcfbedintersect - owner: devteam - revisions: - - 9edfe5145ba8 - tool_panel_section_label: Variant Calling -- name: vcfrandomsample - owner: devteam - revisions: - - 12b570dd0bc5 - tool_panel_section_label: Variant Calling -- name: vcfhethom - owner: devteam - revisions: - - b07ef36cf7e6 - tool_panel_section_label: Variant Calling -- name: vcfsort - owner: devteam - revisions: - - 5b7120c66efc - tool_panel_section_label: Variant Calling -- name: vcfprimers - owner: devteam - revisions: - - d226a7327946 - tool_panel_section_label: Variant Calling -- name: vcfcombine - owner: devteam - revisions: - - 53edb91ed051 - tool_panel_section_label: Variant Calling -- name: vcfleftalign - owner: devteam - revisions: - - d2406f98a782 - tool_panel_section_label: Variant Calling -- name: vcf2tsv - owner: devteam - revisions: - - e92b3c0f9224 - tool_panel_section_label: Variant Calling -- name: vcfaddinfo - owner: devteam - revisions: - - afc0ba768690 - tool_panel_section_label: Variant Calling -- name: vcfcheck - owner: devteam - revisions: - - 5e850c85ba32 - tool_panel_section_label: Variant Calling -- name: varscan_version_2 - owner: devteam - revisions: - - bc1e0cd41241 - tool_panel_section_label: Variant Calling -- name: nanopolish_variants - owner: bgruening - revisions: - - 1ebed8b65752 - tool_panel_section_label: Variant Calling -- name: bcftools - owner: iuc - revisions: - - bdd0cb7fbedf - - e5e78d1e09a6 - tool_panel_section_label: Variant Calling -- name: freebayes - owner: devteam - revisions: - - 156b60c1530f - tool_panel_section_label: Variant Calling -- name: vcfdistance - owner: iuc - revisions: - - c506b8275b1a - tool_panel_section_label: Variant Calling -- name: naive_variant_caller - owner: blankenberg - revisions: - - aff38ea879f1 - tool_panel_section_label: Variant Calling -- name: ococo - owner: iuc - revisions: - - 03cabb6711c5 - tool_panel_section_label: Variant Calling -- name: bcftools_call - owner: iuc - revisions: - - b03984136ce4 - tool_panel_section_label: Variant Calling -- name: snpsift_genesets - owner: iuc - revisions: - - d12a810c837e - tool_panel_section_label: Variant Calling -- name: snpsift_dbnsfp - owner: iuc - revisions: - - 4e21e4f2bc48 - tool_panel_section_label: Variant Calling -- name: snpsift_dbnsfp_generic - owner: iuc - revisions: - - a7cbaf3beadd - tool_panel_section_label: Variant Calling -- name: vcfdistance - owner: devteam - revisions: - - 6e0fc18309f4 - tool_panel_section_label: Variant Calling -- name: allele_counts - owner: nick - revisions: - - 411adeff1eec - tool_panel_section_label: Variant Calling -- name: vcftools_merge - owner: devteam - revisions: - - 71e19ddf52f5 - tool_panel_section_label: Variant Calling -- name: vcftools_isec - owner: devteam - revisions: - - aa232e38338f - tool_panel_section_label: Variant Calling -- name: vt_variant_tools - owner: iuc - revisions: - - 6e073fc99d9c - tool_panel_section_label: Variant Calling -- name: bamleftalign - owner: devteam - revisions: - - e65540a91b87 - tool_panel_section_label: Variant Calling -- name: snpeff_cds_report - owner: jjohnson - revisions: - - fbb6510186df - tool_panel_section_label: Variant Calling -- name: snpeff_to_peptides - owner: jjohnson - revisions: - - 80eff5812b2a - tool_panel_section_label: Variant Calling -- name: vcftools_compare - owner: devteam - revisions: - - ad50c257e758 - tool_panel_section_label: Variant Calling -- name: vcftools_annotate - owner: devteam - revisions: - - 57a6550df582 - tool_panel_section_label: Variant Calling -- name: vcftools_slice - owner: devteam - revisions: - - 1363e5d4a8b8 - tool_panel_section_label: Variant Calling -- name: vcftools_subset - owner: devteam - revisions: - - 23436d1d0fa1 - tool_panel_section_label: Variant Calling diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml deleted file mode 100644 index 9bdd5820..00000000 --- a/usegalaxy.org.au/annotation.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: Annotation -tools: -- name: prokka - owner: crs4 -- name: abricate - owner: iuc -- name: infernal - owner: bgruening -- name: barrnap - owner: iuc -- name: snpeff - owner: iuc -- name: snptools - owner: rreumerman -- name: snpsift - owner: iuc diff --git a/usegalaxy.org.au/annotation.yml.lock b/usegalaxy.org.au/annotation.yml.lock deleted file mode 100644 index 3382f1fc..00000000 --- a/usegalaxy.org.au/annotation.yml.lock +++ /dev/null @@ -1,39 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: prokka - owner: crs4 - revisions: - - eaee459f3d69 - tool_panel_section_label: Annotation -- name: abricate - owner: iuc - revisions: - - 6e9aea89e388 - tool_panel_section_label: Annotation -- name: infernal - owner: bgruening - revisions: - - 477d829d3250 - tool_panel_section_label: Annotation -- name: barrnap - owner: iuc - revisions: - - 8fd427007e93 - tool_panel_section_label: Annotation -- name: snpeff - owner: iuc - revisions: - - 68693743661e - tool_panel_section_label: Annotation -- name: snptools - owner: rreumerman - revisions: - - 8de0ffc2166f - tool_panel_section_label: Annotation -- name: snpsift - owner: iuc - revisions: - - 09d6806c609e - tool_panel_section_label: Annotation diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml deleted file mode 100644 index 69778911..00000000 --- a/usegalaxy.org.au/assembly.yml +++ /dev/null @@ -1,18 +0,0 @@ -tool_panel_section_label: Assembly -tools: -- name: velvetoptimiser - owner: simon-gladman -- name: shovill - owner: iuc -- name: quast - owner: iuc -- name: unicycler - owner: iuc -- name: spades - owner: nml -- name: pilon - owner: iuc -- name: kmergenie - owner: rchikhi -- name: busco - owner: iuc diff --git a/usegalaxy.org.au/assembly.yml.lock b/usegalaxy.org.au/assembly.yml.lock deleted file mode 100644 index b8444fb5..00000000 --- a/usegalaxy.org.au/assembly.yml.lock +++ /dev/null @@ -1,45 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: velvetoptimiser - owner: simon-gladman - revisions: - - 37d88f41c810 - - d81360ea69d8 - tool_panel_section_label: Assembly -- name: shovill - owner: iuc - revisions: - - 57d5928f456e - tool_panel_section_label: Assembly -- name: quast - owner: iuc - revisions: - - 6fcbee531de6 - tool_panel_section_label: Assembly -- name: unicycler - owner: iuc - revisions: - - e92675014ac9 - tool_panel_section_label: Assembly -- name: spades - owner: nml - revisions: - - 9006e5836729 - tool_panel_section_label: Assembly -- name: pilon - owner: iuc - revisions: - - 11e5408fd238 - tool_panel_section_label: Assembly -- name: kmergenie - owner: rchikhi - revisions: - - 2d4b0398cbaf - tool_panel_section_label: Assembly -- name: busco - owner: iuc - revisions: - - 382a4c19007f - tool_panel_section_label: Assembly diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml deleted file mode 100644 index f583ba4c..00000000 --- a/usegalaxy.org.au/bacterial_typing.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Bacterial Typing -tools: -- name: mlst - owner: iuc diff --git a/usegalaxy.org.au/bacterial_typing.yml.lock b/usegalaxy.org.au/bacterial_typing.yml.lock deleted file mode 100644 index 326cfe4a..00000000 --- a/usegalaxy.org.au/bacterial_typing.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: mlst - owner: iuc - revisions: - - 8e8dc9a1e3e5 - tool_panel_section_label: Bacterial Typing diff --git a/usegalaxy.org.au/bed_tools.yml b/usegalaxy.org.au/bed_tools.yml deleted file mode 100644 index 2e0eca51..00000000 --- a/usegalaxy.org.au/bed_tools.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: BED tools -tools: -- name: bedtools - owner: iuc diff --git a/usegalaxy.org.au/bed_tools.yml.lock b/usegalaxy.org.au/bed_tools.yml.lock deleted file mode 100644 index aab99e26..00000000 --- a/usegalaxy.org.au/bed_tools.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: bedtools - owner: iuc - revisions: - - a8eabd2838f6 - tool_panel_section_label: BED tools diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml deleted file mode 100644 index ad107664..00000000 --- a/usegalaxy.org.au/blast.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Blast + -tools: -- name: ncbi_blast_plus - owner: devteam diff --git a/usegalaxy.org.au/blast.yml.lock b/usegalaxy.org.au/blast.yml.lock deleted file mode 100644 index bb692707..00000000 --- a/usegalaxy.org.au/blast.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: ncbi_blast_plus - owner: devteam - revisions: - - 6f386c5dc4fb - tool_panel_section_label: Blast + diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml deleted file mode 100644 index 0aae6f4a..00000000 --- a/usegalaxy.org.au/collection_operations.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Collection Operations -tools: -- name: collapse_collections - owner: nml -- name: bundle_collections - owner: nml -- name: collection_column_join - owner: iuc diff --git a/usegalaxy.org.au/collection_operations.yml.lock b/usegalaxy.org.au/collection_operations.yml.lock deleted file mode 100644 index e1633528..00000000 --- a/usegalaxy.org.au/collection_operations.yml.lock +++ /dev/null @@ -1,19 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: collapse_collections - owner: nml - revisions: - - 25136a2b0cfe - tool_panel_section_label: Collection Operations -- name: bundle_collections - owner: nml - revisions: - - cd6da887a5f4 - tool_panel_section_label: Collection Operations -- name: collection_column_join - owner: iuc - revisions: - - dfde09461b1e - tool_panel_section_label: Collection Operations diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml deleted file mode 100644 index 0287943d..00000000 --- a/usegalaxy.org.au/convert_formats.yml +++ /dev/null @@ -1,18 +0,0 @@ -tool_panel_section_label: Convert Formats -tools: -- name: biom_convert - owner: iuc -- name: biom_add_metadata - owner: iuc -- name: fastq_to_fasta - owner: devteam -- name: fastq_to_tabular - owner: devteam -- name: fasta_to_tabular - owner: devteam -- name: tabular_to_fastq - owner: devteam -- name: tabular_to_fasta - owner: devteam -- name: fml_gff3togtf - owner: vipints diff --git a/usegalaxy.org.au/convert_formats.yml.lock b/usegalaxy.org.au/convert_formats.yml.lock deleted file mode 100644 index 185f4d4d..00000000 --- a/usegalaxy.org.au/convert_formats.yml.lock +++ /dev/null @@ -1,44 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: biom_convert - owner: iuc - revisions: - - 501c21cce614 - tool_panel_section_label: Convert Formats -- name: biom_add_metadata - owner: iuc - revisions: - - 367b1ed91207 - tool_panel_section_label: Convert Formats -- name: fastq_to_fasta - owner: devteam - revisions: - - 186b8d913e6c - tool_panel_section_label: Convert Formats -- name: fastq_to_tabular - owner: devteam - revisions: - - ccf4e1d1fcbe - tool_panel_section_label: Convert Formats -- name: fasta_to_tabular - owner: devteam - revisions: - - 7e801ab2b70e - tool_panel_section_label: Convert Formats -- name: tabular_to_fastq - owner: devteam - revisions: - - b8cdc0507586 - tool_panel_section_label: Convert Formats -- name: tabular_to_fasta - owner: devteam - revisions: - - 0b4e36026794 - tool_panel_section_label: Convert Formats -- name: fml_gff3togtf - owner: vipints - revisions: - - 5c6f33e20fcc - tool_panel_section_label: Convert Formats diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml deleted file mode 100644 index 1bcba07f..00000000 --- a/usegalaxy.org.au/deeptools.yml +++ /dev/null @@ -1,36 +0,0 @@ -tool_panel_section_label: DeepTools -tools: -- name: deeptools_plot_fingerprint - owner: bgruening -- name: deeptools_bam_compare - owner: bgruening -- name: deeptools_plot_coverage - owner: bgruening -- name: deeptools_correct_gc_bias - owner: bgruening -- name: deeptools_bigwig_compare - owner: bgruening -- name: deeptools_bam_coverage - owner: bgruening -- name: deeptools_multi_bigwig_summary - owner: bgruening -- name: deeptools_compute_gc_bias - owner: bgruening -- name: deeptools_multi_bam_summary - owner: bgruening -- name: deeptools_plot_correlation - owner: bgruening -- name: deeptools_bam_pe_fragmentsize - owner: bgruening -- name: deeptools_compute_matrix - owner: bgruening -- name: deeptools_plot_pca - owner: bgruening -- name: deeptools_plot_enrichment - owner: bgruening -- name: deeptools_plot_heatmap - owner: bgruening -- name: deeptools_plot_profile - owner: bgruening -- name: deeptools_compute_matrix_operations - owner: bgruening diff --git a/usegalaxy.org.au/deeptools.yml.lock b/usegalaxy.org.au/deeptools.yml.lock deleted file mode 100644 index 51714dd4..00000000 --- a/usegalaxy.org.au/deeptools.yml.lock +++ /dev/null @@ -1,89 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: deeptools_plot_fingerprint - owner: bgruening - revisions: - - f8fc4e5aff9d - tool_panel_section_label: DeepTools -- name: deeptools_bam_compare - owner: bgruening - revisions: - - a1ca9bccc7f2 - tool_panel_section_label: DeepTools -- name: deeptools_plot_coverage - owner: bgruening - revisions: - - 7e361d147872 - tool_panel_section_label: DeepTools -- name: deeptools_correct_gc_bias - owner: bgruening - revisions: - - a02cfa31e9cb - tool_panel_section_label: DeepTools -- name: deeptools_bigwig_compare - owner: bgruening - revisions: - - bfff7454b59a - tool_panel_section_label: DeepTools -- name: deeptools_bam_coverage - owner: bgruening - revisions: - - 5d11599b8a7d - tool_panel_section_label: DeepTools -- name: deeptools_multi_bigwig_summary - owner: bgruening - revisions: - - db940c262830 - tool_panel_section_label: DeepTools -- name: deeptools_compute_gc_bias - owner: bgruening - revisions: - - 29fcfd36e90a - tool_panel_section_label: DeepTools -- name: deeptools_multi_bam_summary - owner: bgruening - revisions: - - 2d466b530754 - tool_panel_section_label: DeepTools -- name: deeptools_plot_correlation - owner: bgruening - revisions: - - f264afa9fa6f - tool_panel_section_label: DeepTools -- name: deeptools_bam_pe_fragmentsize - owner: bgruening - revisions: - - 81b1e3e1fc6c - tool_panel_section_label: DeepTools -- name: deeptools_compute_matrix - owner: bgruening - revisions: - - fd1275e01605 - tool_panel_section_label: DeepTools -- name: deeptools_plot_pca - owner: bgruening - revisions: - - 38e3f226248b - tool_panel_section_label: DeepTools -- name: deeptools_plot_enrichment - owner: bgruening - revisions: - - 94ca68515826 - tool_panel_section_label: DeepTools -- name: deeptools_plot_heatmap - owner: bgruening - revisions: - - 512155688d98 - tool_panel_section_label: DeepTools -- name: deeptools_plot_profile - owner: bgruening - revisions: - - aac8444d6681 - tool_panel_section_label: DeepTools -- name: deeptools_compute_matrix_operations - owner: bgruening - revisions: - - 72bfafe3330b - tool_panel_section_label: DeepTools diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml deleted file mode 100644 index a6f95ed2..00000000 --- a/usegalaxy.org.au/emboss.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: EMBOSS -tools: -- name: emboss_5 - owner: devteam diff --git a/usegalaxy.org.au/emboss.yml.lock b/usegalaxy.org.au/emboss.yml.lock deleted file mode 100644 index e0909301..00000000 --- a/usegalaxy.org.au/emboss.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: emboss_5 - owner: devteam - revisions: - - 1b6538ec8b56 - tool_panel_section_label: EMBOSS diff --git a/usegalaxy.org.au/fasta_manipulation.yml b/usegalaxy.org.au/fasta_manipulation.yml deleted file mode 100644 index 9e198f16..00000000 --- a/usegalaxy.org.au/fasta_manipulation.yml +++ /dev/null @@ -1,46 +0,0 @@ -tool_panel_section_label: FASTA manipulation -tools: -- name: seq_select_by_id - owner: peterjc -- name: fasta_concatenate_by_species - owner: devteam -- name: fasta_filter_by_length - owner: devteam -- name: clustalw - owner: devteam -- name: fasta_compute_length - owner: devteam -- name: split_paired_reads - owner: devteam -- name: fasta_stats - owner: simon-gladman -- name: fasta_extract - owner: simon-gladman -- name: fasta_nucleotide_changer - owner: devteam -- name: fastx_trimmer - owner: devteam -- name: fastq_quality_converter - owner: devteam -- name: fastx_nucleotides_distribution - owner: devteam -- name: fastq_quality_filter - owner: devteam -- name: fastx_renamer - owner: devteam -- name: fastx_collapser - owner: devteam -- name: fastx_clipper - owner: devteam -- name: fastx_quality_statistics - owner: devteam -- name: fasta_formatter - owner: devteam -- name: fastx_artifacts_filter - owner: devteam -- name: fastx_reverse_complement - owner: devteam -- name: fastx_barcode_splitter - owner: devteam -- name: fasta_clipping_histogram - owner: devteam diff --git a/usegalaxy.org.au/fasta_manipulation.yml.lock b/usegalaxy.org.au/fasta_manipulation.yml.lock deleted file mode 100644 index 79f36726..00000000 --- a/usegalaxy.org.au/fasta_manipulation.yml.lock +++ /dev/null @@ -1,114 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: seq_select_by_id - owner: peterjc - revisions: - - 8e1a90917fa7 - tool_panel_section_label: FASTA manipulation -- name: fasta_concatenate_by_species - owner: devteam - revisions: - - 717aee069681 - tool_panel_section_label: FASTA manipulation -- name: fasta_filter_by_length - owner: devteam - revisions: - - 2fd6033d0e9c - tool_panel_section_label: FASTA manipulation -- name: clustalw - owner: devteam - revisions: - - d6694932c5e0 - tool_panel_section_label: FASTA manipulation -- name: fasta_compute_length - owner: devteam - revisions: - - de2db1bdfbf8 - tool_panel_section_label: FASTA manipulation -- name: split_paired_reads - owner: devteam - revisions: - - 36163bff76cc - tool_panel_section_label: FASTA manipulation -- name: fasta_stats - owner: simon-gladman - revisions: - - 20ca2574216a - tool_panel_section_label: FASTA manipulation -- name: fasta_extract - owner: simon-gladman - revisions: - - 5dfc014a8b3a - tool_panel_section_label: FASTA manipulation -- name: fasta_nucleotide_changer - owner: devteam - revisions: - - f81d4362b6c1 - tool_panel_section_label: FASTA manipulation -- name: fastx_trimmer - owner: devteam - revisions: - - 377ac2829eac - tool_panel_section_label: FASTA manipulation -- name: fastq_quality_converter - owner: devteam - revisions: - - 74db4cffab1f - tool_panel_section_label: FASTA manipulation -- name: fastx_nucleotides_distribution - owner: devteam - revisions: - - 18a51655db17 - tool_panel_section_label: FASTA manipulation -- name: fastq_quality_filter - owner: devteam - revisions: - - e41385662e5e - tool_panel_section_label: FASTA manipulation -- name: fastx_renamer - owner: devteam - revisions: - - 02f8a17a4ebd - tool_panel_section_label: FASTA manipulation -- name: fastx_collapser - owner: devteam - revisions: - - 421f0af4ee95 - tool_panel_section_label: FASTA manipulation -- name: fastx_clipper - owner: devteam - revisions: - - bdf1ce174e39 - tool_panel_section_label: FASTA manipulation -- name: fastx_quality_statistics - owner: devteam - revisions: - - 7306ec78632a - tool_panel_section_label: FASTA manipulation -- name: fasta_formatter - owner: devteam - revisions: - - 9457a20156db - tool_panel_section_label: FASTA manipulation -- name: fastx_artifacts_filter - owner: devteam - revisions: - - 09070cacefd8 - tool_panel_section_label: FASTA manipulation -- name: fastx_reverse_complement - owner: devteam - revisions: - - e246088b6e34 - tool_panel_section_label: FASTA manipulation -- name: fastx_barcode_splitter - owner: devteam - revisions: - - 8abdedf55101 - tool_panel_section_label: FASTA manipulation -- name: fasta_clipping_histogram - owner: devteam - revisions: - - f666895cbebd - tool_panel_section_label: FASTA manipulation diff --git a/usegalaxy.org.au/gatk_tools.yml b/usegalaxy.org.au/gatk_tools.yml deleted file mode 100644 index 1a5907fd..00000000 --- a/usegalaxy.org.au/gatk_tools.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: GATK Tools -tools: -- name: gatk2 - owner: iuc diff --git a/usegalaxy.org.au/gatk_tools.yml.lock b/usegalaxy.org.au/gatk_tools.yml.lock deleted file mode 100644 index 14186112..00000000 --- a/usegalaxy.org.au/gatk_tools.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: gatk2 - owner: iuc - revisions: - - 84584664264c - tool_panel_section_label: GATK Tools diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml deleted file mode 100644 index 05d88921..00000000 --- a/usegalaxy.org.au/gemini_tools.yml +++ /dev/null @@ -1,48 +0,0 @@ -tool_panel_section_label: Gemini Tools -tools: -- name: gemini_db_info - owner: iuc -- name: gemini_windower - owner: iuc -- name: gemini_burden - owner: iuc -- name: gemini_gene_wise - owner: iuc -- name: gemini_stats - owner: iuc -- name: gemini_mendel_errors - owner: iuc -- name: gemini_amend - owner: iuc -- name: gemini_pathways - owner: iuc -- name: gemini_dump - owner: iuc -- name: gemini_region - owner: iuc -- name: gemini_actionable_mutations - owner: iuc -- name: gemini_lof_sieve - owner: iuc -- name: gemini_query - owner: iuc -- name: gemini_fusions - owner: iuc -- name: gemini_load - owner: iuc -- name: gemini_de_novo - owner: iuc -- name: gemini_annotate - owner: iuc -- name: gemini_recessive_and_dominant - owner: iuc -- name: gemini_roh - owner: iuc -- name: gemini_set_somatic - owner: iuc -- name: gemini_qc - owner: iuc -- name: gemini_comp_hets - owner: iuc -- name: gemini_interactions - owner: iuc diff --git a/usegalaxy.org.au/gemini_tools.yml.lock b/usegalaxy.org.au/gemini_tools.yml.lock deleted file mode 100644 index d44251ba..00000000 --- a/usegalaxy.org.au/gemini_tools.yml.lock +++ /dev/null @@ -1,119 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: gemini_db_info - owner: iuc - revisions: - - 4c5f4e9b1931 - tool_panel_section_label: Gemini Tools -- name: gemini_windower - owner: iuc - revisions: - - 8f04952b8882 - tool_panel_section_label: Gemini Tools -- name: gemini_burden - owner: iuc - revisions: - - 1a4c5adcd587 - tool_panel_section_label: Gemini Tools -- name: gemini_gene_wise - owner: iuc - revisions: - - d46017ddbf94 - tool_panel_section_label: Gemini Tools -- name: gemini_stats - owner: iuc - revisions: - - ee894347fcd6 - tool_panel_section_label: Gemini Tools -- name: gemini_mendel_errors - owner: iuc - revisions: - - 61343646155c - tool_panel_section_label: Gemini Tools -- name: gemini_amend - owner: iuc - revisions: - - 4bd4870ecd33 - tool_panel_section_label: Gemini Tools -- name: gemini_pathways - owner: iuc - revisions: - - 6b09debcfc49 - tool_panel_section_label: Gemini Tools -- name: gemini_dump - owner: iuc - revisions: - - 40f85b45e472 - tool_panel_section_label: Gemini Tools -- name: gemini_region - owner: iuc - revisions: - - 33efe43c1dbb - tool_panel_section_label: Gemini Tools -- name: gemini_actionable_mutations - owner: iuc - revisions: - - 3630a6e624d4 - tool_panel_section_label: Gemini Tools -- name: gemini_lof_sieve - owner: iuc - revisions: - - 90021fffff70 - tool_panel_section_label: Gemini Tools -- name: gemini_query - owner: iuc - revisions: - - 666f60a9331a - tool_panel_section_label: Gemini Tools -- name: gemini_fusions - owner: iuc - revisions: - - 91d53f89ca54 - tool_panel_section_label: Gemini Tools -- name: gemini_load - owner: iuc - revisions: - - cf61daf064fe - tool_panel_section_label: Gemini Tools -- name: gemini_de_novo - owner: iuc - revisions: - - d5b01cc263be - tool_panel_section_label: Gemini Tools -- name: gemini_annotate - owner: iuc - revisions: - - 8f53b238a360 - tool_panel_section_label: Gemini Tools -- name: gemini_recessive_and_dominant - owner: iuc - revisions: - - 86f3aac4418d - tool_panel_section_label: Gemini Tools -- name: gemini_roh - owner: iuc - revisions: - - 93967598e18e - tool_panel_section_label: Gemini Tools -- name: gemini_set_somatic - owner: iuc - revisions: - - ef9991a4a9a7 - tool_panel_section_label: Gemini Tools -- name: gemini_qc - owner: iuc - revisions: - - 9e83673fa6d2 - tool_panel_section_label: Gemini Tools -- name: gemini_comp_hets - owner: iuc - revisions: - - 7cf9bc210044 - tool_panel_section_label: Gemini Tools -- name: gemini_interactions - owner: iuc - revisions: - - 184aa4e686e2 - tool_panel_section_label: Gemini Tools diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml deleted file mode 100644 index 3e8ed8f0..00000000 --- a/usegalaxy.org.au/get_data.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Get Data -tools: -- name: sra_tools - owner: iuc diff --git a/usegalaxy.org.au/get_data.yml.lock b/usegalaxy.org.au/get_data.yml.lock deleted file mode 100644 index 4fbcd78f..00000000 --- a/usegalaxy.org.au/get_data.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: sra_tools - owner: iuc - revisions: - - 8c00bc7fd8de - tool_panel_section_label: Get Data diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml deleted file mode 100644 index c67f879b..00000000 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ /dev/null @@ -1,24 +0,0 @@ -tool_panel_section_label: Graph/Display Data -tools: -- name: mummer - owner: peterjc -- name: histogram - owner: devteam -- name: draw_stacked_barplots - owner: devteam -- name: xy_plot - owner: devteam -- name: prop_venn - owner: idot -- name: weblogo3 - owner: devteam -- name: fastq_quality_boxplot - owner: devteam -- name: gmaj - owner: devteam -- name: jbrowse - owner: iuc -- name: circos - owner: iuc -- name: krona_text - owner: saskia-hiltemann diff --git a/usegalaxy.org.au/graphdisplay_data.yml.lock b/usegalaxy.org.au/graphdisplay_data.yml.lock deleted file mode 100644 index 2d6c51b0..00000000 --- a/usegalaxy.org.au/graphdisplay_data.yml.lock +++ /dev/null @@ -1,59 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: mummer - owner: peterjc - revisions: - - d9f3d4779507 - tool_panel_section_label: Graph/Display Data -- name: histogram - owner: devteam - revisions: - - cdb9e89e2970 - tool_panel_section_label: Graph/Display Data -- name: draw_stacked_barplots - owner: devteam - revisions: - - e997b710e38a - tool_panel_section_label: Graph/Display Data -- name: xy_plot - owner: devteam - revisions: - - 319fa5a9fc1b - tool_panel_section_label: Graph/Display Data -- name: prop_venn - owner: idot - revisions: - - cc6707a1e044 - tool_panel_section_label: Graph/Display Data -- name: weblogo3 - owner: devteam - revisions: - - dc25a5169a91 - tool_panel_section_label: Graph/Display Data -- name: fastq_quality_boxplot - owner: devteam - revisions: - - f95284aa2946 - tool_panel_section_label: Graph/Display Data -- name: gmaj - owner: devteam - revisions: - - 2cd5ee197ec7 - tool_panel_section_label: Graph/Display Data -- name: jbrowse - owner: iuc - revisions: - - 836d1aa3e89a - tool_panel_section_label: Graph/Display Data -- name: circos - owner: iuc - revisions: - - ef5f8bbf7730 - tool_panel_section_label: Graph/Display Data -- name: krona_text - owner: saskia-hiltemann - revisions: - - b14f1444e464 - tool_panel_section_label: Graph/Display Data diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml deleted file mode 100644 index 317ae6d5..00000000 --- a/usegalaxy.org.au/mapping.yml +++ /dev/null @@ -1,10 +0,0 @@ -tool_panel_section_label: Mapping -tools: -- name: bwa - owner: devteam -- name: bowtie2 - owner: devteam -- name: lastz_paired_reads - owner: devteam -- name: lastz - owner: devteam diff --git a/usegalaxy.org.au/mapping.yml.lock b/usegalaxy.org.au/mapping.yml.lock deleted file mode 100644 index 466a876c..00000000 --- a/usegalaxy.org.au/mapping.yml.lock +++ /dev/null @@ -1,24 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: bwa - owner: devteam - revisions: - - 4f774c1e6049 - tool_panel_section_label: Mapping -- name: bowtie2 - owner: devteam - revisions: - - dc1639b66f12 - tool_panel_section_label: Mapping -- name: lastz_paired_reads - owner: devteam - revisions: - - ecc974513241 - tool_panel_section_label: Mapping -- name: lastz - owner: devteam - revisions: - - 60afcc2c1d05 - tool_panel_section_label: Mapping diff --git a/usegalaxy.org.au/metagenomic_analyses.yml b/usegalaxy.org.au/metagenomic_analyses.yml deleted file mode 100644 index 0aed71ff..00000000 --- a/usegalaxy.org.au/metagenomic_analyses.yml +++ /dev/null @@ -1,34 +0,0 @@ -tool_panel_section_label: Metagenomic analyses -tools: -- name: phyloseq_ordination_plot - owner: simon-gladman -- name: phyloseq_filter - owner: simon-gladman -- name: usearch_uchime - owner: qfab -- name: kraken_translate - owner: devteam -- name: kraken_report - owner: devteam -- name: kraken - owner: devteam -- name: kraken_filter - owner: devteam -- name: vsearch - owner: iuc -- name: pynast - owner: qfab -- name: fasttree - owner: iuc -- name: collector_curve - owner: qfab -- name: rarefaction - owner: qfab -- name: usearch_cluster_otus - owner: qfab -- name: usearch_map_reads_to_otus - owner: qfab -- name: rdp_multiclassifier - owner: qfab -- name: usearch_dereplication - owner: qfab diff --git a/usegalaxy.org.au/metagenomic_analyses.yml.lock b/usegalaxy.org.au/metagenomic_analyses.yml.lock deleted file mode 100644 index 8d230669..00000000 --- a/usegalaxy.org.au/metagenomic_analyses.yml.lock +++ /dev/null @@ -1,84 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: phyloseq_ordination_plot - owner: simon-gladman - revisions: - - 52f009b255a1 - tool_panel_section_label: Metagenomic analyses -- name: phyloseq_filter - owner: simon-gladman - revisions: - - 54897b7e0551 - tool_panel_section_label: Metagenomic analyses -- name: usearch_uchime - owner: qfab - revisions: - - fd0ab76b83f1 - tool_panel_section_label: Metagenomic analyses -- name: kraken_translate - owner: devteam - revisions: - - 9bdcba262627 - tool_panel_section_label: Metagenomic analyses -- name: kraken_report - owner: devteam - revisions: - - a3a7440fc618 - tool_panel_section_label: Metagenomic analyses -- name: kraken - owner: devteam - revisions: - - 2fdac3e78553 - tool_panel_section_label: Metagenomic analyses -- name: kraken_filter - owner: devteam - revisions: - - 5bee9adae474 - tool_panel_section_label: Metagenomic analyses -- name: vsearch - owner: iuc - revisions: - - 576963db5f1b - tool_panel_section_label: Metagenomic analyses -- name: pynast - owner: qfab - revisions: - - 17b2737094ce - tool_panel_section_label: Metagenomic analyses -- name: fasttree - owner: iuc - revisions: - - c7e73acfa3eb - tool_panel_section_label: Metagenomic analyses -- name: collector_curve - owner: qfab - revisions: - - 13552951d226 - tool_panel_section_label: Metagenomic analyses -- name: rarefaction - owner: qfab - revisions: - - f6c468a79849 - tool_panel_section_label: Metagenomic analyses -- name: usearch_cluster_otus - owner: qfab - revisions: - - 5d05b34a5fdf - tool_panel_section_label: Metagenomic analyses -- name: usearch_map_reads_to_otus - owner: qfab - revisions: - - 87603fcae838 - tool_panel_section_label: Metagenomic analyses -- name: rdp_multiclassifier - owner: qfab - revisions: - - a73ae72b47aa - tool_panel_section_label: Metagenomic analyses -- name: usearch_dereplication - owner: qfab - revisions: - - 88fc52f1c5db - tool_panel_section_label: Metagenomic analyses diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml deleted file mode 100644 index 34ed0c18..00000000 --- a/usegalaxy.org.au/mothur.yml +++ /dev/null @@ -1,256 +0,0 @@ -tool_panel_section_label: Mothur -tools: -- name: mothur_taxonomy_to_krona - owner: iuc -- name: mothur_align_check - owner: iuc -- name: mothur_align_seqs - owner: iuc -- name: mothur_amova - owner: iuc -- name: mothur_anosim - owner: iuc -- name: mothur_bin_seqs - owner: iuc -- name: mothur_chimera_bellerophon - owner: iuc -- name: mothur_chimera_ccode - owner: iuc -- name: mothur_chimera_check - owner: iuc -- name: mothur_chimera_perseus - owner: iuc -- name: mothur_chimera_pintail - owner: iuc -- name: mothur_chimera_slayer - owner: iuc -- name: mothur_chimera_uchime - owner: iuc -- name: mothur_chop_seqs - owner: iuc -- name: mothur_classify_otu - owner: iuc -- name: mothur_classify_rf - owner: iuc -- name: mothur_classify_seqs - owner: iuc -- name: mothur_classify_tree - owner: iuc -- name: mothur_clearcut - owner: iuc -- name: mothur_cluster_classic - owner: iuc -- name: mothur_cluster_fragments - owner: iuc -- name: mothur_cluster_split - owner: iuc -- name: mothur_cluster - owner: iuc -- name: mothur_collect_shared - owner: iuc -- name: mothur_collect_single - owner: iuc -- name: mothur_consensus_seqs - owner: iuc -- name: mothur_cooccurrence - owner: iuc -- name: mothur_corr_axes - owner: iuc -- name: mothur_count_groups - owner: iuc -- name: mothur_count_seqs - owner: iuc -- name: mothur_create_database - owner: iuc -- name: mothur_degap_seqs - owner: iuc -- name: mothur_deunique_seqs - owner: iuc -- name: mothur_deunique_tree - owner: iuc -- name: mothur_dist_seqs - owner: iuc -- name: mothur_dist_shared - owner: iuc -- name: mothur_fastq_info - owner: iuc -- name: mothur_filter_seqs - owner: iuc -- name: mothur_filter_shared - owner: iuc -- name: mothur_get_communitytype - owner: iuc -- name: mothur_get_coremicrobiome - owner: iuc -- name: mothur_get_dists - owner: iuc -- name: mothur_get_groups - owner: iuc -- name: mothur_get_group - owner: iuc -- name: mothur_get_label - owner: iuc -- name: mothur_get_lineage - owner: iuc -- name: mothur_get_mimarkspackage - owner: iuc -- name: mothur_get_otulabels - owner: iuc -- name: mothur_get_otulist - owner: iuc -- name: mothur_get_oturep - owner: iuc -- name: mothur_get_otus - owner: iuc -- name: mothur_get_rabund - owner: iuc -- name: mothur_get_relabund - owner: iuc -- name: mothur_get_sabund - owner: iuc -- name: mothur_get_seqs - owner: iuc -- name: mothur_get_sharedseqs - owner: iuc -- name: mothur_hcluster - owner: iuc -- name: mothur_heatmap_bin - owner: iuc -- name: mothur_heatmap_sim - owner: iuc -- name: mothur_homova - owner: iuc -- name: mothur_indicator - owner: iuc -- name: mothur_lefse - owner: iuc -- name: mothur_libshuff - owner: iuc -- name: mothur_list_otulabels - owner: iuc -- name: mothur_list_seqs - owner: iuc -- name: mothur_make_biom - owner: iuc -- name: mothur_make_contigs - owner: iuc -- name: mothur_make_design - owner: iuc -- name: mothur_make_fastq - owner: iuc -- name: mothur_make_group - owner: iuc -- name: mothur_make_lefse - owner: iuc -- name: mothur_make_lookup - owner: iuc -- name: mothur_make_shared - owner: iuc -- name: mothur_make_sra - owner: iuc -- name: mothur_mantel - owner: iuc -- name: mothur_merge_files - owner: iuc -- name: mothur_merge_groups - owner: iuc -- name: mothur_merge_sfffiles - owner: iuc -- name: mothur_merge_taxsummary - owner: iuc -- name: mothur_metastats - owner: iuc -- name: mothur_mimarks_attributes - owner: iuc -- name: mothur_nmds - owner: iuc -- name: mothur_normalize_shared - owner: iuc -- name: mothur_otu_association - owner: iuc -- name: mothur_otu_hierarchy - owner: iuc -- name: mothur_pairwise_seqs - owner: iuc -- name: mothur_parse_list - owner: iuc -- name: mothur_parsimony - owner: iuc -- name: mothur_pca - owner: iuc -- name: mothur_pcoa - owner: iuc -- name: mothur_pcr_seqs - owner: iuc -- name: mothur_phylo_diversity - owner: iuc -- name: mothur_phylotype - owner: iuc -- name: mothur_pre_cluster - owner: iuc -- name: mothur_primer_design - owner: iuc -- name: mothur_rarefaction_shared - owner: iuc -- name: mothur_rarefaction_single - owner: iuc -- name: mothur_remove_dists - owner: iuc -- name: mothur_remove_groups - owner: iuc -- name: mothur_remove_lineage - owner: iuc -- name: mothur_remove_otulabels - owner: iuc -- name: mothur_remove_otus - owner: iuc -- name: mothur_remove_rare - owner: iuc -- name: mothur_remove_seqs - owner: iuc -- name: mothur_reverse_seqs - owner: iuc -- name: mothur_screen_seqs - owner: iuc -- name: mothur_sens_spec - owner: iuc -- name: mothur_seq_error - owner: iuc -- name: mothur_sffinfo - owner: iuc -- name: mothur_shhh_flows - owner: iuc -- name: mothur_shhh_seqs - owner: iuc -- name: mothur_sort_seqs - owner: iuc -- name: mothur_split_abund - owner: iuc -- name: mothur_split_groups - owner: iuc -- name: mothur_sub_sample - owner: iuc -- name: mothur_summary_qual - owner: iuc -- name: mothur_summary_seqs - owner: iuc -- name: mothur_summary_shared - owner: iuc -- name: mothur_summary_single - owner: iuc -- name: mothur_summary_tax - owner: iuc -- name: mothur_tree_shared - owner: iuc -- name: mothur_trim_flows - owner: iuc -- name: mothur_trim_seqs - owner: iuc -- name: mothur_unifrac_unweighted - owner: iuc -- name: mothur_unifrac_weighted - owner: iuc -- name: mothur_unique_seqs - owner: iuc -- name: mothur_venn - owner: iuc diff --git a/usegalaxy.org.au/mothur.yml.lock b/usegalaxy.org.au/mothur.yml.lock deleted file mode 100644 index e0e23844..00000000 --- a/usegalaxy.org.au/mothur.yml.lock +++ /dev/null @@ -1,639 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: mothur_taxonomy_to_krona - owner: iuc - revisions: - - 71e7d93a593e - tool_panel_section_label: Mothur -- name: mothur_align_check - owner: iuc - revisions: - - dd533a49feed - tool_panel_section_label: Mothur -- name: mothur_align_seqs - owner: iuc - revisions: - - 5d134e0b31fd - tool_panel_section_label: Mothur -- name: mothur_amova - owner: iuc - revisions: - - 5aa5d26efeea - tool_panel_section_label: Mothur -- name: mothur_anosim - owner: iuc - revisions: - - 652d2803062c - tool_panel_section_label: Mothur -- name: mothur_bin_seqs - owner: iuc - revisions: - - 3fc101a0498f - tool_panel_section_label: Mothur -- name: mothur_chimera_bellerophon - owner: iuc - revisions: - - ad0df6ad0499 - tool_panel_section_label: Mothur -- name: mothur_chimera_ccode - owner: iuc - revisions: - - 79255ca0b19a - tool_panel_section_label: Mothur -- name: mothur_chimera_check - owner: iuc - revisions: - - 35c91da65b75 - tool_panel_section_label: Mothur -- name: mothur_chimera_perseus - owner: iuc - revisions: - - 128cbea05aeb - tool_panel_section_label: Mothur -- name: mothur_chimera_pintail - owner: iuc - revisions: - - cc3eef74fe31 - tool_panel_section_label: Mothur -- name: mothur_chimera_slayer - owner: iuc - revisions: - - a899cc1416bc - tool_panel_section_label: Mothur -- name: mothur_chimera_uchime - owner: iuc - revisions: - - 4e3780d096af - tool_panel_section_label: Mothur -- name: mothur_chop_seqs - owner: iuc - revisions: - - 6e1047fa1a51 - tool_panel_section_label: Mothur -- name: mothur_classify_otu - owner: iuc - revisions: - - 29882f4a1ef3 - tool_panel_section_label: Mothur -- name: mothur_classify_rf - owner: iuc - revisions: - - 010296966465 - tool_panel_section_label: Mothur -- name: mothur_classify_seqs - owner: iuc - revisions: - - 65b370206748 - tool_panel_section_label: Mothur -- name: mothur_classify_tree - owner: iuc - revisions: - - 931e9b25e81d - tool_panel_section_label: Mothur -- name: mothur_clearcut - owner: iuc - revisions: - - 20e764494303 - tool_panel_section_label: Mothur -- name: mothur_cluster_classic - owner: iuc - revisions: - - 6ba59950d95c - tool_panel_section_label: Mothur -- name: mothur_cluster_fragments - owner: iuc - revisions: - - 881f9a4013a9 - tool_panel_section_label: Mothur -- name: mothur_cluster_split - owner: iuc - revisions: - - 2c02989afecb - tool_panel_section_label: Mothur -- name: mothur_cluster - owner: iuc - revisions: - - 3bb756df109c - tool_panel_section_label: Mothur -- name: mothur_collect_shared - owner: iuc - revisions: - - 9c78c5ffa049 - tool_panel_section_label: Mothur -- name: mothur_collect_single - owner: iuc - revisions: - - 7f212a2a4a3b - tool_panel_section_label: Mothur -- name: mothur_consensus_seqs - owner: iuc - revisions: - - e432f17722c8 - tool_panel_section_label: Mothur -- name: mothur_cooccurrence - owner: iuc - revisions: - - 57fe046c8fbe - tool_panel_section_label: Mothur -- name: mothur_corr_axes - owner: iuc - revisions: - - 0968daa9b52f - tool_panel_section_label: Mothur -- name: mothur_count_groups - owner: iuc - revisions: - - dc02f3831a1a - tool_panel_section_label: Mothur -- name: mothur_count_seqs - owner: iuc - revisions: - - f00841c6fc14 - tool_panel_section_label: Mothur -- name: mothur_create_database - owner: iuc - revisions: - - 34669a26ea47 - tool_panel_section_label: Mothur -- name: mothur_degap_seqs - owner: iuc - revisions: - - a7fced14ce99 - tool_panel_section_label: Mothur -- name: mothur_deunique_seqs - owner: iuc - revisions: - - 0369aff1be76 - tool_panel_section_label: Mothur -- name: mothur_deunique_tree - owner: iuc - revisions: - - 98083c5a4338 - tool_panel_section_label: Mothur -- name: mothur_dist_seqs - owner: iuc - revisions: - - 57eb5df69242 - tool_panel_section_label: Mothur -- name: mothur_dist_shared - owner: iuc - revisions: - - 5d6d9f0d0652 - tool_panel_section_label: Mothur -- name: mothur_fastq_info - owner: iuc - revisions: - - f02f3ca6dfd1 - tool_panel_section_label: Mothur -- name: mothur_filter_seqs - owner: iuc - revisions: - - a0ce9fb3f260 - tool_panel_section_label: Mothur -- name: mothur_filter_shared - owner: iuc - revisions: - - e44c38a17c7a - tool_panel_section_label: Mothur -- name: mothur_get_communitytype - owner: iuc - revisions: - - beb4e0832f3b - tool_panel_section_label: Mothur -- name: mothur_get_coremicrobiome - owner: iuc - revisions: - - ae1411cffbee - tool_panel_section_label: Mothur -- name: mothur_get_dists - owner: iuc - revisions: - - 6936b18e2a9e - tool_panel_section_label: Mothur -- name: mothur_get_groups - owner: iuc - revisions: - - b1c35f71607f - tool_panel_section_label: Mothur -- name: mothur_get_group - owner: iuc - revisions: - - f2b626fe7082 - tool_panel_section_label: Mothur -- name: mothur_get_label - owner: iuc - revisions: - - bb8b69e90604 - tool_panel_section_label: Mothur -- name: mothur_get_lineage - owner: iuc - revisions: - - b2b145255ece - tool_panel_section_label: Mothur -- name: mothur_get_mimarkspackage - owner: iuc - revisions: - - 6c54b38dd0da - tool_panel_section_label: Mothur -- name: mothur_get_otulabels - owner: iuc - revisions: - - 630ad54722c6 - tool_panel_section_label: Mothur -- name: mothur_get_otulist - owner: iuc - revisions: - - 2478fb777d97 - tool_panel_section_label: Mothur -- name: mothur_get_oturep - owner: iuc - revisions: - - 648b3da84b07 - tool_panel_section_label: Mothur -- name: mothur_get_otus - owner: iuc - revisions: - - 278a9f09614c - tool_panel_section_label: Mothur -- name: mothur_get_rabund - owner: iuc - revisions: - - 398973de93ab - tool_panel_section_label: Mothur -- name: mothur_get_relabund - owner: iuc - revisions: - - 7756edb68ddc - tool_panel_section_label: Mothur -- name: mothur_get_sabund - owner: iuc - revisions: - - c79ecbd31c44 - tool_panel_section_label: Mothur -- name: mothur_get_seqs - owner: iuc - revisions: - - f31e3b8f2336 - tool_panel_section_label: Mothur -- name: mothur_get_sharedseqs - owner: iuc - revisions: - - 75b80a4fa86d - tool_panel_section_label: Mothur -- name: mothur_hcluster - owner: iuc - revisions: - - '989184322514' - tool_panel_section_label: Mothur -- name: mothur_heatmap_bin - owner: iuc - revisions: - - 5e6fddbd1366 - tool_panel_section_label: Mothur -- name: mothur_heatmap_sim - owner: iuc - revisions: - - 0674bdcb3019 - tool_panel_section_label: Mothur -- name: mothur_homova - owner: iuc - revisions: - - 68005ede9e6e - tool_panel_section_label: Mothur -- name: mothur_indicator - owner: iuc - revisions: - - 0232e2fe594c - tool_panel_section_label: Mothur -- name: mothur_lefse - owner: iuc - revisions: - - 772e6a5b7358 - tool_panel_section_label: Mothur -- name: mothur_libshuff - owner: iuc - revisions: - - eefbe872fd04 - tool_panel_section_label: Mothur -- name: mothur_list_otulabels - owner: iuc - revisions: - - 0c9eb32683bf - tool_panel_section_label: Mothur -- name: mothur_list_seqs - owner: iuc - revisions: - - ea1a32c7927e - tool_panel_section_label: Mothur -- name: mothur_make_biom - owner: iuc - revisions: - - 143cd841de28 - tool_panel_section_label: Mothur -- name: mothur_make_contigs - owner: iuc - revisions: - - 4b72b6c43327 - tool_panel_section_label: Mothur -- name: mothur_make_design - owner: iuc - revisions: - - 5280cc8135eb - tool_panel_section_label: Mothur -- name: mothur_make_fastq - owner: iuc - revisions: - - e9b12c5ad27f - tool_panel_section_label: Mothur -- name: mothur_make_group - owner: iuc - revisions: - - afc13b55ead3 - tool_panel_section_label: Mothur -- name: mothur_make_lefse - owner: iuc - revisions: - - 678c90b43e17 - tool_panel_section_label: Mothur -- name: mothur_make_lookup - owner: iuc - revisions: - - d56e5a7a9cef - tool_panel_section_label: Mothur -- name: mothur_make_shared - owner: iuc - revisions: - - b5f98810181e - tool_panel_section_label: Mothur -- name: mothur_make_sra - owner: iuc - revisions: - - 33a3f68dc34b - tool_panel_section_label: Mothur -- name: mothur_mantel - owner: iuc - revisions: - - 17b471efdc40 - tool_panel_section_label: Mothur -- name: mothur_merge_files - owner: iuc - revisions: - - 12b1bd17d614 - tool_panel_section_label: Mothur -- name: mothur_merge_groups - owner: iuc - revisions: - - 052bc33e134e - tool_panel_section_label: Mothur -- name: mothur_merge_sfffiles - owner: iuc - revisions: - - ec717c8dce9b - tool_panel_section_label: Mothur -- name: mothur_merge_taxsummary - owner: iuc - revisions: - - 80bd73567a2c - tool_panel_section_label: Mothur -- name: mothur_metastats - owner: iuc - revisions: - - 10866c1f8e06 - tool_panel_section_label: Mothur -- name: mothur_mimarks_attributes - owner: iuc - revisions: - - 247d1bacbefe - tool_panel_section_label: Mothur -- name: mothur_nmds - owner: iuc - revisions: - - 98f1cc2bc428 - tool_panel_section_label: Mothur -- name: mothur_normalize_shared - owner: iuc - revisions: - - ad80d646ed1c - tool_panel_section_label: Mothur -- name: mothur_otu_association - owner: iuc - revisions: - - 0fb08aeb215e - tool_panel_section_label: Mothur -- name: mothur_otu_hierarchy - owner: iuc - revisions: - - 7590f83a6419 - tool_panel_section_label: Mothur -- name: mothur_pairwise_seqs - owner: iuc - revisions: - - c05906ab8c41 - tool_panel_section_label: Mothur -- name: mothur_parse_list - owner: iuc - revisions: - - 3b803b7f3388 - tool_panel_section_label: Mothur -- name: mothur_parsimony - owner: iuc - revisions: - - 65955ae23f29 - tool_panel_section_label: Mothur -- name: mothur_pca - owner: iuc - revisions: - - 7474b222205d - tool_panel_section_label: Mothur -- name: mothur_pcoa - owner: iuc - revisions: - - c9fc98593dec - tool_panel_section_label: Mothur -- name: mothur_pcr_seqs - owner: iuc - revisions: - - 2b8dce0751e5 - tool_panel_section_label: Mothur -- name: mothur_phylo_diversity - owner: iuc - revisions: - - 3868f54b097e - tool_panel_section_label: Mothur -- name: mothur_phylotype - owner: iuc - revisions: - - 58f143161d30 - tool_panel_section_label: Mothur -- name: mothur_pre_cluster - owner: iuc - revisions: - - fbbe2b081299 - tool_panel_section_label: Mothur -- name: mothur_primer_design - owner: iuc - revisions: - - 6e8cdd7e6825 - tool_panel_section_label: Mothur -- name: mothur_rarefaction_shared - owner: iuc - revisions: - - 419266a5e29e - tool_panel_section_label: Mothur -- name: mothur_rarefaction_single - owner: iuc - revisions: - - 8091da04fbac - tool_panel_section_label: Mothur -- name: mothur_remove_dists - owner: iuc - revisions: - - ea7b70e1a61b - tool_panel_section_label: Mothur -- name: mothur_remove_groups - owner: iuc - revisions: - - 7c5b7dddd02e - tool_panel_section_label: Mothur -- name: mothur_remove_lineage - owner: iuc - revisions: - - 2f633c057c0d - tool_panel_section_label: Mothur -- name: mothur_remove_otulabels - owner: iuc - revisions: - - ba9df7320629 - tool_panel_section_label: Mothur -- name: mothur_remove_otus - owner: iuc - revisions: - - ce3c9cb04314 - tool_panel_section_label: Mothur -- name: mothur_remove_rare - owner: iuc - revisions: - - 196b1583580a - tool_panel_section_label: Mothur -- name: mothur_remove_seqs - owner: iuc - revisions: - - 2fa446f85b18 - tool_panel_section_label: Mothur -- name: mothur_reverse_seqs - owner: iuc - revisions: - - 03450507aa98 - tool_panel_section_label: Mothur -- name: mothur_screen_seqs - owner: iuc - revisions: - - 94d8dbac60d8 - tool_panel_section_label: Mothur -- name: mothur_sens_spec - owner: iuc - revisions: - - ddda05cfccb4 - tool_panel_section_label: Mothur -- name: mothur_seq_error - owner: iuc - revisions: - - a03c9ebf1959 - tool_panel_section_label: Mothur -- name: mothur_sffinfo - owner: iuc - revisions: - - 12507ed33710 - tool_panel_section_label: Mothur -- name: mothur_shhh_flows - owner: iuc - revisions: - - 7cca6773bc2a - tool_panel_section_label: Mothur -- name: mothur_shhh_seqs - owner: iuc - revisions: - - 6ee54b761c3c - tool_panel_section_label: Mothur -- name: mothur_sort_seqs - owner: iuc - revisions: - - cbe644faff63 - tool_panel_section_label: Mothur -- name: mothur_split_abund - owner: iuc - revisions: - - d850b4b9659d - tool_panel_section_label: Mothur -- name: mothur_split_groups - owner: iuc - revisions: - - 68c20caae797 - tool_panel_section_label: Mothur -- name: mothur_sub_sample - owner: iuc - revisions: - - 34e1fbd32a04 - tool_panel_section_label: Mothur -- name: mothur_summary_qual - owner: iuc - revisions: - - d50fdfdc2a0c - tool_panel_section_label: Mothur -- name: mothur_summary_seqs - owner: iuc - revisions: - - 411ddfefe041 - tool_panel_section_label: Mothur -- name: mothur_summary_shared - owner: iuc - revisions: - - 74c8ebee088c - tool_panel_section_label: Mothur -- name: mothur_summary_single - owner: iuc - revisions: - - 2857a688a7e9 - tool_panel_section_label: Mothur -- name: mothur_summary_tax - owner: iuc - revisions: - - 5eb0f670aa35 - tool_panel_section_label: Mothur -- name: mothur_tree_shared - owner: iuc - revisions: - - 40d8938eaa24 - tool_panel_section_label: Mothur -- name: mothur_trim_flows - owner: iuc - revisions: - - 4d56c7e82ba6 - tool_panel_section_label: Mothur -- name: mothur_trim_seqs - owner: iuc - revisions: - - c49a6454726c - tool_panel_section_label: Mothur -- name: mothur_unifrac_unweighted - owner: iuc - revisions: - - 3597ca9089a5 - tool_panel_section_label: Mothur -- name: mothur_unifrac_weighted - owner: iuc - revisions: - - 136cb4f4b996 - tool_panel_section_label: Mothur -- name: mothur_unique_seqs - owner: iuc - revisions: - - 7c3f9c0850ac - tool_panel_section_label: Mothur -- name: mothur_venn - owner: iuc - revisions: - - e4f4c1c0d193 - tool_panel_section_label: Mothur diff --git a/usegalaxy.org.au/none.yml.lock b/usegalaxy.org.au/none.yml.lock deleted file mode 100644 index f7a4012d..00000000 --- a/usegalaxy.org.au/none.yml.lock +++ /dev/null @@ -1,64 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: data_manager_bwa_mem_index_builder - owner: devteam - revisions: - - 46066df8813d - tool_panel_section_label: None -- name: rnachipintegrator - owner: pjbriggs - revisions: - - b695071de766 - tool_panel_section_label: None -- name: data_manager_sam_fasta_index_builder - owner: devteam - revisions: - - 1865e693d8b2 - tool_panel_section_label: None -- name: data_manager_kallisto_index_builder - owner: iuc - revisions: - - 6843a0db2da0 - tool_panel_section_label: None -- name: data_manager_snpeff - owner: iuc - revisions: - - a6400027d849 - tool_panel_section_label: None -- name: data_manager_gatk_picard_index_builder - owner: devteam - revisions: - - b31f1fcb203c - tool_panel_section_label: None -- name: data_manager_hisat2_index_builder - owner: iuc - revisions: - - d210e1f185bd - tool_panel_section_label: None -- name: data_manager_twobit_builder - owner: devteam - revisions: - - 9946bc39c834 - tool_panel_section_label: None -- name: data_manager_fetch_genome_dbkeys_all_fasta - owner: devteam - revisions: - - b1bc53e9bbc5 - tool_panel_section_label: None -- name: data_manager_gemini_database_downloader - owner: iuc - revisions: - - 172815da3d41 - tool_panel_section_label: None -- name: data_manager_bowtie2_index_builder - owner: devteam - revisions: - - 83da94c0e4a6 - tool_panel_section_label: None -- name: data_manager_fetch_busco - owner: iuc - revisions: - - 53eec20e8fb6 - tool_panel_section_label: None diff --git a/usegalaxy.org.au/operate_on_genomic_intervals.yml b/usegalaxy.org.au/operate_on_genomic_intervals.yml deleted file mode 100644 index b3373276..00000000 --- a/usegalaxy.org.au/operate_on_genomic_intervals.yml +++ /dev/null @@ -1,26 +0,0 @@ -tool_panel_section_label: Operate on Genomic Intervals -tools: -- name: merge - owner: devteam -- name: basecoverage - owner: devteam -- name: coverage - owner: devteam -- name: intersect - owner: devteam -- name: complement - owner: devteam -- name: subtract - owner: devteam -- name: concat - owner: devteam -- name: join - owner: devteam -- name: subtract_query - owner: devteam -- name: get_flanks - owner: devteam -- name: flanking_features - owner: devteam -- name: cluster - owner: devteam diff --git a/usegalaxy.org.au/operate_on_genomic_intervals.yml.lock b/usegalaxy.org.au/operate_on_genomic_intervals.yml.lock deleted file mode 100644 index eada65cc..00000000 --- a/usegalaxy.org.au/operate_on_genomic_intervals.yml.lock +++ /dev/null @@ -1,64 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: merge - owner: devteam - revisions: - - 381cd27bf67a - tool_panel_section_label: Operate on Genomic Intervals -- name: basecoverage - owner: devteam - revisions: - - 2cedec3759e4 - tool_panel_section_label: Operate on Genomic Intervals -- name: coverage - owner: devteam - revisions: - - 4ef9819dc7fb - tool_panel_section_label: Operate on Genomic Intervals -- name: intersect - owner: devteam - revisions: - - 33b3f3688db4 - tool_panel_section_label: Operate on Genomic Intervals -- name: complement - owner: devteam - revisions: - - 38c8bb402872 - tool_panel_section_label: Operate on Genomic Intervals -- name: subtract - owner: devteam - revisions: - - 0145969324c4 - tool_panel_section_label: Operate on Genomic Intervals -- name: concat - owner: devteam - revisions: - - 32e1c8dac438 - tool_panel_section_label: Operate on Genomic Intervals -- name: join - owner: devteam - revisions: - - a10f49d9218a - tool_panel_section_label: Operate on Genomic Intervals -- name: subtract_query - owner: devteam - revisions: - - ff3901618482 - tool_panel_section_label: Operate on Genomic Intervals -- name: get_flanks - owner: devteam - revisions: - - 077f404ae1bb - tool_panel_section_label: Operate on Genomic Intervals -- name: flanking_features - owner: devteam - revisions: - - a09d13b108fd - tool_panel_section_label: Operate on Genomic Intervals -- name: cluster - owner: devteam - revisions: - - 05696474ee89 - tool_panel_section_label: Operate on Genomic Intervals diff --git a/usegalaxy.org.au/peak_calling.yml b/usegalaxy.org.au/peak_calling.yml deleted file mode 100644 index 726ba5b7..00000000 --- a/usegalaxy.org.au/peak_calling.yml +++ /dev/null @@ -1,16 +0,0 @@ -tool_panel_section_label: Peak Calling -tools: -- name: sicer - owner: devteam -- name: macs2 - owner: iuc -- name: idr_package - owner: modencode-dcc -- name: diffbind - owner: bgruening -- name: spp_tool - owner: stemcellcommons -- name: macs21 - owner: pjbriggs -- name: rnachipintegrator - owner: pjbriggs diff --git a/usegalaxy.org.au/peak_calling.yml.lock b/usegalaxy.org.au/peak_calling.yml.lock deleted file mode 100644 index 5707e0a8..00000000 --- a/usegalaxy.org.au/peak_calling.yml.lock +++ /dev/null @@ -1,39 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: sicer - owner: devteam - revisions: - - 4a14714649b4 - tool_panel_section_label: Peak Calling -- name: macs2 - owner: iuc - revisions: - - f5d67c722d67 - tool_panel_section_label: Peak Calling -- name: idr_package - owner: modencode-dcc - revisions: - - 6f6a9fbe264e - tool_panel_section_label: Peak Calling -- name: diffbind - owner: bgruening - revisions: - - fa56d93f7980 - tool_panel_section_label: Peak Calling -- name: spp_tool - owner: stemcellcommons - revisions: - - 23b22c1692fa - tool_panel_section_label: Peak Calling -- name: macs21 - owner: pjbriggs - revisions: - - 4124781932db - tool_panel_section_label: Peak Calling -- name: rnachipintegrator - owner: pjbriggs - revisions: - - b695071de766 - tool_panel_section_label: Peak Calling diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml deleted file mode 100644 index 7524fbed..00000000 --- a/usegalaxy.org.au/phylogenetics.yml +++ /dev/null @@ -1,8 +0,0 @@ -tool_panel_section_label: Phylogenetics -tools: -- name: raxml - owner: iuc -- name: gubbins - owner: iuc -- name: roary - owner: iuc diff --git a/usegalaxy.org.au/phylogenetics.yml.lock b/usegalaxy.org.au/phylogenetics.yml.lock deleted file mode 100644 index 66f88233..00000000 --- a/usegalaxy.org.au/phylogenetics.yml.lock +++ /dev/null @@ -1,19 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: raxml - owner: iuc - revisions: - - ba29b5e2a4be - tool_panel_section_label: Phylogenetics -- name: gubbins - owner: iuc - revisions: - - 637ec5d5368c - tool_panel_section_label: Phylogenetics -- name: roary - owner: iuc - revisions: - - f1ccc8a6eb05 - tool_panel_section_label: Phylogenetics diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml deleted file mode 100644 index 44fb2253..00000000 --- a/usegalaxy.org.au/picard.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_label: Picard -tools: -- name: picard - owner: devteam diff --git a/usegalaxy.org.au/picard.yml.lock b/usegalaxy.org.au/picard.yml.lock deleted file mode 100644 index 52b45dff..00000000 --- a/usegalaxy.org.au/picard.yml.lock +++ /dev/null @@ -1,9 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: picard - owner: devteam - revisions: - - fc288950c3b7 - tool_panel_section_label: Picard diff --git a/usegalaxy.org.au/qc_and_manipulation.yml b/usegalaxy.org.au/qc_and_manipulation.yml deleted file mode 100644 index c28c6370..00000000 --- a/usegalaxy.org.au/qc_and_manipulation.yml +++ /dev/null @@ -1,40 +0,0 @@ -tool_panel_section_label: QC and manipulation -tools: -- name: fastqc - owner: devteam -- name: pear - owner: iuc -- name: multiqc - owner: engineson -- name: trim_galore - owner: bgruening -- name: trimmomatic - owner: pjbriggs -- name: fastq_trimmer - owner: devteam -- name: fastq_stats - owner: devteam -- name: fastq_paired_end_joiner - owner: devteam -- name: fastq_masker_by_quality - owner: devteam -- name: fastq_paired_end_splitter - owner: devteam -- name: fastq_paired_end_interlacer - owner: devteam -- name: fastq_manipulation - owner: devteam -- name: fastq_groomer - owner: devteam -- name: fastq_paired_end_deinterlacer - owner: devteam -- name: fastq_combiner - owner: devteam -- name: fastq_filter - owner: devteam -- name: fastq_trimmer_by_quality - owner: devteam -- name: ngsutils_bam_filter - owner: iuc -- name: cutadapt - owner: lparsons diff --git a/usegalaxy.org.au/qc_and_manipulation.yml.lock b/usegalaxy.org.au/qc_and_manipulation.yml.lock deleted file mode 100644 index c014a50e..00000000 --- a/usegalaxy.org.au/qc_and_manipulation.yml.lock +++ /dev/null @@ -1,99 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: fastqc - owner: devteam - revisions: - - 3e1cdf5406db - tool_panel_section_label: QC and manipulation -- name: pear - owner: iuc - revisions: - - 2f804526f5fd - tool_panel_section_label: QC and manipulation -- name: multiqc - owner: engineson - revisions: - - 5e4080791d90 - tool_panel_section_label: QC and manipulation -- name: trim_galore - owner: bgruening - revisions: - - 949f01671246 - tool_panel_section_label: QC and manipulation -- name: trimmomatic - owner: pjbriggs - revisions: - - 53af7b5b1b56 - tool_panel_section_label: QC and manipulation -- name: fastq_trimmer - owner: devteam - revisions: - - 2d0d13b0b0f1 - tool_panel_section_label: QC and manipulation -- name: fastq_stats - owner: devteam - revisions: - - e2cf940128d5 - tool_panel_section_label: QC and manipulation -- name: fastq_paired_end_joiner - owner: devteam - revisions: - - 822cc1e6274e - tool_panel_section_label: QC and manipulation -- name: fastq_masker_by_quality - owner: devteam - revisions: - - eb592e9ec47a - tool_panel_section_label: QC and manipulation -- name: fastq_paired_end_splitter - owner: devteam - revisions: - - 9bbe5b7ffa12 - tool_panel_section_label: QC and manipulation -- name: fastq_paired_end_interlacer - owner: devteam - revisions: - - ef49268ee579 - tool_panel_section_label: QC and manipulation -- name: fastq_manipulation - owner: devteam - revisions: - - 4ac14b275aca - tool_panel_section_label: QC and manipulation -- name: fastq_groomer - owner: devteam - revisions: - - 71e5fa25b8a2 - tool_panel_section_label: QC and manipulation -- name: fastq_paired_end_deinterlacer - owner: devteam - revisions: - - b7ce72b00e62 - tool_panel_section_label: QC and manipulation -- name: fastq_combiner - owner: devteam - revisions: - - 56389130cb63 - tool_panel_section_label: QC and manipulation -- name: fastq_filter - owner: devteam - revisions: - - 06934412f56d - tool_panel_section_label: QC and manipulation -- name: fastq_trimmer_by_quality - owner: devteam - revisions: - - c64d534a763c - tool_panel_section_label: QC and manipulation -- name: ngsutils_bam_filter - owner: iuc - revisions: - - aecfe10118ed - tool_panel_section_label: QC and manipulation -- name: cutadapt - owner: lparsons - revisions: - - 8665bcc8b847 - tool_panel_section_label: QC and manipulation diff --git a/usegalaxy.org.au/rna_analysis.yml b/usegalaxy.org.au/rna_analysis.yml deleted file mode 100644 index 26a10a0c..00000000 --- a/usegalaxy.org.au/rna_analysis.yml +++ /dev/null @@ -1,86 +0,0 @@ -tool_panel_section_label: RNA Analysis -tools: -- name: kallisto_quant - owner: iuc -- name: kallisto_pseudo - owner: iuc -- name: trinotate - owner: iuc -- name: trinity - owner: iuc -- name: transdecoder - owner: iuc -- name: htseq_count - owner: lparsons -- name: sailfish - owner: bgruening -- name: gffcompare - owner: iuc -- name: edger - owner: iuc -- name: dexseq - owner: iuc -- name: rseqc - owner: nilesh -- name: featurecounts - owner: iuc -- name: generate_count_matrix - owner: jchung -- name: stringtie - owner: iuc -- name: trinity_run_de_analysis - owner: iuc -- name: trinity_filter_low_expr_transcripts - owner: iuc -- name: describe_samples - owner: iuc -- name: trinity_gene_to_trans_map - owner: iuc -- name: trinity_analyze_diff_expr - owner: iuc -- name: trinity_align_and_estimate_abundance - owner: iuc -- name: trinity_define_clusters_by_cutting_tree - owner: iuc -- name: trinity_abundance_estimates_to_matrix - owner: iuc -- name: trinity_samples_qccheck - owner: iuc -- name: trinity_contig_exn50_statistic - owner: iuc -- name: salmon - owner: bgruening -- name: deseq2 - owner: iuc -- name: differential_count_models - owner: fubar -- name: htseq_bams_to_count_matrix - owner: fubar -- name: express - owner: devteam -- name: filter_transcripts_via_tracking - owner: devteam -- name: cummerbund - owner: devteam -- name: cuffcompare - owner: devteam -- name: cuffmerge - owner: devteam -- name: cuffnorm - owner: devteam -- name: cuffquant - owner: devteam -- name: cuffdiff - owner: devteam -- name: cufflinks - owner: devteam -- name: tophat_fusion_post - owner: devteam -- name: tophat2 - owner: devteam -- name: rgrnastar - owner: iuc -- name: hisat2 - owner: iuc -- name: rsem - owner: jjohnson diff --git a/usegalaxy.org.au/rna_analysis.yml.lock b/usegalaxy.org.au/rna_analysis.yml.lock deleted file mode 100644 index db75f9e3..00000000 --- a/usegalaxy.org.au/rna_analysis.yml.lock +++ /dev/null @@ -1,214 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: kallisto_quant - owner: iuc - revisions: - - 10c98fab6c5a - tool_panel_section_label: RNA Analysis -- name: kallisto_pseudo - owner: iuc - revisions: - - 1c75aa5de15e - tool_panel_section_label: RNA Analysis -- name: trinotate - owner: iuc - revisions: - - 6fd16fad465d - tool_panel_section_label: RNA Analysis -- name: trinity - owner: iuc - revisions: - - cee61b3fcf78 - tool_panel_section_label: RNA Analysis -- name: transdecoder - owner: iuc - revisions: - - 0db979fead3a - tool_panel_section_label: RNA Analysis -- name: htseq_count - owner: lparsons - revisions: - - 7f5a8d427b39 - tool_panel_section_label: RNA Analysis -- name: sailfish - owner: bgruening - revisions: - - a8f343909c17 - tool_panel_section_label: RNA Analysis -- name: gffcompare - owner: iuc - revisions: - - 3c97c841a443 - tool_panel_section_label: RNA Analysis -- name: edger - owner: iuc - revisions: - - 9bdff28ae1b1 - tool_panel_section_label: RNA Analysis -- name: dexseq - owner: iuc - revisions: - - f1c406f9554c - tool_panel_section_label: RNA Analysis -- name: rseqc - owner: nilesh - revisions: - - 080fd5739bb4 - tool_panel_section_label: RNA Analysis -- name: featurecounts - owner: iuc - revisions: - - e6a2a912677a - tool_panel_section_label: RNA Analysis -- name: generate_count_matrix - owner: jchung - revisions: - - 56768aac1758 - tool_panel_section_label: RNA Analysis -- name: stringtie - owner: iuc - revisions: - - 76d290331481 - tool_panel_section_label: RNA Analysis -- name: trinity_run_de_analysis - owner: iuc - revisions: - - 047c22569787 - tool_panel_section_label: RNA Analysis -- name: trinity_filter_low_expr_transcripts - owner: iuc - revisions: - - 6f0fb35b799c - tool_panel_section_label: RNA Analysis -- name: describe_samples - owner: iuc - revisions: - - 8f0181aacb7a - tool_panel_section_label: RNA Analysis -- name: trinity_gene_to_trans_map - owner: iuc - revisions: - - c2c039e421af - tool_panel_section_label: RNA Analysis -- name: trinity_analyze_diff_expr - owner: iuc - revisions: - - c5f02e00d596 - tool_panel_section_label: RNA Analysis -- name: trinity_align_and_estimate_abundance - owner: iuc - revisions: - - 04bd98a9c751 - tool_panel_section_label: RNA Analysis -- name: trinity_define_clusters_by_cutting_tree - owner: iuc - revisions: - - c5fbddcac63a - tool_panel_section_label: RNA Analysis -- name: trinity_abundance_estimates_to_matrix - owner: iuc - revisions: - - 74217fbfba4d - tool_panel_section_label: RNA Analysis -- name: trinity_samples_qccheck - owner: iuc - revisions: - - 1812dbc5bb7b - tool_panel_section_label: RNA Analysis -- name: trinity_contig_exn50_statistic - owner: iuc - revisions: - - 4687ecf0eb2d - tool_panel_section_label: RNA Analysis -- name: salmon - owner: bgruening - revisions: - - 53e9709776a0 - tool_panel_section_label: RNA Analysis -- name: deseq2 - owner: iuc - revisions: - - 24a09ca67621 - tool_panel_section_label: RNA Analysis -- name: differential_count_models - owner: fubar - revisions: - - 3107df74056e - tool_panel_section_label: RNA Analysis -- name: htseq_bams_to_count_matrix - owner: fubar - revisions: - - d300bc688e95 - tool_panel_section_label: RNA Analysis -- name: express - owner: devteam - revisions: - - 7b0708761d05 - tool_panel_section_label: RNA Analysis -- name: filter_transcripts_via_tracking - owner: devteam - revisions: - - 45f89dcf0b4c - tool_panel_section_label: RNA Analysis -- name: cummerbund - owner: devteam - revisions: - - 78fcfc04fcfe - tool_panel_section_label: RNA Analysis -- name: cuffcompare - owner: devteam - revisions: - - e66b9b5b8580 - tool_panel_section_label: RNA Analysis -- name: cuffmerge - owner: devteam - revisions: - - cf747d1bd79a - tool_panel_section_label: RNA Analysis -- name: cuffnorm - owner: devteam - revisions: - - f5b2ee725d34 - tool_panel_section_label: RNA Analysis -- name: cuffquant - owner: devteam - revisions: - - 6dc45faebc1d - tool_panel_section_label: RNA Analysis -- name: cuffdiff - owner: devteam - revisions: - - d3ae7d9c2202 - tool_panel_section_label: RNA Analysis -- name: cufflinks - owner: devteam - revisions: - - e04dbae2abe0 - tool_panel_section_label: RNA Analysis -- name: tophat_fusion_post - owner: devteam - revisions: - - f83394a2c2da - tool_panel_section_label: RNA Analysis -- name: tophat2 - owner: devteam - revisions: - - 16c4255042be - tool_panel_section_label: RNA Analysis -- name: rgrnastar - owner: iuc - revisions: - - 99b17b74a8cd - tool_panel_section_label: RNA Analysis -- name: hisat2 - owner: iuc - revisions: - - 764756ab0eb5 - tool_panel_section_label: RNA Analysis -- name: rsem - owner: jjohnson - revisions: - - 14267d364365 - tool_panel_section_label: RNA Analysis diff --git a/usegalaxy.org.au/sam_tools.yml b/usegalaxy.org.au/sam_tools.yml deleted file mode 100644 index f414b3d6..00000000 --- a/usegalaxy.org.au/sam_tools.yml +++ /dev/null @@ -1,44 +0,0 @@ -tool_panel_section_label: SAM Tools -tools: -- name: pileup_parser - owner: devteam -- name: sam_merge - owner: devteam -- name: samtool_filter2 - owner: devteam -- name: sam_pileup - owner: devteam -- name: sam_bitwise_flag_filter - owner: devteam -- name: sam2interval - owner: devteam -- name: samtools_phase - owner: devteam -- name: pileup_interval - owner: devteam -- name: samtools_mpileup - owner: devteam -- name: samtools_idxstats - owner: devteam -- name: samtools_flagstat - owner: devteam -- name: sam_to_bam - owner: devteam -- name: samtools_reheader - owner: devteam -- name: samtools_split - owner: devteam -- name: samtools_stats - owner: devteam -- name: samtools_bedcov - owner: devteam -- name: samtools_slice_bam - owner: devteam -- name: samtools_calmd - owner: devteam -- name: samtools_sort - owner: devteam -- name: bam_to_sam - owner: devteam -- name: samtools_rmdup - owner: devteam diff --git a/usegalaxy.org.au/sam_tools.yml.lock b/usegalaxy.org.au/sam_tools.yml.lock deleted file mode 100644 index 4917df5e..00000000 --- a/usegalaxy.org.au/sam_tools.yml.lock +++ /dev/null @@ -1,109 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: pileup_parser - owner: devteam - revisions: - - 85bedbea8a12 - tool_panel_section_label: SAM Tools -- name: sam_merge - owner: devteam - revisions: - - 1977f1637890 - tool_panel_section_label: SAM Tools -- name: samtool_filter2 - owner: devteam - revisions: - - dc6ff68ea5e8 - tool_panel_section_label: SAM Tools -- name: sam_pileup - owner: devteam - revisions: - - 890d97772e2a - tool_panel_section_label: SAM Tools -- name: sam_bitwise_flag_filter - owner: devteam - revisions: - - 0b2424a404d9 - tool_panel_section_label: SAM Tools -- name: sam2interval - owner: devteam - revisions: - - 8c737b8ddc45 - tool_panel_section_label: SAM Tools -- name: samtools_phase - owner: devteam - revisions: - - 6166013090c0 - tool_panel_section_label: SAM Tools -- name: pileup_interval - owner: devteam - revisions: - - ef11139d4545 - tool_panel_section_label: SAM Tools -- name: samtools_mpileup - owner: devteam - revisions: - - 583abf29fc8e - tool_panel_section_label: SAM Tools -- name: samtools_idxstats - owner: devteam - revisions: - - 88b8c2916784 - tool_panel_section_label: SAM Tools -- name: samtools_flagstat - owner: devteam - revisions: - - cc61ade70eb8 - tool_panel_section_label: SAM Tools -- name: sam_to_bam - owner: devteam - revisions: - - f7a0d41036c7 - tool_panel_section_label: SAM Tools -- name: samtools_reheader - owner: devteam - revisions: - - db000c6007a0 - tool_panel_section_label: SAM Tools -- name: samtools_split - owner: devteam - revisions: - - b7f7826ef1cd - tool_panel_section_label: SAM Tools -- name: samtools_stats - owner: devteam - revisions: - - 24c5d43cb545 - tool_panel_section_label: SAM Tools -- name: samtools_bedcov - owner: devteam - revisions: - - 12749212f61b - tool_panel_section_label: SAM Tools -- name: samtools_slice_bam - owner: devteam - revisions: - - a4a10c7924d1 - tool_panel_section_label: SAM Tools -- name: samtools_calmd - owner: devteam - revisions: - - 33208952b99d - tool_panel_section_label: SAM Tools -- name: samtools_sort - owner: devteam - revisions: - - cab3f8d35989 - tool_panel_section_label: SAM Tools -- name: bam_to_sam - owner: devteam - revisions: - - f57df915aa10 - tool_panel_section_label: SAM Tools -- name: samtools_rmdup - owner: devteam - revisions: - - 9129584416e2 - tool_panel_section_label: SAM Tools diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml deleted file mode 100644 index 57956d8d..00000000 --- a/usegalaxy.org.au/statistics.yml +++ /dev/null @@ -1,34 +0,0 @@ -tool_panel_section_label: Statistics -tools: -- name: row_means - owner: simon-gladman -- name: count_gff_features - owner: devteam -- name: datamash_ops - owner: iuc -- name: plot_from_lda - owner: devteam -- name: dwt_ivc_all - owner: devteam -- name: dwt_cor_ava_perclass - owner: devteam -- name: correlation - owner: devteam -- name: compute_motif_frequencies_for_all_motifs - owner: devteam -- name: t_test_two_samples - owner: devteam -- name: poisson2test - owner: devteam -- name: categorize_elements_satisfying_criteria - owner: devteam -- name: dwt_cor_avb_all - owner: devteam -- name: generate_pc_lda_matrix - owner: devteam -- name: compute_motifs_frequency - owner: devteam -- name: dwt_var_perfeature - owner: devteam -- name: dwt_var_perclass - owner: devteam diff --git a/usegalaxy.org.au/statistics.yml.lock b/usegalaxy.org.au/statistics.yml.lock deleted file mode 100644 index a8b5af20..00000000 --- a/usegalaxy.org.au/statistics.yml.lock +++ /dev/null @@ -1,84 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: row_means - owner: simon-gladman - revisions: - - 33493e25c51c - tool_panel_section_label: Statistics -- name: count_gff_features - owner: devteam - revisions: - - 188392a0d0a8 - tool_panel_section_label: Statistics -- name: datamash_ops - owner: iuc - revisions: - - 2f3c6f2dcf39 - tool_panel_section_label: Statistics -- name: plot_from_lda - owner: devteam - revisions: - - 08affc5d2aef - tool_panel_section_label: Statistics -- name: dwt_ivc_all - owner: devteam - revisions: - - 0b89b03ad760 - tool_panel_section_label: Statistics -- name: dwt_cor_ava_perclass - owner: devteam - revisions: - - a0defff5cf89 - tool_panel_section_label: Statistics -- name: correlation - owner: devteam - revisions: - - 24e01abf9e34 - tool_panel_section_label: Statistics -- name: compute_motif_frequencies_for_all_motifs - owner: devteam - revisions: - - 5319efa51514 - tool_panel_section_label: Statistics -- name: t_test_two_samples - owner: devteam - revisions: - - c2ffc9885b5a - tool_panel_section_label: Statistics -- name: poisson2test - owner: devteam - revisions: - - 5ff18ec88181 - tool_panel_section_label: Statistics -- name: categorize_elements_satisfying_criteria - owner: devteam - revisions: - - 586c1f0e1515 - tool_panel_section_label: Statistics -- name: dwt_cor_avb_all - owner: devteam - revisions: - - 8564f6927b87 - tool_panel_section_label: Statistics -- name: generate_pc_lda_matrix - owner: devteam - revisions: - - 04cdbd00dcec - tool_panel_section_label: Statistics -- name: compute_motifs_frequency - owner: devteam - revisions: - - 1f8ee7f9701b - tool_panel_section_label: Statistics -- name: dwt_var_perfeature - owner: devteam - revisions: - - cb1c59d69557 - tool_panel_section_label: Statistics -- name: dwt_var_perclass - owner: devteam - revisions: - - cb422b6f49d2 - tool_panel_section_label: Statistics diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml deleted file mode 100644 index 4a092491..00000000 --- a/usegalaxy.org.au/text_manipulation.yml +++ /dev/null @@ -1,14 +0,0 @@ -tool_panel_section_label: Text Manipulation -tools: -- name: column_arrange_by_header - owner: bgruening -- name: cut_include_exclude - owner: r-lannes -- name: concatenate_multiple_datasets - owner: artbio -- name: condense_characters - owner: devteam -- name: column_maker - owner: devteam -- name: regex_find_replace - owner: galaxyp diff --git a/usegalaxy.org.au/text_manipulation.yml.lock b/usegalaxy.org.au/text_manipulation.yml.lock deleted file mode 100644 index 63aca350..00000000 --- a/usegalaxy.org.au/text_manipulation.yml.lock +++ /dev/null @@ -1,34 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: column_arrange_by_header - owner: bgruening - revisions: - - f18f67056946 - tool_panel_section_label: Text Manipulation -- name: cut_include_exclude - owner: r-lannes - revisions: - - d28ee835a561 - tool_panel_section_label: Text Manipulation -- name: concatenate_multiple_datasets - owner: artbio - revisions: - - 6f54dc6b37da - tool_panel_section_label: Text Manipulation -- name: condense_characters - owner: devteam - revisions: - - 381ed54c5e39 - tool_panel_section_label: Text Manipulation -- name: column_maker - owner: devteam - revisions: - - 626658afe4cb - tool_panel_section_label: Text Manipulation -- name: regex_find_replace - owner: galaxyp - revisions: - - 209b7c5ee9d7 - tool_panel_section_label: Text Manipulation diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml deleted file mode 100644 index 5da89676..00000000 --- a/usegalaxy.org.au/variant_calling.yml +++ /dev/null @@ -1,22 +0,0 @@ -tool_panel_section_label: Variant Calling -tools: -- name: snippy - owner: iuc -- name: substitution_rates - owner: devteam -- name: snpfreq - owner: devteam -- name: vcf_extract - owner: devteam -- name: vcf_intersect - owner: devteam -- name: vcf_annotate - owner: devteam -- name: vcf_filter - owner: devteam -- name: freebayes - owner: devteam -- name: varscan_version_2 - owner: devteam -- name: vcftools_merge - owner: devteam diff --git a/usegalaxy.org.au/variant_calling.yml.lock b/usegalaxy.org.au/variant_calling.yml.lock deleted file mode 100644 index a3ad143b..00000000 --- a/usegalaxy.org.au/variant_calling.yml.lock +++ /dev/null @@ -1,54 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: snippy - owner: iuc - revisions: - - c9a8ef2aa380 - tool_panel_section_label: Variant Calling -- name: substitution_rates - owner: devteam - revisions: - - 3d9544198582 - tool_panel_section_label: Variant Calling -- name: snpfreq - owner: devteam - revisions: - - 5c3ac057608b - tool_panel_section_label: Variant Calling -- name: vcf_extract - owner: devteam - revisions: - - 76ad0b7865b9 - tool_panel_section_label: Variant Calling -- name: vcf_intersect - owner: devteam - revisions: - - 9d162bde4113 - tool_panel_section_label: Variant Calling -- name: vcf_annotate - owner: devteam - revisions: - - b001b50f2009 - tool_panel_section_label: Variant Calling -- name: vcf_filter - owner: devteam - revisions: - - da1a6f33b504 - tool_panel_section_label: Variant Calling -- name: freebayes - owner: devteam - revisions: - - 156b60c1530f - tool_panel_section_label: Variant Calling -- name: varscan_version_2 - owner: devteam - revisions: - - bc1e0cd41241 - tool_panel_section_label: Variant Calling -- name: vcftools_merge - owner: devteam - revisions: - - 71e19ddf52f5 - tool_panel_section_label: Variant Calling diff --git a/usegalaxy.org.au/vcf_manipulation.yml b/usegalaxy.org.au/vcf_manipulation.yml deleted file mode 100644 index 3e9556ff..00000000 --- a/usegalaxy.org.au/vcf_manipulation.yml +++ /dev/null @@ -1,48 +0,0 @@ -tool_panel_section_label: VCF Manipulation -tools: -- name: vcf2tsv - owner: devteam -- name: vcfaddinfo - owner: devteam -- name: vcfallelicprimitives - owner: devteam -- name: vcfannotate - owner: devteam -- name: vcfannotategenotypes - owner: devteam -- name: vcfbedintersect - owner: devteam -- name: vcfbreakcreatemulti - owner: devteam -- name: vcfcheck - owner: devteam -- name: vcfcombine - owner: devteam -- name: vcfcommonsamples - owner: devteam -- name: vcfdistance - owner: devteam -- name: vcffilter - owner: devteam -- name: vcffixup - owner: devteam -- name: vcfflatten - owner: devteam -- name: vcfgeno2haplo - owner: devteam -- name: vcfgenotypes - owner: devteam -- name: vcfhethom - owner: devteam -- name: vcfleftalign - owner: devteam -- name: vcfprimers - owner: devteam -- name: vcfrandomsample - owner: devteam -- name: vcfselectsamples - owner: devteam -- name: vcfsort - owner: devteam -- name: vcfvcfintersect - owner: devteam diff --git a/usegalaxy.org.au/vcf_manipulation.yml.lock b/usegalaxy.org.au/vcf_manipulation.yml.lock deleted file mode 100644 index 8a247d3e..00000000 --- a/usegalaxy.org.au/vcf_manipulation.yml.lock +++ /dev/null @@ -1,119 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: vcf2tsv - owner: devteam - revisions: - - e92b3c0f9224 - tool_panel_section_label: VCF Manipulation -- name: vcfaddinfo - owner: devteam - revisions: - - afc0ba768690 - tool_panel_section_label: VCF Manipulation -- name: vcfallelicprimitives - owner: devteam - revisions: - - a8a4f94aa321 - tool_panel_section_label: VCF Manipulation -- name: vcfannotate - owner: devteam - revisions: - - 6faa2c4c71d2 - tool_panel_section_label: VCF Manipulation -- name: vcfannotategenotypes - owner: devteam - revisions: - - 70bc6ced57f7 - tool_panel_section_label: VCF Manipulation -- name: vcfbedintersect - owner: devteam - revisions: - - 9edfe5145ba8 - tool_panel_section_label: VCF Manipulation -- name: vcfbreakcreatemulti - owner: devteam - revisions: - - 690b1d846263 - tool_panel_section_label: VCF Manipulation -- name: vcfcheck - owner: devteam - revisions: - - 5e850c85ba32 - tool_panel_section_label: VCF Manipulation -- name: vcfcombine - owner: devteam - revisions: - - 53edb91ed051 - tool_panel_section_label: VCF Manipulation -- name: vcfcommonsamples - owner: devteam - revisions: - - 254f285dbaaa - tool_panel_section_label: VCF Manipulation -- name: vcfdistance - owner: devteam - revisions: - - 48e458c721b3 - tool_panel_section_label: VCF Manipulation -- name: vcffilter - owner: devteam - revisions: - - 6b935ab36d7b - tool_panel_section_label: VCF Manipulation -- name: vcffixup - owner: devteam - revisions: - - fc5a64fdd5b2 - tool_panel_section_label: VCF Manipulation -- name: vcfflatten - owner: devteam - revisions: - - b24e368ae7b1 - tool_panel_section_label: VCF Manipulation -- name: vcfgeno2haplo - owner: devteam - revisions: - - b890055e07bd - tool_panel_section_label: VCF Manipulation -- name: vcfgenotypes - owner: devteam - revisions: - - f5653ed90dfd - tool_panel_section_label: VCF Manipulation -- name: vcfhethom - owner: devteam - revisions: - - b07ef36cf7e6 - tool_panel_section_label: VCF Manipulation -- name: vcfleftalign - owner: devteam - revisions: - - d2406f98a782 - tool_panel_section_label: VCF Manipulation -- name: vcfprimers - owner: devteam - revisions: - - d226a7327946 - tool_panel_section_label: VCF Manipulation -- name: vcfrandomsample - owner: devteam - revisions: - - 12b570dd0bc5 - tool_panel_section_label: VCF Manipulation -- name: vcfselectsamples - owner: devteam - revisions: - - 958b6484a7f1 - tool_panel_section_label: VCF Manipulation -- name: vcfsort - owner: devteam - revisions: - - 5b7120c66efc - tool_panel_section_label: VCF Manipulation -- name: vcfvcfintersect - owner: devteam - revisions: - - 6f6bf10618d7 - tool_panel_section_label: VCF Manipulation diff --git a/usegalaxy.org.au/vcfbcf_tools.yml b/usegalaxy.org.au/vcfbcf_tools.yml deleted file mode 100644 index f19ccbb4..00000000 --- a/usegalaxy.org.au/vcfbcf_tools.yml +++ /dev/null @@ -1,70 +0,0 @@ -tool_panel_section_label: VCF/BCF Tools -tools: -- name: bcftools_roh - owner: iuc -- name: bcftools_stats - owner: iuc -- name: bcftools_annotate - owner: iuc -- name: bcftools_csq - owner: iuc -- name: bcftools_view - owner: iuc -- name: bcftools_plugin_setgt - owner: iuc -- name: bcftools_plugin_fill_an_ac - owner: iuc -- name: bcftools_convert_to_vcf - owner: iuc -- name: bcftools_filter - owner: iuc -- name: bcftools_plugin_fill_tags - owner: iuc -- name: bcftools_norm - owner: iuc -- name: bcftools_convert_from_vcf - owner: iuc -- name: bcftools_mpileup - owner: iuc -- name: bcftools_plugin_missing2ref - owner: iuc -- name: bcftools_cnv - owner: iuc -- name: bcftools_consensus - owner: iuc -- name: bcftools_query_list_samples - owner: iuc -- name: bcftools_reheader - owner: iuc -- name: bcftools_query - owner: iuc -- name: bcftools_plugin_fixploidy - owner: iuc -- name: bcftools_plugin_mendelian - owner: iuc -- name: bcftools_isec - owner: iuc -- name: bcftools_gtcheck - owner: iuc -- name: bcftools_plugin_counts - owner: iuc -- name: bcftools_plugin_impute_info - owner: iuc -- name: bcftools_plugin_tag2tag - owner: iuc -- name: bcftools_call - owner: iuc -- name: bcftools_concat - owner: iuc -- name: bcftools_merge - owner: iuc -- name: bcftools_plugin_dosage - owner: iuc -- name: vcftools_slice - owner: devteam -- name: vcftools_isec - owner: devteam -- name: vcftools_subset - owner: devteam -- name: vcftools_annotate - owner: devteam diff --git a/usegalaxy.org.au/vcfbcf_tools.yml.lock b/usegalaxy.org.au/vcfbcf_tools.yml.lock deleted file mode 100644 index 02605786..00000000 --- a/usegalaxy.org.au/vcfbcf_tools.yml.lock +++ /dev/null @@ -1,174 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: false -tools: -- name: bcftools_roh - owner: iuc - revisions: - - 5296d26b0373 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_stats - owner: iuc - revisions: - - b641062a2587 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_annotate - owner: iuc - revisions: - - 265fe0f9ea64 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_csq - owner: iuc - revisions: - - 7cbf3c66d4ad - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_view - owner: iuc - revisions: - - 3a233c8eb814 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_setgt - owner: iuc - revisions: - - 46eb13bc2c73 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_fill_an_ac - owner: iuc - revisions: - - 0a62420cb9cd - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_convert_to_vcf - owner: iuc - revisions: - - 1f2183a23823 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_filter - owner: iuc - revisions: - - 963a3635b2e1 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_fill_tags - owner: iuc - revisions: - - bca7ce81688f - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_norm - owner: iuc - revisions: - - a404f786a94c - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_convert_from_vcf - owner: iuc - revisions: - - 92c0aff8b53e - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_mpileup - owner: iuc - revisions: - - 9c711df3258d - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_missing2ref - owner: iuc - revisions: - - 96d0145c041a - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_cnv - owner: iuc - revisions: - - 8408bffd5616 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_consensus - owner: iuc - revisions: - - 1829900b5dcd - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_query_list_samples - owner: iuc - revisions: - - adee7e8b746f - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_reheader - owner: iuc - revisions: - - d43eb39b989e - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_query - owner: iuc - revisions: - - c9935c9e8a24 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_fixploidy - owner: iuc - revisions: - - 157ffcdd3fa7 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_mendelian - owner: iuc - revisions: - - a367a15c6de5 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_isec - owner: iuc - revisions: - - c803c34361e0 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_gtcheck - owner: iuc - revisions: - - 501bfb078342 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_counts - owner: iuc - revisions: - - 5ad5d4243987 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_impute_info - owner: iuc - revisions: - - 29ba253e2e05 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_tag2tag - owner: iuc - revisions: - - 0594ea1417c8 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_call - owner: iuc - revisions: - - b03984136ce4 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_concat - owner: iuc - revisions: - - f430a1ec7ee4 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_merge - owner: iuc - revisions: - - 85ee7e6c4204 - tool_panel_section_label: VCF/BCF Tools -- name: bcftools_plugin_dosage - owner: iuc - revisions: - - 0fe007201caf - tool_panel_section_label: VCF/BCF Tools -- name: vcftools_slice - owner: devteam - revisions: - - 1363e5d4a8b8 - tool_panel_section_label: VCF/BCF Tools -- name: vcftools_isec - owner: devteam - revisions: - - aa232e38338f - tool_panel_section_label: VCF/BCF Tools -- name: vcftools_subset - owner: devteam - revisions: - - 23436d1d0fa1 - tool_panel_section_label: VCF/BCF Tools -- name: vcftools_annotate - owner: devteam - revisions: - - 57a6550df582 - tool_panel_section_label: VCF/BCF Tools diff --git a/usegalaxy.org/annotation.yml b/usegalaxy.org/annotation.yml index fe009981..dfb6528d 100644 --- a/usegalaxy.org/annotation.yml +++ b/usegalaxy.org/annotation.yml @@ -50,8 +50,6 @@ tools: owner: iuc - name: progressivemauve owner: iuc -- name: repeat_masker - owner: bgruening - name: roary owner: iuc - name: snap_training @@ -70,3 +68,45 @@ tools: owner: iuc - name: transtermhp owner: iuc +- name: find_nested_alt_orfs + owner: iuc +- name: bicodon_counts_from_fasta + owner: iuc +- name: codon_freq_from_bicodons + owner: iuc +- name: antismash + owner: bgruening +- name: orfipy + owner: iuc +- name: sortmerna + owner: rnateam +- name: clinod + owner: peterjc +- name: read_it_and_keep + owner: iuc +- name: freyja_demix + owner: iuc +- name: freyja_aggregate_plot + owner: iuc +- name: cooc_mutbamscan + owner: iuc +- name: cooc_tabmut + owner: iuc +- name: repeatmodeler + owner: csbl +- name: red + owner: iuc +- name: funannotate_compare + owner: iuc +- name: funannotate_annotate + owner: iuc +- name: funannotate_predict + owner: iuc +- name: interproscan + owner: bgruening +- name: pfamscan + owner: bgruening +- name: cpat + owner: bgruening +- name: mitos2 + owner: iuc diff --git a/usegalaxy.org/annotation.yml.lock b/usegalaxy.org/annotation.yml.lock index 52cca4c3..e38c008a 100644 --- a/usegalaxy.org/annotation.yml.lock +++ b/usegalaxy.org/annotation.yml.lock @@ -6,10 +6,10 @@ tools: - name: prokka owner: crs4 revisions: + - 111884f0d912 - 8a22554cdde2 - bf68eb663bc3 - eaee459f3d69 - - 111884f0d912 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: abricate @@ -23,8 +23,9 @@ tools: - name: augustus owner: bgruening revisions: - - ca6d970d931c - 09855551d713 + - 28433faa6e42 + - ca6d970d931c tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: augustus_training @@ -32,6 +33,7 @@ tools: revisions: - 6519ebe25019 - 7be22100e5e1 + - dc027fa56d55 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: bp_genbank2gff3 @@ -50,12 +52,16 @@ tools: - name: busco owner: iuc revisions: + - 0d243f458b53 - 1e62c28ba91d + - 2a5b8b9936bf - 4048d82f0c88 + - 41030a6c03b7 + - 46ae58b1d792 - 602fb8e63aa7 + - 94170eee0ad8 - cf13a1e03e5b - - 0d243f458b53 - - 46ae58b1d792 + - e4bd1e99bacf tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: exonerate @@ -69,6 +75,7 @@ tools: owner: iuc revisions: - 239ce9f24386 + - b982a9ea939c tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: fgsea @@ -123,6 +130,7 @@ tools: owner: iuc revisions: - 637ec5d5368c + - 96e6283e4745 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: jcvi_gff_stats @@ -140,60 +148,57 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ade773848c3d - - d7540a923c7b + - 39b40a9a6296 + - 3f987772e283 - 438f65cb1d14 - 72aade318318 + - ade773848c3d + - ba6d2c32f797 + - d7540a923c7b tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: maker_map_ids owner: iuc revisions: + - 2e3535db1bfa - 326f9c294b09 - e408aa831db3 - - 2e3535db1bfa + - e906fa778440 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: maker owner: iuc revisions: + - 370c210d9541 + - 3c1a01127868 - 5e96efe6e6c6 - d46d803ca6cc - - 3c1a01127868 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: mlst owner: iuc revisions: - 1f5641a52664 + - 31812e7a1315 - ded48b36f3b7 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: progressivemauve owner: iuc revisions: - - bdb752f3c6bb - 97a43bcbf44d + - bdb752f3c6bb - ce795616bd9c tool_panel_section_id: annotation tool_panel_section_label: Annotation -- name: repeat_masker - owner: bgruening - revisions: - - ade773848c3d - - d7540a923c7b - - 438f65cb1d14 - - 72aade318318 - tool_panel_section_id: annotation - tool_panel_section_label: Annotation - name: roary owner: iuc revisions: - - 91887494eb97 - - 809e42326fc2 - - dbe2b2204555 - 15ac71df11a0 - 78608ec02d62 + - 809e42326fc2 + - 91887494eb97 + - dbe2b2204555 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: snap_training @@ -211,33 +216,39 @@ tools: - name: spaln owner: iuc revisions: - - 95ea8d97abb4 + - 2e92e1929cb1 - 37b5e1f0b544 + - 95ea8d97abb4 - dd0cd2319ae5 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: tbprofiler owner: iuc revisions: - - 200c378d85f3 - - c2656b729ee9 - 037a11682176 - - ba6f87115e13 + - 200c378d85f3 + - 2c68b0c38785 - 809dfc93d593 + - ac8250086ac3 + - ba6f87115e13 + - c2656b729ee9 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: tb_variant_filter owner: iuc revisions: + - 32f14a2723ec - 3b1e7c170b10 - 40f0591deda0 - e7aff4a85df5 + - ee4a90760848 tool_panel_section_id: annotation tool_panel_section_label: Annotation - name: tbvcfreport owner: iuc revisions: - 02d81b994ef5 + - 4934c0ac6197 - adc0645b945c tool_panel_section_id: annotation tool_panel_section_label: Annotation @@ -255,3 +266,164 @@ tools: - 012171ba9fce tool_panel_section_id: annotation tool_panel_section_label: Annotation +- name: find_nested_alt_orfs + owner: iuc + revisions: + - 14f4c7a8a962 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: bicodon_counts_from_fasta + owner: iuc + revisions: + - e13169dca7c8 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: codon_freq_from_bicodons + owner: iuc + revisions: + - cc5a776acd47 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: antismash + owner: bgruening + revisions: + - 3f0077c88c16 + - 5784e268efca + - 593bb8f5488b + - 5db064bbb3be + - bc88856eddab + - e78e25d3b4bd + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: orfipy + owner: iuc + revisions: + - 45d4d26e01b5 + - c147914c9f02 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: sortmerna + owner: rnateam + revisions: + - 10b84b577117 + - 1eafcc450052 + - 65c38d020fea + - eb35257d2e29 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: clinod + owner: peterjc + revisions: + - 4863b1dbe8f0 + - 77cfe958b5ea + - f61366a4a14e + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: read_it_and_keep + owner: iuc + revisions: + - 1563b58905f4 + - 554aa2a63f04 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: freyja_demix + owner: iuc + revisions: + - c0a0e79d7196 + - fc6252e78d5b + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: freyja_aggregate_plot + owner: iuc + revisions: + - 0ceb9fb0f4ce + - 1f89eeba299a + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: cooc_mutbamscan + owner: iuc + revisions: + - 373c1735d31f + - 9f1660129403 + - cd0484c5f9f1 + - d58a57db7a96 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: cooc_tabmut + owner: iuc + revisions: + - 4be399803856 + - 52bd683c6d3f + - 579538ff939d + - eeb5c054ecf8 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: repeatmodeler + owner: csbl + revisions: + - 8661b2607b7e + - fbe22cb3c869 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: red + owner: iuc + revisions: + - 18a46265455b + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: funannotate_compare + owner: iuc + revisions: + - 30f08d74024f + - 57c6718cbfcc + - a7ce2601500c + - b69c46064ec7 + - e94187d661df + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: funannotate_annotate + owner: iuc + revisions: + - 3bbe70fef6df + - 582fd74dc2a1 + - 756376aeb1ae + - 9feee7fc49a1 + - d0336d67702b + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: funannotate_predict + owner: iuc + revisions: + - 1bc5a03faf2e + - 51b6ee65ef7f + - f31125bb85ea + - f77d7b685bb3 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: interproscan + owner: bgruening + revisions: + - 74810db257cc + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: pfamscan + owner: bgruening + revisions: + - 15cff34c2005 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: cpat + owner: bgruening + revisions: + - 8e9e228c54c4 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: mitos2 + owner: iuc + revisions: + - 033755194fe9 + - af3c1dc1d141 + - b815ec682418 + - e95d52d295d7 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation diff --git a/usegalaxy.org/assembly.yml b/usegalaxy.org/assembly.yml index c07a77c0..c6e350eb 100644 --- a/usegalaxy.org/assembly.yml +++ b/usegalaxy.org/assembly.yml @@ -24,6 +24,18 @@ tools: owner: iuc - name: rnaspades owner: iuc +- name: spades_rnaviralspades + owner: iuc +- name: spades_metaplasmidspades + owner: iuc +- name: spades_coronaspades + owner: iuc +- name: spades_biosyntheticspades + owner: iuc +- name: spades_plasmidspades + owner: iuc +- name: spades_metaviralspades + owner: iuc - name: shovill owner: iuc - name: spades @@ -52,3 +64,15 @@ tools: owner: iuc - name: pretext_snapshot owner: iuc +- name: gfastats + owner: bgruening +- name: yahs + owner: iuc +- name: smudgeplot + owner: galaxy-australia +- name: velvet + owner: devteam +- name: aegean_parseval + owner: iuc +- name: mitohifi + owner: bgruening \ No newline at end of file diff --git a/usegalaxy.org/assembly.yml.lock b/usegalaxy.org/assembly.yml.lock index 709834c6..8838e1bc 100644 --- a/usegalaxy.org/assembly.yml.lock +++ b/usegalaxy.org/assembly.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Assembly tools: @@ -7,17 +7,23 @@ tools: owner: iuc revisions: - 0a3a602cd1e3 + - 6e26c9afd301 - 88c240872a65 + - 8f9f06995f98 - 9e3e80cc4ad4 + - d10bdad2fd17 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: quast owner: iuc revisions: + - 3061c8b029e5 - 59db8ea8c845 - - ebb0dcdb621a + - 675488238c96 + - 72472698a2df - 7594365c546b - 875d0f36d66f + - ebb0dcdb621a tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: trinity_psc @@ -36,6 +42,7 @@ tools: - name: idba_hybrid owner: iuc revisions: + - 5c5806e23338 - 5ece301faf6b - a81c5169e9fc tool_panel_section_id: assembly @@ -43,6 +50,7 @@ tools: - name: idba_tran owner: iuc revisions: + - 03de4e0f84c2 - 33f00ff1cb22 - a30d991a3fdd tool_panel_section_id: assembly @@ -50,6 +58,7 @@ tools: - name: idba_ud owner: iuc revisions: + - 1542a2fffe0c - 2ed5c0795f99 - 694b0f55b744 tool_panel_section_id: assembly @@ -57,25 +66,28 @@ tools: - name: megahit owner: iuc revisions: + - 14ddfc8ffb93 - 7518ee87b53d + - a96f3ad4e0d8 - de387b2b2803 - - 14ddfc8ffb93 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: metaspades owner: nml revisions: - 05c394313b1c + - e731ea24e48d + - fd128c111ab0 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: miniasm owner: iuc revisions: - 2dcd07f40204 + - 80d1250bd5fd - 8b6d0d85252b - 8dee0218ac7d - a7b889b90140 - - 80d1250bd5fd tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: pilon @@ -88,24 +100,92 @@ tools: owner: iuc revisions: - 03fd468e158f - - 9e58ff014088 - - a8a278849c18 - 1035adb112c0 + - 1d06c8b38e77 + - 28189050e437 - 53c2bc8c2ae3 + - 675ee1aa5952 + - 9e58ff014088 + - a8a278849c18 + - e122f9101584 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: spades_rnaviralspades + owner: iuc + revisions: + - 48cf45a53456 + - b65a43f70b99 + - d159735a6a9f + - d5fb354f745d + - de1260f8a300 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: spades_metaplasmidspades + owner: iuc + revisions: + - 037f9927c4ff + - 4a01e0d2892c + - 6b5a5842531e + - b8002c3f7141 + - e5a3b75a271f + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: spades_coronaspades + owner: iuc + revisions: + - 34305b013402 + - 9678993ca5bd + - ad8b536d1caa + - d6e617c4e338 + - ff41a00a6745 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: spades_biosyntheticspades + owner: iuc + revisions: + - 051fd2db8a27 + - 604782a8a53a + - 7490b213baa9 + - 904bf932cf78 + - d89ced9439f3 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: spades_plasmidspades + owner: iuc + revisions: + - 1708851f8804 + - 340bc17f49cf + - 75405f5e2cc5 + - 7bb235ff0746 + - 85fb02c43042 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: spades_metaviralspades + owner: iuc + revisions: + - 2a10645aeadd + - 328aa71f0f3c + - 5b26685e5d3b + - 9de69775f512 + - e060c3987513 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: shovill owner: iuc revisions: + - 2a9baa0c4316 - 83ead2be47b2 - 8d1af5db538d + - ad80238462c1 - d9f6a00b6db7 - - 2a9baa0c4316 + - ee17a294d3a3 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: spades owner: nml revisions: + - 33368fec3b70 + - 7897763d14ec - b8c00ce5dfa0 tool_panel_section_id: assembly tool_panel_section_label: Assembly @@ -113,75 +193,102 @@ tools: owner: iuc revisions: - 067592b6b312 + - 21e491ad532a - 94fe43e75ddc - b2860df42e16 - b9e31c5c01c7 + - ddddce450736 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: racon owner: bgruening revisions: - - aa39b19ca11e + - 39bed8de8017 + - 78c533842eeb - 7c847ec300b8 + - 936f0b5e7fcc + - a199cd7ac344 + - aa39b19ca11e + - e100a765370e tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: hifiasm owner: bgruening revisions: + - 045c7c3d8e59 + - 0ee0c3089254 + - 366a11d316a7 + - 3f7be05a1597 + - 5bec28269d95 + - 5f625c63b8bc - 6505bd37670d - - bf0a4667e3ce + - 71740308d412 - 9ef6920c3089 - - 045c7c3d8e59 + - bf0a4667e3ce + - df25d4fb79b7 + - f3c89da3af16 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: purge_dups owner: iuc revisions: - 29151e779524 - - cf13a1e03e5b - 76d4cbefff85 - a315c25dc813 + - cf13a1e03e5b + - e9bd16ba5ebd tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: meryl owner: iuc revisions: + - 29dabd8db6f2 - 31fa26c0692b - 5ae3496f9ca3 + - 9cd178127b19 - eadfd71dde37 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: merqury owner: iuc revisions: - - 9d79beb19ac3 + - 09c589057ee8 - 39edec572bae + - 589078edd230 + - 9d79beb19ac3 + - d7edbc9c3a07 + - f8113c25bc6b tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: genomescope owner: iuc revisions: - - b2f674562a18 + - 01210c4e9144 - 3169a38c2656 + - b2f674562a18 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: bionano_scaffold owner: bgruening revisions: - - 96cacb31d571 + - 3371c5bdc17a - 5258e18bbe23 + - 96cacb31d571 + - faee8629b460 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: bellerophon owner: iuc revisions: - - eca6296a091a - 25ca5d73aedf + - 321347bd0494 + - eca6296a091a tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: salsa owner: iuc revisions: + - 9a22227bb6d0 - ba7b0f11e470 - f77f7a7f3b83 tool_panel_section_id: assembly @@ -190,15 +297,66 @@ tools: owner: iuc revisions: - 02831bf9e95f - - 8fef980d48b5 - 2b16ba799da9 + - 511e5e3cd55e + - 79b48f02db49 + - 8fef980d48b5 - dfb8a4497339 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 + - 0a10fddd97d2 - 44c66e8d21e6 + - 6c571966cfb9 + - 7c9417381ad5 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: gfastats + owner: bgruening + revisions: + - 2b8b4cacb83d + - 3ef480892a9f + - 3fba9c77550a + - 5127a713de83 + - 5799092ffdff + - 690c2caa367e + - 8ccbf07a5433 + - ad1149b4f795 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: yahs + owner: iuc + revisions: + - 39495e107274 + - 425e63adcc5d + - d87433f2a54d + - fc925f53cae7 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: smudgeplot + owner: galaxy-australia + revisions: + - 24e471d13fe9 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: velvet + owner: devteam + revisions: + - 920677cd220f + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: aegean_parseval + owner: iuc + revisions: + - 1b52f0c8ad7f + - d6c074a93c51 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: mitohifi + owner: bgruening + revisions: + - 99ddbf037d98 tool_panel_section_id: assembly tool_panel_section_label: Assembly diff --git a/usegalaxy.org/bbtools.yml b/usegalaxy.org/bbtools.yml new file mode 100644 index 00000000..47b7f9ca --- /dev/null +++ b/usegalaxy.org/bbtools.yml @@ -0,0 +1,14 @@ +tool_panel_section_label: BBTools +tools: +- name: bbtools_bbduk + owner: iuc +- name: bbtools_bbmap + owner: iuc +- name: bbtools_bbmerge + owner: iuc +- name: bbtools_bbnorm + owner: iuc +- name: bbtools_callvariants + owner: iuc +- name: bbtools_tadpole + owner: iuc diff --git a/usegalaxy.org/bbtools.yml.lock b/usegalaxy.org/bbtools.yml.lock new file mode 100644 index 00000000..97cda460 --- /dev/null +++ b/usegalaxy.org/bbtools.yml.lock @@ -0,0 +1,47 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: BBTools +tools: +- name: bbtools_bbduk + owner: iuc + revisions: + - 0840ba83860c + - 159b04e36791 + tool_panel_section_id: bbtools + tool_panel_section_label: BBTools +- name: bbtools_bbmap + owner: iuc + revisions: + - 3171f7f52576 + - 517464809c33 + tool_panel_section_id: bbtools + tool_panel_section_label: BBTools +- name: bbtools_bbmerge + owner: iuc + revisions: + - 6d084528a6f1 + - c05232655d00 + tool_panel_section_id: bbtools + tool_panel_section_label: BBTools +- name: bbtools_bbnorm + owner: iuc + revisions: + - 1ef267476a17 + - a9329b77db78 + tool_panel_section_id: bbtools + tool_panel_section_label: BBTools +- name: bbtools_callvariants + owner: iuc + revisions: + - adec76ebc868 + - ee407fae3ccd + tool_panel_section_id: bbtools + tool_panel_section_label: BBTools +- name: bbtools_tadpole + owner: iuc + revisions: + - 20aef74d20a1 + - e4fb34b79770 + tool_panel_section_id: bbtools + tool_panel_section_label: BBTools diff --git a/usegalaxy.org/bed.yml b/usegalaxy.org/bed.yml index a97a3e41..e04f1435 100644 --- a/usegalaxy.org/bed.yml +++ b/usegalaxy.org/bed.yml @@ -2,3 +2,5 @@ tool_panel_section_label: BED tools: - name: bedtools owner: iuc +- name: bedops_sortbed + owner: iuc diff --git a/usegalaxy.org/bed.yml.lock b/usegalaxy.org/bed.yml.lock index 21df6250..ad4bfc43 100644 --- a/usegalaxy.org/bed.yml.lock +++ b/usegalaxy.org/bed.yml.lock @@ -1,15 +1,23 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: BED tools: - name: bedtools owner: iuc revisions: + - 07e8b80f278c - 0a5c785ac6db + - 7ab85ac5f64b + - a1a923cd89e8 - b28e0cfa7ba1 - ce3c7f062223 - fe5b4cb8356c - - 7ab85ac5f64b + tool_panel_section_id: bed + tool_panel_section_label: BED +- name: bedops_sortbed + owner: iuc + revisions: + - baeee32175e8 tool_panel_section_id: bed tool_panel_section_label: BED diff --git a/usegalaxy.org/biodiversity_data_exploration.yml b/usegalaxy.org/biodiversity_data_exploration.yml new file mode 100644 index 00000000..c2e47ad0 --- /dev/null +++ b/usegalaxy.org/biodiversity_data_exploration.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Biodiversity data exploration +tools: +- name: obisindicators + owner: ecology diff --git a/usegalaxy.org/biodiversity_data_exploration.yml.lock b/usegalaxy.org/biodiversity_data_exploration.yml.lock new file mode 100644 index 00000000..236092b2 --- /dev/null +++ b/usegalaxy.org/biodiversity_data_exploration.yml.lock @@ -0,0 +1,11 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Biodiversity data exploration +tools: +- name: obisindicators + owner: ecology + revisions: + - 4e7c1fb5e894 + tool_panel_section_id: biodiversity_data_exploration + tool_panel_section_label: Biodiversity data exploration diff --git a/usegalaxy.org/chemicaltoolbox.yml b/usegalaxy.org/chemicaltoolbox.yml index 350ab150..6ec96883 100644 --- a/usegalaxy.org/chemicaltoolbox.yml +++ b/usegalaxy.org/chemicaltoolbox.yml @@ -38,6 +38,8 @@ tools: owner: chemteam - name: gmx_merge_topology_files owner: chemteam +- name: gmx_energy + owner: chemteam - name: parmconv owner: chemteam - name: md_converter @@ -50,3 +52,191 @@ tools: owner: chemteam - name: mmpbsa_mmgbsa owner: chemteam +- name: openms_openpepxl + owner: galaxyp +- name: gmx_get_builtin_file + owner: chemteam +- name: gmx_rg + owner: chemteam +- name: gmx_restraints + owner: chemteam +- name: gmx_trj + owner: chemteam +- name: alphafold2 + owner: galaxy-australia +- name: gromacs_extract_topology + owner: chemteam +- name: tleap + owner: chemteam +- name: rdconf + owner: bgruening +- name: traj_selections_and_merge + owner: chemteam +- name: autodock_vina + owner: bgruening +- name: acpype_amber2gromacs + owner: chemteam +- name: ambertools_parmchk2 + owner: chemteam +- name: fpocket + owner: bgruening +- name: align_it + owner: bgruening +- name: autodock_vina_prepare_box + owner: bgruening +- name: gmx_md + owner: chemteam +- name: chembl + owner: bgruening +- name: openbabel_subsearch + owner: bgruening +- name: biomd_rmsd_clustering + owner: chemteam +- name: biomd_extract_clusters + owner: chemteam +- name: mdanalysis_extract_rmsd + owner: chemteam +- name: openbabel_addh + owner: bgruening +- name: openbabel_remions + owner: bgruening +- name: chembl_structure_pipeline + owner: bgruening +- name: qed + owner: bgruening +- name: gromacs_modify_topology + owner: chemteam +- name: openbabel_remove_protonation_state + owner: bgruening +- name: mdanalysis_ramachandran_protein + owner: chemteam +- name: mdanalysis_endtoend + owner: chemteam +- name: mdanalysis_cosine_analysis + owner: chemteam +- name: mdanalysis_hbonds + owner: chemteam +- name: mdanalysis_ramachandran_plot + owner: chemteam +- name: mdanalysis_distance + owner: chemteam +- name: mdanalysis_dihedral + owner: chemteam +- name: openbabel_change_title + owner: bgruening +- name: mdanalysis_rdf + owner: chemteam +- name: openbabel_spectrophore_search + owner: bgruening +- name: mdanalysis_angle + owner: chemteam +- name: apoc + owner: earlhaminst +- name: smina + owner: earlhaminst +- name: autodock_vina_prepare_receptor + owner: bgruening +- name: sdf_to_tab + owner: bgruening +- name: mordred + owner: bgruening +- name: get_pubchem + owner: bgruening +- name: autodock_vina_prepare_ligand + owner: bgruening +- name: openbabel_remduplicates + owner: bgruening +- name: openbabel_filter + owner: bgruening +- name: openbabel_svg_depiction + owner: bgruening +- name: openbabel_genprop + owner: bgruening +- name: openbabel_obgrep + owner: bgruening +- name: openbabel_remsmall + owner: bgruening +- name: prepare_ligands_for_docking + owner: bgruening +- name: sucos_clustering + owner: bgruening +- name: sucos_max_score + owner: bgruening +- name: openbabel_structure_distance_finder + owner: bgruening +- name: rdock_rbcavity + owner: bgruening +- name: rdock_rbdock + owner: bgruening +- name: rxdock_sort_filter + owner: bgruening +- name: ctb_im_pbf_ev + owner: bgruening +- name: ctb_im_rxn_smarts_filter + owner: bgruening +- name: ctb_im_conformers + owner: bgruening +- name: ctb_im_constrained_conf_gen + owner: bgruening +- name: ctb_im_cluster_butina_matrix + owner: bgruening +- name: ctb_im_o3dalign + owner: bgruening +- name: ctb_im_standardize + owner: bgruening +- name: ctb_im_cluster_butina + owner: bgruening +- name: ctb_im_max_min_picker + owner: bgruening +- name: ctb_im_rxn_maker + owner: bgruening +- name: ctb_im_screen + owner: bgruening +- name: ctb_im_xcos + owner: bgruening +- name: featurestein + owner: bgruening +- name: openduck_chunk + owner: bgruening +- name: openduck_run_smd + owner: bgruening +- name: xchem_transfs_scoring + owner: bgruening +- name: fastpca + owner: chemteam +- name: alchemical_analysis + owner: chemteam +- name: goseq + owner: iuc +- name: vmd_hbonds + owner: chemteam +- name: bio3d_pca_visualize + owner: chemteam +- name: bio3d_rmsf + owner: chemteam +- name: bio3d_pca + owner: chemteam +- name: bio3d_rmsd + owner: chemteam +- name: bio3d_dccm + owner: chemteam +- name: packmol + owner: chemteam +- name: padel + owner: bgruening +- name: openbabel_multi_obgrep + owner: bgruening +- name: openbabel + owner: bgruening +- name: osra + owner: bgruening +- name: natural_product_likeness + owner: bgruening +- name: simsearch + owner: bgruening +- name: confab + owner: bgruening +- name: ctb_machine_learning + owner: bgruening +- name: openmg + owner: bgruening diff --git a/usegalaxy.org/chemicaltoolbox.yml.lock b/usegalaxy.org/chemicaltoolbox.yml.lock index 2eeba069..22ac1069 100644 --- a/usegalaxy.org/chemicaltoolbox.yml.lock +++ b/usegalaxy.org/chemicaltoolbox.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: ChemicalToolBox tools: @@ -12,7 +12,7 @@ tools: - name: chemfp owner: bgruening revisions: - - 43a9e7d9b24f + - 3b14765c22ee tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: get_pdb @@ -54,18 +54,19 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - bbbf5fb356dd + - 67ee76f0e497 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: ctb_rdkit_descriptors owner: bgruening revisions: - - a1c53f0533b0 + - 0993ac4f4a23 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: openbabel_compound_convert owner: bgruening revisions: + - b59c91adeac1 - e2c36f62e22f tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox @@ -78,61 +79,107 @@ tools: - name: gmx_setup owner: chemteam revisions: + - 070e3ecc3fda + - 2c349b027a01 - 4da9ee404eab + - a66c193fafdb + - cac1886249a2 + - ed736e6eee39 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: gmx_editconf owner: chemteam revisions: + - 0fac8e2afc13 + - 3b8a9d5ced85 + - 79cfd9ead848 + - 88076940fa94 + - b9e25ec471eb - bfb65cb551d8 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: gmx_solvate owner: chemteam revisions: + - 1809414a9454 - 27ea4e1a3f95 + - 2c8ed1b52bf7 + - 598e0078040b + - 61094e01eff9 + - 7568ae18908a + - 8ad46f918541 + - c4fbab8e03c5 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: gmx_em owner: chemteam revisions: + - 1b46398cc8ca - 55918daa5651 + - 59c662ca4211 + - b46d4b4d995c + - eb6564a60136 + - f5d979cb4b54 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: gmx_sim owner: chemteam revisions: - - a97dcfc23b4b + - 2e219a2d9327 + - 525ca7c8065f + - 73008ef1f487 + - b7cebf442209 + - c0c9a5024177 + - f197e34c33a9 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: gmx_makendx owner: chemteam revisions: - 5f9f51642a24 + - 9acc0fc74373 + - e3e536aa2633 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: gmx_merge_topology_files owner: chemteam revisions: + - 04abdf96978b + - 319a28774da9 - 534ff13ea227 + - bc31d02be922 + - d1d0efda35c0 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: gmx_energy + owner: chemteam + revisions: + - 593c63b5aff8 + - d2f955aea23a + - f26afd1b7104 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: parmconv owner: chemteam revisions: - - 5a97cb53a456 + - 6d0677a148fe tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: md_converter owner: chemteam revisions: + - 79e8ab8f1e81 - ba83f0923369 + - d7ec25187599 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: ambertools_acpype owner: chemteam revisions: + - 095ad4d096d1 + - 6ca543ec1bf8 - a0c154146234 + - f4230f116196 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: biomd_neqgamma @@ -145,11 +192,593 @@ tools: owner: chemteam revisions: - 4fff93efc0f9 + - 8a839e6a1e3e tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: mmpbsa_mmgbsa owner: chemteam revisions: - - 45dc2555933c + - 608098b3668d + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openms_openpepxl + owner: galaxyp + revisions: + - 4d2b77fd7a28 + - fc36cfd19834 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: gmx_get_builtin_file + owner: chemteam + revisions: + - 124c21408519 + - 42dfec375136 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: gmx_rg + owner: chemteam + revisions: + - 2b19cec3cca9 + - b01f3db44534 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: gmx_restraints + owner: chemteam + revisions: + - 25b8272872c8 + - 509aa136d4e3 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: gmx_trj + owner: chemteam + revisions: + - 32052c6c3310 + - 72459c3ea5f6 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: alphafold2 + owner: galaxy-australia + revisions: + - 5b85006245f3 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: gromacs_extract_topology + owner: chemteam + revisions: + - 9faa4f4b8b76 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: tleap + owner: chemteam + revisions: + - 3de1359b86cc + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: rdconf + owner: bgruening + revisions: + - 5c501eb8d56c + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: traj_selections_and_merge + owner: chemteam + revisions: + - a26c4750c7c7 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: autodock_vina + owner: bgruening + revisions: + - 90ea16534012 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: acpype_amber2gromacs + owner: chemteam + revisions: + - 5b4ae74b7f0b + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ambertools_parmchk2 + owner: chemteam + revisions: + - ecc43bf27a49 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: fpocket + owner: bgruening + revisions: + - 4cc9d85c3bae + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: align_it + owner: bgruening + revisions: + - 06d9381593a4 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: autodock_vina_prepare_box + owner: bgruening + revisions: + - 8f766d9652a2 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: gmx_md + owner: chemteam + revisions: + - 2e28934c1d8c + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: chembl + owner: bgruening + revisions: + - a446ea7e2bc1 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_subsearch + owner: bgruening + revisions: + - c19608db6b15 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: biomd_rmsd_clustering + owner: chemteam + revisions: + - b9c46dbe9605 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: biomd_extract_clusters + owner: chemteam + revisions: + - e0ecaf2d05fb + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: mdanalysis_extract_rmsd + owner: chemteam + revisions: + - 589f8ef21e58 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_addh + owner: bgruening + revisions: + - 6e4b7e0c61a6 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_remions + owner: bgruening + revisions: + - 4e3b2049a4d3 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: chembl_structure_pipeline + owner: bgruening + revisions: + - 2f59c6239f25 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: qed + owner: bgruening + revisions: + - 52a8d34dd08f + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: gromacs_modify_topology + owner: chemteam + revisions: + - 5521a057ed6a + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_remove_protonation_state + owner: bgruening + revisions: + - e376ba0fcde0 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: mdanalysis_ramachandran_protein + owner: chemteam + revisions: + - 060b9d9ec8cf + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: mdanalysis_endtoend + owner: chemteam + revisions: + - 795a5996cdc8 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: mdanalysis_cosine_analysis + owner: chemteam + revisions: + - 48d6a6eb438b + - 9a3a1f698fc6 + - ebeb72aa39a8 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: mdanalysis_hbonds + owner: chemteam + revisions: + - b17ce46509ad + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: mdanalysis_ramachandran_plot + owner: chemteam + revisions: + - be5eaea0b2d1 + - d710c7f00ae6 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: mdanalysis_distance + owner: chemteam + revisions: + - 489b25966bb9 + - fd987ff06ceb + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: mdanalysis_dihedral + owner: chemteam + 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tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_filter + owner: bgruening + revisions: + - df4dc55197dd + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_svg_depiction + owner: bgruening + revisions: + - 7672039a0bb0 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_genprop + owner: bgruening + revisions: + - b249bf9be0d1 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_obgrep + owner: bgruening + revisions: + - 274193d6c443 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_remsmall + owner: bgruening + revisions: + - d7f0ca1f2669 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: prepare_ligands_for_docking + owner: bgruening + revisions: + - 5486f7a2b0cb + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: sucos_clustering + owner: bgruening + revisions: + - b8725fec8c7b + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: sucos_max_score + owner: bgruening + revisions: + - 9b48456a96fe + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_structure_distance_finder + owner: bgruening + revisions: + - 2c5c7da26e08 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: rdock_rbcavity + owner: bgruening + revisions: + - 7e5c2e4bc227 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: rdock_rbdock + owner: bgruening + revisions: + - c362398df83b + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: rxdock_sort_filter + owner: bgruening + revisions: + - 3e4244e74d41 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_pbf_ev + owner: bgruening + revisions: + - 1c7a7b74f677 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_rxn_smarts_filter + owner: bgruening + revisions: + - d219d934cf1c + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_conformers + owner: bgruening + revisions: + - a4b1474efada + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_constrained_conf_gen + owner: bgruening + revisions: + - ac204d3f7312 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_cluster_butina_matrix + owner: bgruening + revisions: + - d804c6e6d5ad + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_o3dalign + owner: bgruening + revisions: + - 46fe89ea20ef + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_standardize + owner: bgruening + revisions: + - 8ac4f037fdde + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_cluster_butina + owner: bgruening + revisions: + - 65316a9205f5 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_max_min_picker + owner: bgruening + revisions: + - a20b87a3dc19 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_rxn_maker + owner: bgruening + revisions: + - 8ef5428fb809 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_screen + owner: bgruening + revisions: + - 05cc95060024 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_im_xcos + owner: bgruening + revisions: + - 9b6210854c8c + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: featurestein + owner: bgruening + revisions: + - 0eb24d808e75 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openduck_chunk + owner: bgruening + revisions: + - 89c3bd4f50a3 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openduck_run_smd + owner: bgruening + revisions: + - 05c95b16823b + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: xchem_transfs_scoring + owner: bgruening + revisions: + - f6f9b47d02b6 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: fastpca + owner: chemteam + revisions: + - 9ca30ad95444 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: alchemical_analysis + owner: chemteam + revisions: + - c1fa72716efc + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: goseq + owner: iuc + revisions: + - 43798b4caee0 + - 602de62d995b + - 8b3e3657034e + - ef2ad746b589 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: vmd_hbonds + owner: chemteam + revisions: + - 8aa5e465b043 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: bio3d_pca_visualize + owner: chemteam + revisions: + - f61a718993fd + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: bio3d_rmsf + owner: chemteam + revisions: + - 4354d92dc1aa + - 6bcb804a54c3 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: bio3d_pca + owner: chemteam + revisions: + - 24867ab16f36 + - 994c509873db + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: bio3d_rmsd + owner: chemteam + revisions: + - 77e28e1da9f4 + - f871c9a8cb7c + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: bio3d_dccm + owner: chemteam + revisions: + - c9ae0c833ded + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: packmol + owner: chemteam + revisions: + - 539fb45630e6 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: padel + owner: bgruening + revisions: + - a84bcb007b09 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel_multi_obgrep + owner: bgruening + revisions: + - 09640954740c + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openbabel + owner: bgruening + revisions: + - 125da3a296ca + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: osra + owner: bgruening + revisions: + - b2edf498e8fb + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: natural_product_likeness + owner: bgruening + revisions: + - 6052dd3fa475 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: simsearch + owner: bgruening + revisions: + - 425469deb136 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: confab + owner: bgruening + revisions: + - 461f64330945 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: ctb_machine_learning + owner: bgruening + revisions: + - fe542273784f + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: openmg + owner: bgruening + revisions: + - 473a07404e83 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox diff --git a/usegalaxy.org/chip_seq.yml.lock b/usegalaxy.org/chip_seq.yml.lock index 16c68be0..bcbf8c63 100644 --- a/usegalaxy.org/chip_seq.yml.lock +++ b/usegalaxy.org/chip_seq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: ChIP-seq tools: @@ -7,6 +7,7 @@ tools: owner: rnateam revisions: - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_id: chip_seq tool_panel_section_label: ChIP-seq - name: cwpair2 @@ -25,13 +26,15 @@ tools: owner: iuc revisions: - 424aefbd7777 + - 640d3af5d833 + - 86e2413cf3f8 tool_panel_section_id: chip_seq tool_panel_section_label: ChIP-seq - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 tool_panel_section_id: chip_seq tool_panel_section_label: ChIP-seq - name: ngsutils_bam_filter @@ -49,7 +52,9 @@ tools: - name: diffbind owner: bgruening revisions: + - 163688bb8f73 - 194e3f2c1d86 + - 2605cbdaa7d8 tool_panel_section_id: chip_seq tool_panel_section_label: ChIP-seq - name: tag_pileup_frequency diff --git a/usegalaxy.org/chromosome_conformation.yml.lock b/usegalaxy.org/chromosome_conformation.yml.lock index 30cd3d9e..5bbe2efa 100644 --- a/usegalaxy.org/chromosome_conformation.yml.lock +++ b/usegalaxy.org/chromosome_conformation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Chromosome Conformation tools: diff --git a/usegalaxy.org/climate_analysis.yml b/usegalaxy.org/climate_analysis.yml index b50848ca..495cf3f0 100644 --- a/usegalaxy.org/climate_analysis.yml +++ b/usegalaxy.org/climate_analysis.yml @@ -2,3 +2,7 @@ tool_panel_section_label: Climate Analysis tools: - name: ctsm_fates owner: climate +- name: climate_stripes + owner: climate +- name: c3s + owner: climate diff --git a/usegalaxy.org/climate_analysis.yml.lock b/usegalaxy.org/climate_analysis.yml.lock index 531767dc..22f0185a 100644 --- a/usegalaxy.org/climate_analysis.yml.lock +++ b/usegalaxy.org/climate_analysis.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Climate Analysis tools: @@ -9,3 +9,15 @@ tools: - b525b88bc941 tool_panel_section_id: climate_analysis tool_panel_section_label: Climate Analysis +- name: climate_stripes + owner: climate + revisions: + - c6f2435d680b + tool_panel_section_id: climate_analysis + tool_panel_section_label: Climate Analysis +- name: c3s + owner: climate + revisions: + - 250554670f72 + tool_panel_section_id: climate_analysis + tool_panel_section_label: Climate Analysis diff --git a/usegalaxy.org/cloudmap__deprecated_.yml.lock b/usegalaxy.org/cloudmap__deprecated_.yml.lock index bcb39a58..f6fde597 100644 --- a/usegalaxy.org/cloudmap__deprecated_.yml.lock +++ b/usegalaxy.org/cloudmap__deprecated_.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: CloudMap (deprecated) tools: diff --git a/usegalaxy.org/collection_operations.yml.lock b/usegalaxy.org/collection_operations.yml.lock index 4e89945f..88acad69 100644 --- a/usegalaxy.org/collection_operations.yml.lock +++ b/usegalaxy.org/collection_operations.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Collection Operations tools: @@ -27,9 +27,10 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - e77b954f0da5 - - d57735dd27b0 - 0046692724f9 - 6cbe2f30c2d7 + - baabc30154cd + - d57735dd27b0 + - e77b954f0da5 tool_panel_section_id: collection_operations tool_panel_section_label: Collection Operations diff --git a/usegalaxy.org/compose_text_param.yml b/usegalaxy.org/compose_text_param.yml deleted file mode 100644 index 2324c832..00000000 --- a/usegalaxy.org/compose_text_param.yml +++ /dev/null @@ -1,4 +0,0 @@ -tool_panel_section_id: expression_tools -tools: - - name: compose_text_param - owner: iuc diff --git a/usegalaxy.org/compose_text_param.yml.lock b/usegalaxy.org/compose_text_param.yml.lock deleted file mode 100644 index 13948886..00000000 --- a/usegalaxy.org/compose_text_param.yml.lock +++ /dev/null @@ -1,11 +0,0 @@ -install_repository_dependencies: false -install_resolver_dependencies: true -install_tool_dependencies: false -tool_panel_section_id: expression_tools -tools: -- name: compose_text_param - owner: iuc - revisions: - - feb3acba1e0a - - e188c9826e0f - tool_panel_section_id: expression_tools diff --git a/usegalaxy.org/compute_indicators_for_satellite_remote_sensing.yml b/usegalaxy.org/compute_indicators_for_satellite_remote_sensing.yml new file mode 100644 index 00000000..e3af6392 --- /dev/null +++ b/usegalaxy.org/compute_indicators_for_satellite_remote_sensing.yml @@ -0,0 +1,10 @@ +tool_panel_section_label: Compute indicators for satellite remote sensing +tools: +- name: srs_diversity_maps + owner: ecology +- name: srs_global_indices + owner: ecology +- name: srs_preprocess_s2 + owner: ecology +- name: srs_spectral_indices + owner: ecology diff --git a/usegalaxy.org/compute_indicators_for_satellite_remote_sensing.yml.lock b/usegalaxy.org/compute_indicators_for_satellite_remote_sensing.yml.lock new file mode 100644 index 00000000..fc6ac1bc --- /dev/null +++ b/usegalaxy.org/compute_indicators_for_satellite_remote_sensing.yml.lock @@ -0,0 +1,29 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Compute indicators for satellite remote sensing +tools: +- name: srs_diversity_maps + owner: ecology + revisions: + - 9adccd3da70c + tool_panel_section_id: compute_indicators_for_satellite_remote_sensing + tool_panel_section_label: Compute indicators for satellite remote sensing +- name: srs_global_indices + owner: ecology + revisions: + - 5cae678042ec + tool_panel_section_id: compute_indicators_for_satellite_remote_sensing + tool_panel_section_label: Compute indicators for satellite remote sensing +- name: srs_preprocess_s2 + owner: ecology + revisions: + - 33a1e15f7252 + tool_panel_section_id: compute_indicators_for_satellite_remote_sensing + tool_panel_section_label: Compute indicators for satellite remote sensing +- name: srs_spectral_indices + owner: ecology + revisions: + - b40aba3d9e5c + tool_panel_section_id: compute_indicators_for_satellite_remote_sensing + tool_panel_section_label: Compute indicators for satellite remote sensing diff --git a/usegalaxy.org/convert_formats.yml b/usegalaxy.org/convert_formats.yml index a603bfe1..d550d935 100644 --- a/usegalaxy.org/convert_formats.yml +++ b/usegalaxy.org/convert_formats.yml @@ -45,4 +45,8 @@ tools: - name: gffread owner: devteam - name: compress_file - owner: iuc \ No newline at end of file + owner: iuc +- name: graphicsmagick_image_montage + owner: bgruening +- name: msconvert + owner: galaxyp diff --git a/usegalaxy.org/convert_formats.yml.lock b/usegalaxy.org/convert_formats.yml.lock index abacda54..ceba7878 100644 --- a/usegalaxy.org/convert_formats.yml.lock +++ b/usegalaxy.org/convert_formats.yml.lock @@ -1,14 +1,14 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Convert Formats tools: - name: bioext_bam2msa owner: iuc revisions: - - f5792425ea50 - - b226e0c805a5 - 359e043a285c + - b226e0c805a5 + - f5792425ea50 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: tabular_to_fasta @@ -42,6 +42,8 @@ tools: owner: devteam revisions: - 02a5f43cd5d1 + - 77b41c89d856 + - 8979c288aefb - e282bc27be9a tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats @@ -72,17 +74,18 @@ tools: - name: bax2bam owner: iuc revisions: - - ee356d7a5518 - 5bd67e012d54 + - ee356d7a5518 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: crossmap_bam owner: iuc revisions: - 0f0cf480051b + - 158b5b2a164a - 60ca8d013263 - - e5340c09200a - e13f565068d6 + - e5340c09200a tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: crossmap_bed @@ -90,40 +93,44 @@ tools: revisions: - 91efc13d3ec1 - cdbdce00f5f6 + - ee86b27291b5 - f4a70882a71b tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: crossmap_wig owner: iuc revisions: - - e8d84292e510 - - 5f893ed3c5ed - 282a658c6569 + - 5f893ed3c5ed + - e72c320c17c1 + - e8d84292e510 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: crossmap_vcf owner: iuc revisions: + - 18f7e96459d2 + - 6e96c77f5824 + - 71730c177cdf - 97979c3d179f - b21851ddcc79 - - 71730c177cdf - - 6e96c77f5824 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: crossmap_gff owner: iuc revisions: - 09c6a9e067f9 - - 88d180fb6d67 + - 42b239a32349 - 4d97434ea0fb + - 88d180fb6d67 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 49d6f8ef63b3 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: gtftobed12 @@ -138,6 +145,7 @@ tools: owner: iuc revisions: - 356dc923f8d3 + - 8067dfa00ed2 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: bed_to_protein_map @@ -157,6 +165,7 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: + - 8190f6083c0d - e34bdac5b157 - f5c632894818 tool_panel_section_id: convert_formats @@ -164,9 +173,10 @@ tools: - name: gffread owner: devteam revisions: + - 154d00cbbf2d + - 3e436657dcd0 - 4dea02886337 - 69e0806b63a4 - - 154d00cbbf2d tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats - name: compress_file @@ -175,3 +185,17 @@ tools: - 09ea79f9f260 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats +- name: graphicsmagick_image_montage + owner: bgruening + revisions: + - 39881709807e + - 8dbc700cb940 + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats +- name: msconvert + owner: galaxyp + revisions: + - 3cf310697624 + - 6153e8ada1ee + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org/data_managers.yml similarity index 51% rename from usegalaxy.org.au/none.yml rename to usegalaxy.org/data_managers.yml index 8d2fc7ed..1d96033c 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org/data_managers.yml @@ -1,26 +1,38 @@ -tool_panel_section_label: None +tool_panel_section_label: Data Managers tools: +- name: data_manager_fetch_genome_dbkeys_all_fasta + owner: devteam +- name: data_manager_bowtie2_index_builder + owner: devteam - name: data_manager_bwa_mem_index_builder owner: devteam -- name: rnachipintegrator - owner: pjbriggs +- name: data_manager_hisat_index_builder + owner: devteam +- name: data_manager_twobit_builder + owner: devteam +- name: data_manager_picard_index_builder + owner: devteam - name: data_manager_sam_fasta_index_builder owner: devteam +- name: data_manager_hisat2_index_builder + owner: iuc +- name: data_manager_star_index_builder + owner: iuc +- name: data_manager_bowtie_index_builder + owner: iuc - name: data_manager_kallisto_index_builder owner: iuc - name: data_manager_snpeff owner: iuc -- name: data_manager_gatk_picard_index_builder - owner: devteam -- name: data_manager_hisat2_index_builder +- name: data_manager_plant_tribes_scaffolds_downloader owner: iuc -- name: data_manager_twobit_builder - owner: devteam -- name: data_manager_fetch_genome_dbkeys_all_fasta +- name: data_manager_fetch_ncbi_taxonomy owner: devteam - name: data_manager_gemini_database_downloader owner: iuc -- name: data_manager_bowtie2_index_builder - owner: devteam -- name: data_manager_fetch_busco +- name: data_manager_build_kraken2_database + owner: iuc +- name: data_manager_build_bracken_database + owner: iuc +- name: data_manager_mapseq owner: iuc diff --git a/usegalaxy.org/data_managers.yml.lock b/usegalaxy.org/data_managers.yml.lock new file mode 100644 index 00000000..c163715d --- /dev/null +++ b/usegalaxy.org/data_managers.yml.lock @@ -0,0 +1,114 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Data Managers +tools: +- name: data_manager_fetch_genome_dbkeys_all_fasta + owner: devteam + revisions: + - 4d3eff1bc421 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_bowtie2_index_builder + owner: devteam + revisions: + - 9dd107db92c2 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_bwa_mem_index_builder + owner: devteam + revisions: + - 9e993022c762 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_hisat_index_builder + owner: devteam + revisions: + - ba11fef120cd + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_twobit_builder + owner: devteam + revisions: + - 94a50db37d1a + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_picard_index_builder + owner: devteam + revisions: + - 7124d2c14e4b + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_sam_fasta_index_builder + owner: devteam + revisions: + - a256278e5bff + - ad90c2da4f38 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_hisat2_index_builder + owner: iuc + revisions: + - d74c740bdb25 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_star_index_builder + owner: iuc + revisions: + - d63c1442407f + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_bowtie_index_builder + owner: iuc + revisions: + - cb157f55b4fd + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_kallisto_index_builder + owner: iuc + revisions: + - 4c7ebbad42cf + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_snpeff + owner: iuc + revisions: + - def511e8e005 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_plant_tribes_scaffolds_downloader + owner: iuc + revisions: + - 1550b1741780 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_fetch_ncbi_taxonomy + owner: devteam + revisions: + - 6dd9e00dea95 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_gemini_database_downloader + owner: iuc + revisions: + - 27a6a256cd23 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_build_kraken2_database + owner: iuc + revisions: + - e4b4837f06f5 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_build_bracken_database + owner: iuc + revisions: + - 5c8a23ccb14a + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers +- name: data_manager_mapseq + owner: iuc + revisions: + - dbf2735e8480 + tool_panel_section_id: data_managers + tool_panel_section_label: Data Managers diff --git a/usegalaxy.org/datamash.yml.lock b/usegalaxy.org/datamash.yml.lock index c70a8d8f..c60291af 100644 --- a/usegalaxy.org/datamash.yml.lock +++ b/usegalaxy.org/datamash.yml.lock @@ -1,23 +1,30 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Datamash tools: - name: datamash_ops owner: iuc revisions: - - 562f3c677828 + - 2f3c6f2dcf39 + - 4c07ddedc198 + - 746e8e4bf929 tool_panel_section_id: datamash tool_panel_section_label: Datamash - name: datamash_transpose owner: iuc revisions: - 22c2a1ac7ae3 + - 374cb875d38a + - a513e3fbb4c5 + - ac092723240d tool_panel_section_id: datamash tool_panel_section_label: Datamash - name: datamash_reverse owner: iuc revisions: - 0f1724dd59d2 + - b8a457820315 + - f198773344e4 tool_panel_section_id: datamash tool_panel_section_label: Datamash diff --git a/usegalaxy.org/deeptools.yml b/usegalaxy.org/deeptools.yml index f4bb2bff..cf25fbfc 100644 --- a/usegalaxy.org/deeptools.yml +++ b/usegalaxy.org/deeptools.yml @@ -32,3 +32,5 @@ tools: owner: bgruening - name: deeptools_bam_compare owner: bgruening +- name: deeptools_bigwig_average + owner: bgruening diff --git a/usegalaxy.org/deeptools.yml.lock b/usegalaxy.org/deeptools.yml.lock index 1bf0cdb7..314773c2 100644 --- a/usegalaxy.org/deeptools.yml.lock +++ b/usegalaxy.org/deeptools.yml.lock @@ -1,26 +1,39 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: deepTools tools: - name: deeptools_plot_profile owner: bgruening revisions: + - 10301d137111 + - 6662b1a8d326 + - aac8444d6681 - c361b12d207a - d806504e96d9 + - e9429e484e25 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_bam_coverage owner: bgruening revisions: + - 0e143b4c3987 + - 0e49b109abc2 + - 2d2cf5c1ea8a + - 4df95152a39e - 7a7fd0f5f15d - bb1e4f63e0e6 + - c2b4dd18f09d + - fe7cc56090ea tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_pca owner: bgruening revisions: + - 00d869ea03a1 + - 443d9a9d6d11 - 69264da0ce77 + - 7784523d9743 - aa200e4f3939 tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -28,20 +41,29 @@ tools: owner: bgruening revisions: - 010e58e9d822 + - 25d830337d31 + - 42cb23d80271 - a4dfb122e52b - a7849312d328 + - e4c7985d4585 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_fingerprint owner: bgruening revisions: - 2da482e408b8 + - 4ed32329e0ed + - b88ebb3672a1 + - ca8a7f0ea872 - d57251071381 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_enrichment owner: bgruening revisions: + - 4431f39ede55 + - 88ce7fed1488 + - c03c3384cd81 - d9114ef1c8a5 - e65d16fb2724 tool_panel_section_id: deeptools @@ -49,71 +71,114 @@ tools: - name: deeptools_plot_coverage owner: bgruening revisions: + - 231994413f89 - 4e12ea27f788 - 56bce3c82278 + - 7fda5607e777 + - 9368fbc49c8b tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_correlation owner: bgruening revisions: + - 2c66e43f1c86 - 32e451def88c + - bad3ca889618 - bd7db9e2f2cb + - e44978659400 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 137c4beed34b - 2f9e4843f480 - 3c9f0c486cca + - 459cfa861f0b + - d9ce4897dbb2 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 01fb6a7654e6 + - 1fcb7adc39b8 - 69a8621ca2f0 - 78f405266706 + - b4e53394fced tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_correct_gc_bias owner: bgruening revisions: + - 00a71ff7c06b - 2c37ce318bc3 + - 5bffaa8354a1 - c34d11ea4ba6 + - e479c7ca5570 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_compute_matrix owner: bgruening revisions: + - 167788df3b46 + - 19bb3e6d9e31 - 514fa53b5efb + - a2e50c362097 + - a60c359ec43c + - a69f124a198d - b73e213add0c + - c1bc6406b3bb + - d9a637e83828 + - f305afa8ff0d - fb9cf9c97ec4 + - fd1275e01605 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 26983857c91a - 2bc10a9ca58b + - 56d5b797ce84 + - 5be24eba848d - b8858746dc1f tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_bigwig_compare owner: bgruening revisions: + - 07418a30ed01 - 26e7304d6737 + - 3d211717a775 - 71aa86af6762 + - 7989c6ddf634 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: + - 195e98217334 - 1d848bc4585f + - 3f9dc453c0e8 - 62eb6d63f582 + - c06951d10364 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_bam_compare owner: bgruening revisions: - 268e91e540ee + - 29451af70c52 + - c89b665b45e4 + - c929a006727f - e821645ef8fc tool_panel_section_id: deeptools tool_panel_section_label: deepTools +- name: deeptools_bigwig_average + owner: bgruening + revisions: + - 4a53856a5b85 + - f6f246438eda + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools diff --git a/usegalaxy.org/du_novo.yml.lock b/usegalaxy.org/du_novo.yml.lock index 750ebdcc..b114ba92 100644 --- a/usegalaxy.org/du_novo.yml.lock +++ b/usegalaxy.org/du_novo.yml.lock @@ -1,34 +1,36 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Du Novo tools: - name: dunovo owner: nick revisions: - - 9dc43bf7d1db - 0f8e0dc73d1d + - 9dc43bf7d1db tool_panel_section_id: du_novo tool_panel_section_label: Du Novo - name: sequence_content_trimmer owner: nick revisions: + - 464aee13e2df - 7f170cb06e2e tool_panel_section_id: du_novo tool_panel_section_label: Du Novo - name: duplex_family_size_distribution owner: iuc revisions: + - 6cc65a11d922 - 7fc3c8704c05 - ec5a92514113 - - 6cc65a11d922 + - f85557b9707a tool_panel_section_id: du_novo tool_panel_section_label: Du Novo - name: variant_analyzer owner: iuc revisions: - 3556001ff2db - - 8d29173d49a9 - 3f1dbd2c59bf + - 8d29173d49a9 tool_panel_section_id: du_novo tool_panel_section_label: Du Novo diff --git a/usegalaxy.org/emboss.yml.lock b/usegalaxy.org/emboss.yml.lock index b6462d7d..18ab4852 100644 --- a/usegalaxy.org/emboss.yml.lock +++ b/usegalaxy.org/emboss.yml.lock @@ -1,13 +1,14 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: EMBOSS tools: - name: emboss_5 owner: devteam revisions: + - 63dd26468588 + - ce385837c160 - dba489bfcd62 - dc492eb6a4fc - - ce385837c160 tool_panel_section_id: emboss tool_panel_section_label: EMBOSS diff --git a/usegalaxy.eu/epigenetics.yml b/usegalaxy.org/epigenetics.yml similarity index 56% rename from usegalaxy.eu/epigenetics.yml rename to usegalaxy.org/epigenetics.yml index ef5d768a..4f203dd3 100644 --- a/usegalaxy.eu/epigenetics.yml +++ b/usegalaxy.org/epigenetics.yml @@ -1,11 +1,5 @@ tool_panel_section_label: Epigenetics tools: -- name: vcf_filter - owner: devteam -- name: pileometh - owner: bgruening -- name: nanopolish_methylation - owner: bgruening - name: hicup_truncater owner: bgruening - name: hicup_hicup @@ -16,13 +10,15 @@ tools: owner: bgruening - name: hicup_deduplicator owner: bgruening -- name: epicseg - owner: rnateam -- name: bwameth - owner: iuc - name: hicup_mapper owner: bgruening -- name: metilene - owner: rnateam -- name: rnbeads - owner: pavlo-lutsik +- name: hicup2juicer + owner: bgruening +- name: cooler_makebins + owner: lldelisle +- name: cooler_csort_tabix + owner: lldelisle +- name: cooler_cload_tabix + owner: lldelisle +- name: cooler_balance + owner: lldelisle diff --git a/usegalaxy.org/epigenetics.yml.lock b/usegalaxy.org/epigenetics.yml.lock new file mode 100644 index 00000000..985b0eb5 --- /dev/null +++ b/usegalaxy.org/epigenetics.yml.lock @@ -0,0 +1,86 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Epigenetics +tools: +- name: hicup_truncater + owner: bgruening + revisions: + - 71278c4f1b2e + - cc413be789ea + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: hicup_hicup + owner: bgruening + revisions: + - 68fb19094f84 + - 852e1fac4802 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: hicup_filter + owner: bgruening + revisions: + - 2d4a34c00c67 + - 6c26354dabe0 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: hicup_digester + owner: bgruening + revisions: + - 8b1d0e4e8f22 + - e79c38f1752c + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: hicup_deduplicator + owner: bgruening + revisions: + - 2107c2f7a5d7 + - 44b121185562 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: hicup_mapper + owner: bgruening + revisions: + - 70427be35bf2 + - be104dee2833 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: hicup2juicer + owner: bgruening + revisions: + - b4e7244246e2 + - f8cb84c49623 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: cooler_makebins + owner: lldelisle + revisions: + - c3dc51297bf8 + - ebd2a52eb245 + - f67664a4e1d6 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: cooler_csort_tabix + owner: lldelisle + revisions: + - 5cb855a2dc9e + - 8c3cba559c99 + - d56db0e1555d + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: cooler_cload_tabix + owner: lldelisle + revisions: + - 0641e1c892c6 + - 3ff6eeca667e + - c639f60ae76a + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: cooler_balance + owner: lldelisle + revisions: + - 8f71aaf6e59d + - 8f9fe0667b89 + - 9655af207032 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics diff --git a/usegalaxy.org/evolution.yml.lock b/usegalaxy.org/evolution.yml.lock index 64fc22c7..679d9bfe 100644 --- a/usegalaxy.org/evolution.yml.lock +++ b/usegalaxy.org/evolution.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Evolution tools: @@ -19,37 +19,41 @@ tools: - name: iqtree owner: iuc revisions: - - 563c3aa769f2 - - c1d53e95327f - 524d31add34a + - 563c3aa769f2 - 973a28be3b7f - - b8476e82ac20 - 9b892d7f82cc + - b8476e82ac20 + - c1d53e95327f tool_panel_section_id: evolution tool_panel_section_label: Evolution - name: tn93 owner: iuc revisions: - - ccebde0e2d61 - 9d793e88e15f + - b38f620a3628 + - ccebde0e2d61 tool_panel_section_id: evolution tool_panel_section_label: Evolution - name: tn93_filter owner: iuc revisions: - ba95715078c9 + - cf50aeb956f2 tool_panel_section_id: evolution tool_panel_section_label: Evolution - name: tn93_cluster owner: iuc revisions: + - 112d80c9ccca - af03f3398f03 tool_panel_section_id: evolution tool_panel_section_label: Evolution - name: tn93_readreduce owner: iuc revisions: - - bdaadfd0c843 + - 1d2ec0b0a0a7 - 84849140a3bc + - bdaadfd0c843 tool_panel_section_id: evolution tool_panel_section_label: Evolution diff --git a/usegalaxy.org/expression_tools.yml b/usegalaxy.org/expression_tools.yml new file mode 100644 index 00000000..16cb06b8 --- /dev/null +++ b/usegalaxy.org/expression_tools.yml @@ -0,0 +1,8 @@ +tool_panel_section_label: Expression Tools +tools: + - name: compose_text_param + owner: iuc + - name: map_param_value + owner: iuc + - name: pick_value + owner: iuc \ No newline at end of file diff --git a/usegalaxy.org/expression_tools.yml.lock b/usegalaxy.org/expression_tools.yml.lock new file mode 100644 index 00000000..8b0461eb --- /dev/null +++ b/usegalaxy.org/expression_tools.yml.lock @@ -0,0 +1,26 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Expression Tools +tools: +- name: compose_text_param + owner: iuc + revisions: + - e188c9826e0f + - feb3acba1e0a + tool_panel_section_id: expression_tools + tool_panel_section_label: Expression Tools +- name: map_param_value + owner: iuc + revisions: + - 43d7b3642a30 + - 5ac8a4bf7a8d + - a01f088d0e5e + tool_panel_section_id: expression_tools + tool_panel_section_label: Expression Tools +- name: pick_value + owner: iuc + revisions: + - b19e21af9c52 + tool_panel_section_id: expression_tools + tool_panel_section_label: Expression Tools diff --git a/usegalaxy.org/extract_features.yml b/usegalaxy.org/extract_features.yml new file mode 100644 index 00000000..69714543 --- /dev/null +++ b/usegalaxy.org/extract_features.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Extract Features +tools: +- name: parse_mito_blast + owner: iuc diff --git a/usegalaxy.org/extract_features.yml.lock b/usegalaxy.org/extract_features.yml.lock new file mode 100644 index 00000000..edb56292 --- /dev/null +++ b/usegalaxy.org/extract_features.yml.lock @@ -0,0 +1,11 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tools: +- name: parse_mito_blast + owner: iuc + revisions: + - 3c9ad4adf8d2 + - f172b1f77d6c + tool_panel_section_id: extract_features + tool_panel_section_label: Extract Features diff --git a/usegalaxy.org/fasta_fastq.yml b/usegalaxy.org/fasta_fastq.yml index 8c92c146..ef985d9c 100644 --- a/usegalaxy.org/fasta_fastq.yml +++ b/usegalaxy.org/fasta_fastq.yml @@ -90,3 +90,11 @@ tools: owner: peterjc - name: umi_tools_extract owner: iuc +- name: umi_tools_whitelist + owner: iuc +- name: umi_tools_dedup + owner: iuc +- name: umi_tools_group + owner: iuc +- name: fasta_regex_finder + owner: mbernt diff --git a/usegalaxy.org/fasta_fastq.yml.lock b/usegalaxy.org/fasta_fastq.yml.lock index 5b1cc6a2..c76ff1c7 100644 --- a/usegalaxy.org/fasta_fastq.yml.lock +++ b/usegalaxy.org/fasta_fastq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: FASTA/FASTQ tools: @@ -12,17 +12,26 @@ tools: - name: cutadapt owner: lparsons revisions: + - 02c5a84971c8 + - 135b80fb1ac2 + - 288f97432497 + - 44e2cc14f75b - 49370cb85f0f + - 4e5056fefd88 + - 64172f1c1202 - 660cffd8d92a + - 8c0175e03cee + - c053d4cad713 + - c5e2e5902201 + - de6cebe3c043 - e4691e1589d3 - f5fdf41c08b8 - - 288f97432497 - - c053d4cad713 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: flash owner: iuc revisions: + - 01a4ebf1f237 - a27654fc4270 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -30,6 +39,7 @@ tools: owner: iuc revisions: - 1d8fe9bc4cb0 + - 65b93b623c77 - dbf9c561ef29 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -38,12 +48,14 @@ tools: revisions: - 547e8d00f11c - 61b4cedc8934 + - 73194cdd4f57 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fastx_reverse_complement owner: devteam revisions: - 0c2907307ba4 + - 177f0621c266 - 6027ef51ef91 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -51,12 +63,15 @@ tools: owner: devteam revisions: - 736b8f6ee456 + - 90858c306551 - b8658f852bc7 + - cb1e251cac37 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fastq_quality_filter owner: devteam revisions: + - 64e9a6afdd0c - 7b4468117008 - ce9cd02d5b88 tool_panel_section_id: fasta_fastq @@ -64,6 +79,7 @@ tools: - name: length_and_gc_content owner: iuc revisions: + - e3ba567abdf5 - f088370d2a3c tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -72,17 +88,20 @@ tools: revisions: - 3599f5451ee2 - b29d37ca9e41 + - f984bb114520 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fastx_barcode_splitter owner: devteam revisions: + - 0b7ec11b3c7c - 4bedca26c133 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fastx_artifacts_filter owner: devteam revisions: + - 529bccd5e4a1 - 567d5b3c52b1 - d5e9e83cd3d8 tool_panel_section_id: fasta_fastq @@ -90,6 +109,7 @@ tools: - name: fastq_quality_converter owner: devteam revisions: + - 045f0e1043f7 - 54053ea6c77e tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -129,6 +149,7 @@ tools: - 249c8393f2d4 - 35e38452bb3f - 9bbe5b7ffa12 + - e39cc71d3ed6 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fastq_masker_by_quality @@ -194,6 +215,7 @@ tools: - name: fastx_collapser owner: devteam revisions: + - 07497255281e - 7ce1891db6f5 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -217,11 +239,13 @@ tools: revisions: - 091ca73f5804 - ec0b5076173a + - f773e98b26cf tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fasta_formatter owner: devteam revisions: + - 516b97a23d7e - 859422bcb689 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -252,14 +276,16 @@ tools: - name: fasta_stats owner: iuc revisions: - - 9c620a950d3a - - 56022eb50bbd - 0dbb995c7d35 + - 56022eb50bbd + - 9c620a950d3a tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: filtlong owner: iuc revisions: + - 1f296803dfa3 + - 41b2ad601cf0 - 8880fb74ef56 - a72af9de6bf5 tool_panel_section_id: fasta_fastq @@ -268,6 +294,7 @@ tools: owner: iuc revisions: - 2f804526f5fd + - b4c6f054210a tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: sickle @@ -280,6 +307,7 @@ tools: owner: iuc revisions: - 71f649c23021 + - bf04bd405d5b tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: umi_tools_count @@ -299,6 +327,7 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: + - 3c623e81be77 - dff7df6fcab5 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -323,3 +352,27 @@ tools: - f3759eec3018 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ +- name: umi_tools_whitelist + owner: iuc + revisions: + - 953b4821b183 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: umi_tools_dedup + owner: iuc + revisions: + - f1d33e4c7bd8 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: umi_tools_group + owner: iuc + revisions: + - d6255614afd7 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: fasta_regex_finder + owner: mbernt + revisions: + - 9a811adb714f + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ diff --git a/usegalaxy.org/fastq_quality_control.yml b/usegalaxy.org/fastq_quality_control.yml index a8ac9bfe..300a3ea2 100644 --- a/usegalaxy.org/fastq_quality_control.yml +++ b/usegalaxy.org/fastq_quality_control.yml @@ -18,3 +18,5 @@ tools: owner: iuc - name: fastqe owner: iuc +- name: fastq_info + owner: bgruening diff --git a/usegalaxy.org/fastq_quality_control.yml.lock b/usegalaxy.org/fastq_quality_control.yml.lock index 1efdedb1..04c08646 100644 --- a/usegalaxy.org/fastq_quality_control.yml.lock +++ b/usegalaxy.org/fastq_quality_control.yml.lock @@ -1,11 +1,13 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: FASTQ Quality Control tools: - name: fastqc owner: devteam revisions: + - 3d0c7bdf12f5 + - 5ec9f6bceaee - e7b2202befea - ff9530579d1f tool_panel_section_id: fastq_quality_control @@ -14,6 +16,7 @@ tools: owner: pjbriggs revisions: - 898b67846b47 + - d94aff5ee623 - dfa082f84068 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control @@ -23,11 +26,12 @@ tools: - 1c2db0054039 - 3d93dd18d9f8 - 5e33b465d8d5 + - 75c93c70d094 + - 9a913cdee30e + - abfd8a6544d7 - b2f1f75d49c4 - bf675f34b056 - f7985e0479b9 - - 75c93c70d094 - - 9a913cdee30e tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: fastq_stats @@ -42,6 +46,7 @@ tools: owner: devteam revisions: - 59003d0543cd + - cc0fd298cc17 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: fastx_nucleotides_distribution @@ -49,6 +54,7 @@ tools: revisions: - 21796f46e0ba - ad116ae3f4d9 + - b6b54ba71bd8 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: fastq_quality_boxplot @@ -56,21 +62,31 @@ tools: revisions: - 3987db70a4b0 - 7cf5b1d072b5 + - 867ab348287d tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: prinseq owner: iuc revisions: - 02befcb391f5 + - 1ee282794de3 - 654b3a274ed5 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: fastqe owner: iuc revisions: - - a252d8415583 - 819b8c1657d5 - - ecb38e2798cd - 89d299153577 + - a252d8415583 + - c1a33f603da2 + - d77a9c2a242d + - ecb38e2798cd + tool_panel_section_id: fastq_quality_control + tool_panel_section_label: FASTQ Quality Control +- name: fastq_info + owner: bgruening + revisions: + - 7a821cd57b43 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control diff --git a/usegalaxy.org/fetch_sequences_alignments.yml.lock b/usegalaxy.org/fetch_sequences_alignments.yml.lock index ad98bfb5..ccec6eba 100644 --- a/usegalaxy.org/fetch_sequences_alignments.yml.lock +++ b/usegalaxy.org/fetch_sequences_alignments.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Fetch Sequences/Alignments tools: diff --git a/usegalaxy.org/filter_and_sort.yml b/usegalaxy.org/filter_and_sort.yml new file mode 100644 index 00000000..180f91a2 --- /dev/null +++ b/usegalaxy.org/filter_and_sort.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Filter and Sort +tools: +- name: sample_seqs + owner: peterjc diff --git a/usegalaxy.org/filter_and_sort.yml.lock b/usegalaxy.org/filter_and_sort.yml.lock new file mode 100644 index 00000000..cf081c4a --- /dev/null +++ b/usegalaxy.org/filter_and_sort.yml.lock @@ -0,0 +1,11 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Filter and Sort +tools: +- name: sample_seqs + owner: peterjc + revisions: + - 7c40a1fbc82e + tool_panel_section_id: filter_and_sort + tool_panel_section_label: Filter and Sort diff --git a/usegalaxy.org/gatk.yml.lock b/usegalaxy.org/gatk.yml.lock index 2280854b..af5f9ef6 100644 --- a/usegalaxy.org/gatk.yml.lock +++ b/usegalaxy.org/gatk.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: GATK tools: diff --git a/usegalaxy.org/gemini.yml b/usegalaxy.org/gemini.yml new file mode 100644 index 00000000..716484ea --- /dev/null +++ b/usegalaxy.org/gemini.yml @@ -0,0 +1,10 @@ +tool_panel_section_label: Gemini +tools: +- name: gemini_annotate + owner: iuc +- name: gemini_inheritance + owner: iuc +- name: gemini_load + owner: iuc +- name: gemini_query + owner: iuc diff --git a/usegalaxy.org/gemini.yml.lock b/usegalaxy.org/gemini.yml.lock new file mode 100644 index 00000000..c2374719 --- /dev/null +++ b/usegalaxy.org/gemini.yml.lock @@ -0,0 +1,33 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Gemini +tools: +- name: gemini_annotate + owner: iuc + revisions: + - cf0f0f05ba9f + - f2f3bc622a16 + tool_panel_section_id: gemini + tool_panel_section_label: Gemini +- name: gemini_inheritance + owner: iuc + revisions: + - 18d13111692b + - 2c68e29c3527 + tool_panel_section_id: gemini + tool_panel_section_label: Gemini +- name: gemini_load + owner: iuc + revisions: + - 2270a8b83c12 + - 45296e47d565 + tool_panel_section_id: gemini + tool_panel_section_label: Gemini +- name: gemini_query + owner: iuc + revisions: + - 77a1e60fd1de + - da74170c55c7 + tool_panel_section_id: gemini + tool_panel_section_label: Gemini diff --git a/usegalaxy.org/genome_diversity.yml b/usegalaxy.org/genome_diversity.yml index 1607e2ba..4c2411a1 100644 --- a/usegalaxy.org/genome_diversity.yml +++ b/usegalaxy.org/genome_diversity.yml @@ -1,4 +1,4 @@ tool_panel_section_label: Genome Diversity tools: -- name: genome_diversity - owner: miller-lab +- name: raxml + owner: iuc diff --git a/usegalaxy.org/genome_diversity.yml.lock b/usegalaxy.org/genome_diversity.yml.lock index 3818ead9..c2939ef2 100644 --- a/usegalaxy.org/genome_diversity.yml.lock +++ b/usegalaxy.org/genome_diversity.yml.lock @@ -1,11 +1,12 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Genome Diversity tools: -- name: genome_diversity - owner: miller-lab +- name: raxml + owner: iuc revisions: - - e56023008e36 + - b1e68bbe4cef + - ea30d3089354 tool_panel_section_id: genome_diversity tool_panel_section_label: Genome Diversity diff --git a/usegalaxy.org/genome_editing.yml b/usegalaxy.org/genome_editing.yml new file mode 100644 index 00000000..f92902a9 --- /dev/null +++ b/usegalaxy.org/genome_editing.yml @@ -0,0 +1,8 @@ +tool_panel_section_label: Genome Editing +tools: +- name: mageck_mle + owner: iuc +- name: mageck_test + owner: iuc +- name: mageck_count + owner: iuc diff --git a/usegalaxy.org/genome_editing.yml.lock b/usegalaxy.org/genome_editing.yml.lock new file mode 100644 index 00000000..90cd8a7c --- /dev/null +++ b/usegalaxy.org/genome_editing.yml.lock @@ -0,0 +1,23 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Genome Editing +tools: +- name: mageck_mle + owner: iuc + revisions: + - 26126538a86f + tool_panel_section_id: genome_editing + tool_panel_section_label: Genome Editing +- name: mageck_test + owner: iuc + revisions: + - 9b4f4533c9ee + tool_panel_section_id: genome_editing + tool_panel_section_label: Genome Editing +- name: mageck_count + owner: iuc + revisions: + - e329d44424d7 + tool_panel_section_id: genome_editing + tool_panel_section_label: Genome Editing diff --git a/usegalaxy.org/get_data.yml b/usegalaxy.org/get_data.yml index facd2d09..29dfdecf 100644 --- a/usegalaxy.org/get_data.yml +++ b/usegalaxy.org/get_data.yml @@ -2,6 +2,8 @@ tool_panel_section_label: Get Data tools: - name: sra_tools owner: iuc +- name: ncbi_datasets + owner: iuc - name: ebi_metagenomics_run_downloader owner: iuc - name: ebi_search_rest_results @@ -12,3 +14,5 @@ tools: owner: iuc - name: unipept owner: galaxyp +- name: ega_download_client + owner: iuc diff --git a/usegalaxy.org/get_data.yml.lock b/usegalaxy.org/get_data.yml.lock index c92378d5..ee7c54aa 100644 --- a/usegalaxy.org/get_data.yml.lock +++ b/usegalaxy.org/get_data.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Get Data tools: @@ -7,15 +7,35 @@ tools: owner: iuc revisions: - 248f85ff0733 + - 4317d3cb6cba + - 4df8de2d0e48 - 653e89d73fc4 + - 6591f049cf7e + - 69ebb7f46e45 + - 6ea73833cf67 - 7068f48d0ef9 + - 734abc7ac21d + - 83c7d564b128 - 964579f93c54 - aad3885b3216 - c441583adae5 - - f5ea3ce9b9b0 - e08a7ad4378b - - 69ebb7f46e45 - - 83c7d564b128 + - e407b9da183a + - f5ea3ce9b9b0 + tool_panel_section_id: get_data + tool_panel_section_label: Get Data +- name: ncbi_datasets + owner: iuc + revisions: + - 0622d99c2619 + - 18eed8fa7f23 + - 1e188c9610c3 + - 5a2656cc84cb + - 6c829a430475 + - 75acf92c8fd5 + - a3395b1d871b + - b2ae7186d41f + - c47a0a93ffd2 tool_panel_section_id: get_data tool_panel_section_label: Get Data - name: ebi_metagenomics_run_downloader @@ -41,12 +61,22 @@ tools: revisions: - 1c58de56d587 - 28587613264f + - e063168e0a81 tool_panel_section_id: get_data tool_panel_section_label: Get Data - name: unipept owner: galaxyp revisions: - 34758ab8aaa4 + - 7863f1abcdda - 9aaa46d45472 tool_panel_section_id: get_data tool_panel_section_label: Get Data +- name: ega_download_client + owner: iuc + revisions: + - 6cb20e130473 + - 7d87a9d58aa1 + - f9db47f68e5e + tool_panel_section_id: get_data + tool_panel_section_label: Get Data diff --git a/usegalaxy.org/gis_data_handling.yml b/usegalaxy.org/gis_data_handling.yml index a063a64f..c8433b31 100644 --- a/usegalaxy.org/gis_data_handling.yml +++ b/usegalaxy.org/gis_data_handling.yml @@ -4,3 +4,9 @@ tools: owner: ecology - name: xarray_select owner: ecology +- name: xarray_netcdf2netcdf + owner: ecology +- name: xarray_coords_info + owner: ecology +- name: xarray_mapplot + owner: ecology diff --git a/usegalaxy.org/gis_data_handling.yml.lock b/usegalaxy.org/gis_data_handling.yml.lock index 514207dc..88f8c1f0 100644 --- a/usegalaxy.org/gis_data_handling.yml.lock +++ b/usegalaxy.org/gis_data_handling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: GIS Data Handling tools: @@ -15,3 +15,21 @@ tools: - 6baac361495b tool_panel_section_id: gis_data_handling tool_panel_section_label: GIS Data Handling +- name: xarray_netcdf2netcdf + owner: ecology + revisions: + - 1a91e551f3a9 + tool_panel_section_id: gis_data_handling + tool_panel_section_label: GIS Data Handling +- name: xarray_coords_info + owner: ecology + revisions: + - 6015f30a7258 + tool_panel_section_id: gis_data_handling + tool_panel_section_label: GIS Data Handling +- name: xarray_mapplot + owner: ecology + revisions: + - d7479b6dfbe8 + tool_panel_section_id: gis_data_handling + tool_panel_section_label: GIS Data Handling diff --git a/usegalaxy.org/graph_display_data.yml.lock b/usegalaxy.org/graph_display_data.yml.lock index 53442965..8b28109f 100644 --- a/usegalaxy.org/graph_display_data.yml.lock +++ b/usegalaxy.org/graph_display_data.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Graph/Display Data tools: @@ -7,9 +7,15 @@ tools: owner: bgruening revisions: - 05143043ca13 + - 1588f9076e32 - 222c02df5d55 - 4a229a7ad638 + - 6fabdcde0214 + - 8334dc98c48e + - a536d2736c2d - c7655b5a94af + - c80db5d6fd8c + - e88c782a127d tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: plotly_parallel_coordinates_plot @@ -35,9 +41,11 @@ tools: revisions: - 17359b808b01 - 1cfc579079a6 + - 2bb2e07a7a21 - 4542035c1075 - 667e17248bfe - 6cd09d7b5f37 + - 836d1aa3e89a - a6e57ff585c0 - edb534491f92 - fd5dbf0f732e @@ -58,18 +66,21 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - 53460afd5115 + - '566197475670' - ca7cb0eaad62 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: circos owner: iuc revisions: + - 290a11559985 - 4b519282a05b - a64dc31ab7f2 + - c4bde687c846 - df7356989ac1 - e6cbe3190642 - fd59d783248a - - 290a11559985 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: venn_list @@ -81,6 +92,7 @@ tools: - name: ucsc_custom_track owner: devteam revisions: + - 3d87079756e1 - 760f588e8a26 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data @@ -124,13 +136,18 @@ tools: - name: bandage owner: iuc revisions: + - 067592b6b312 + - 21e491ad532a - 94fe43e75ddc + - b2860df42e16 - b9e31c5c01c7 + - ddddce450736 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: export2graphlan owner: iuc revisions: + - 635c90a27692 - b16989c1e3a7 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data @@ -143,40 +160,56 @@ tools: - name: ggplot2_heatmap owner: iuc revisions: + - 10515715c940 + - 3d059e9c2fba - a4d83ba2a1bc - - de002ba2b849 - d3a9e32672ec + - da4c086cff5b + - de002ba2b849 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: ggplot2_histogram owner: iuc revisions: + - 11869c5becd8 + - 355a82227003 - 497d700a5229 - 536078949ae4 - - 355a82227003 + - b0d96516e6a5 + - fb50ab943396 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: ggplot2_pca owner: iuc revisions: - 1b9406a1a769 + - 2bf238af068d + - 7f2ef7216cf8 - 90928b255abb + - b1268b7544d3 - fcb6a19960c6 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: ggplot2_point owner: iuc revisions: + - 1acf88921176 + - 299307abd804 + - 3b12bf9b4b87 + - 5fe1dc76176e - 87908c76ca8d - 9cec81e1b90e - a36551483a8f - - 1acf88921176 + - d0fc8b746d57 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: ggplot2_violin owner: iuc revisions: + - 0e7290688b50 - 637cf21db396 + - 9c52a8130729 + - d6c41b454cc1 - d8305f18060e - e44775efb2dc tool_panel_section_id: graph_display_data @@ -184,12 +217,16 @@ tools: - name: graphlan owner: iuc revisions: + - 6e8eb0c0d91f + - 8f62f666dcb6 - a490b70e46fc tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: graphlan_annotate owner: iuc revisions: + - 5d6f8f0bef7c + - 97e3b735ed22 - cf1df6b2220a tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data @@ -197,6 +234,8 @@ tools: owner: iuc revisions: - 08780101bc36 + - 21beb30956c2 + - 33b8c5eedc04 - f5fa293605ca tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data @@ -218,6 +257,7 @@ tools: revisions: - 03c13085aecc - bd99e8fbde97 + - f1691de443a7 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: pe_histogram @@ -229,17 +269,24 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 + - 0a10fddd97d2 - 44c66e8d21e6 + - 6c571966cfb9 + - 7c9417381ad5 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: pygenometracks owner: iuc revisions: + - 14e7c35f3d00 - 2824d77cd8f8 - 326a3db8d9d1 + - 360df4999907 - 4ac4e7083b7e + - 59fd173ac850 - 5cec5fb749f0 + - 7dd841a32245 + - a1abfa420d9d - eca03db4f612 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data diff --git a/usegalaxy.org/hyphy.yml b/usegalaxy.org/hyphy.yml index 83c6dc22..64b90780 100644 --- a/usegalaxy.org/hyphy.yml +++ b/usegalaxy.org/hyphy.yml @@ -2,10 +2,16 @@ tool_panel_section_label: HyPhy tools: - name: hyphy_absrel owner: iuc +- name: hyphy_annotate + owner: iuc - name: hyphy_bgm owner: iuc - name: hyphy_busted owner: iuc +- name: hyphy_cfel + owner: iuc +- name: hyphy_conv + owner: iuc - name: hyphy_fade owner: iuc - name: hyphy_fel @@ -24,9 +30,11 @@ tools: owner: iuc - name: hyphy_sm19 owner: iuc +- name: hyphy_strike_ambigs + owner: iuc - name: hyphy_summary owner: iuc - name: sarscov2summary owner: iuc - name: sarscov2formatter - owner: iuc \ No newline at end of file + owner: iuc diff --git a/usegalaxy.org/hyphy.yml.lock b/usegalaxy.org/hyphy.yml.lock index ec4f8961..7854a519 100644 --- a/usegalaxy.org/hyphy.yml.lock +++ b/usegalaxy.org/hyphy.yml.lock @@ -1,315 +1,366 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: HyPhy tools: - name: hyphy_absrel owner: iuc revisions: - - 5f2ca10db92a - - 9275e81b5590 - - d033ffc1c161 + - 107d3ba7024a + - '113854308427' + - 212c958f6cee - 3b8b5bde0bd9 - - b89cac5156ec - - d7c7ef3353fe - - 6a457678efcb + - 3f59ebfbfe3d + - 4aad5b48d5b2 - 4cc4dbca2f02 + - 5f2ca10db92a + - 6a457678efcb - 81e66674859e + - '841557158611' - 8834daeb9892 - - 107d3ba7024a - - 4aad5b48d5b2 + - 9275e81b5590 + - a6619171428e - ad0af446d496 + - b89cac5156ec - c78f3d7dd1db - cce7b18495e4 - - '113854308427' - - 3f59ebfbfe3d + - d033ffc1c161 + - d7c7ef3353fe tool_panel_section_id: hyphy tool_panel_section_label: HyPhy - name: hyphy_annotate owner: iuc revisions: - - f7810488bd92 + - 2318841ec191 + - 68cd2d8e3840 + - 91cf1290ba6f - a88848771d2d - df56795c3d89 - - 68cd2d8e3840 + - e6009f23582c + - f7810488bd92 - fa913c2975da tool_panel_section_id: hyphy tool_panel_section_label: HyPhy - name: hyphy_bgm owner: iuc revisions: - - d1c977aee228 - - d88bbb287923 - - 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revisions: + - 193dcaef2169 + - 31e7f5a25db3 - 4bf743518e41 - - 7c86ceaf523c - 50554f806e16 + - 7c86ceaf523c - dc8875a13914 + - f5bbd4b34541 tool_panel_section_id: hyphy tool_panel_section_label: HyPhy - name: hyphy_summary owner: iuc revisions: - - f304c108aa1f - - bd90215b7d15 - 11dd1a96ffe9 + - 4e7f1a7d18be + - 81b23515db14 + - bd90215b7d15 + - f304c108aa1f + - f3e408cc2546 tool_panel_section_id: hyphy tool_panel_section_label: HyPhy - name: sarscov2summary @@ -322,7 +373,7 @@ tools: owner: iuc revisions: - 1c664ff29354 - - e3a7995dce75 - 2e993ff8e7dc + - e3a7995dce75 tool_panel_section_id: hyphy tool_panel_section_label: HyPhy diff --git a/usegalaxy.org/iwtomics.yml.lock b/usegalaxy.org/iwtomics.yml.lock index 8ac920a6..f6a460bb 100644 --- a/usegalaxy.org/iwtomics.yml.lock +++ b/usegalaxy.org/iwtomics.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: IWTomics tools: diff --git a/usegalaxy.org/join__subtract_and_group.yml.lock b/usegalaxy.org/join__subtract_and_group.yml.lock index 9386136f..6063a1fa 100644 --- a/usegalaxy.org/join__subtract_and_group.yml.lock +++ b/usegalaxy.org/join__subtract_and_group.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Join, Subtract and Group tools: diff --git a/usegalaxy.org/machine_learning.yml b/usegalaxy.org/machine_learning.yml index 0cd394b1..9977ef74 100644 --- a/usegalaxy.org/machine_learning.yml +++ b/usegalaxy.org/machine_learning.yml @@ -64,3 +64,5 @@ tools: owner: bgruening - name: create_tool_recommendation_model owner: bgruening +- name: chopin2 + owner: iuc diff --git a/usegalaxy.org/machine_learning.yml.lock b/usegalaxy.org/machine_learning.yml.lock index 703a5a7b..cfa5bc85 100644 --- a/usegalaxy.org/machine_learning.yml.lock +++ b/usegalaxy.org/machine_learning.yml.lock @@ -1,14 +1,20 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Machine Learning tools: - name: model_prediction owner: bgruening revisions: + - 1e088aa741eb + - 25b46af53232 + - 29e4122c90de - 60c726f5cc5e - 65820fb7257b - 83228baae3c5 + - 948eca2af157 + - 980bf31faa05 + - 9991c4ddde14 - b237f27a8afc - ce00f1cccb03 tool_panel_section_id: machine_learning @@ -18,9 +24,15 @@ tools: revisions: - 0c933465d70e - 2a853a2d2e72 + - 2b8d85927742 - 2d8478144bb2 + - 4d81e3e2fb63 + - 61a6132df9e0 + - 8a794e6d3388 - 94d91334c787 + - b9906ce4756c - bedbda03c573 + - f22a9297440f tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: keras_model_builder @@ -28,18 +40,30 @@ tools: revisions: - 053570bac5ea - 1f0c955fabc7 + - 20cd4269deb2 + - 522137aaa9c4 + 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tool_panel_section_label: Machine Learning - name: sklearn_estimator_attributes owner: bgruening revisions: - 07843f917990 + - 30d21a6041f6 + - 5a125d1ac9b9 + - 5ae00d2908f2 - 867caa39eaa4 - 89deaf399ff7 + - 9fda0b82f419 + - adaf2457d6ec - bd27a211182a - c9ddd20d25d0 + - d0352e8b4c10 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_model_validation owner: bgruening revisions: - 0474777be433 + - 30f892a9b46d - 4b359039f09f + - 5d5d9cc554f9 + - 61e76fb65daf + - 65f18ab91132 - 805194c3cdfb - 887e0aaa482e + - 9dc28a4b6ca8 - bfc7bdfcb423 + - e06ab1e112cc tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_svm_classifier owner: bgruening revisions: - 02d2be90dedb + - 0630258dcf35 - 14fa42b095c4 + - 6d23883e0b94 - 73d2ef652879 + - 80852884053f + - b7c3e9a3b954 - d2afc87db26b + - f458724cc317 - f9639b488779 + - fa9d6a4d95ad tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_sample_generator owner: bgruening revisions: - 0f460421b212 + - 1fe020b2108f - 7068b5fcd623 + - 7c2e71e4acf3 - ab2c393080f9 + - ab9977548806 - b4ba9602a36e - db7eb7302fc9 + - e99cccc3ca13 + - eb41d87cb1de + - fed1850f01c3 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_searchcv @@ -106,39 +162,63 @@ tools: revisions: - 103aaea17119 - 1ae5dfd5ac17 + - 1ddf415cb349 - 25ab6b4e376e + - 301e07345c93 + - 36e8d6d5d01b + - 7626ea9c2e1b - a36a45cb96fa + - d37a7f17e35d - e5a5ad882f1f + - f0d2e8a3c575 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_build_pipeline owner: bgruening revisions: - 0c74d3164ac8 + - 118e230e85ce + - 3f25f37ee3db + - 4c4ec859c31a - 7388ffedf12c + - 7442b94d6a1e - 840f29aad145 + - 9160cb4069c2 - 97dce66fe158 - 9c3e1d3235c8 + - b1eda492f063 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_pairwise_metrics owner: bgruening revisions: + - 053e7f32d37e - 09bfbef3dd90 - 1682b64aad9e - 226524df8c6c + - 2a1afd3481ce - 7366e5108e9f + - 7614281473da + - b07416ec8d16 + - c84ab9ca4e5c + - e79200975daf - f24deab884d0 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_nn_classifier owner: bgruening revisions: + - 2c58b83c9bad + - 309cc7c6af56 - 39ae3c043096 + - 4db563e8d453 + - 7ae443e6217d - 823ecc0bce45 + - 8b1b2b91f8d0 - 9871a634540f - aa83e7e3c398 - cd02bf168d23 + - d33d37f32e54 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_numeric_clustering @@ -147,47 +227,77 @@ tools: - 1dd433d2c92c - 2d7c60aa6c62 - 73e7f1c76ece + - 7dd3fb35904f + - 8eed73e8e04d - ad7e0b4291ee + - aeca97d9a214 + - bb9fc9d46ea4 + - e10e776f2109 + - e13a7c05b3a4 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: sklearn_ensemble owner: bgruening revisions: + - 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bgruening revisions: + - 03e0da430d44 - 24c1cc2dd4a4 + - 3af626081467 + - 945a53c248de + - c17f3eacdb14 + - caf164dd0e18 + - f06ad033c114 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: keras_train_and_eval owner: bgruening revisions: + - 0af678661e20 + - 2af1346e68c9 + - 470aed90aa41 + - 818f9b69d8a0 + - e1317b5502fa + - e29894cdea47 - ead8f1822587 + - f1b9a42d6809 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: scipy_sparse owner: bgruening revisions: + - 42b513bed40b + - 4efac966af2a + - 6d1a9fae57eb - 92e09b827300 + - 9f9cf31e3111 + - b7e93c1deb3f + - e6893a4bcb7b tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning - name: create_tool_recommendation_model owner: bgruening revisions: + - 4f7e6612906b - afec8c595124 + - e94dc7945639 + tool_panel_section_id: machine_learning + tool_panel_section_label: Machine Learning +- name: chopin2 + owner: iuc + revisions: + - d49893faf877 tool_panel_section_id: machine_learning tool_panel_section_label: Machine Learning diff --git a/usegalaxy.org/mapping.yml b/usegalaxy.org/mapping.yml index a7fbc969..fd9ced1f 100644 --- a/usegalaxy.org/mapping.yml +++ b/usegalaxy.org/mapping.yml @@ -24,3 +24,11 @@ tools: owner: iuc - name: rna_starsolo owner: iuc +- name: bwa_mem2 + owner: iuc +- name: pileometh + owner: bgruening +- name: bbtools_bbmap + owner: iuc +- name: metilene + owner: rnateam \ No newline at end of file diff --git a/usegalaxy.org/mapping.yml.lock b/usegalaxy.org/mapping.yml.lock index 02d55aeb..af7af428 100644 --- a/usegalaxy.org/mapping.yml.lock +++ b/usegalaxy.org/mapping.yml.lock @@ -1,31 +1,35 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Mapping tools: - name: bioext_bealign owner: iuc revisions: + - a07a2d9ddd42 + - a287431cdf4f - d8b6f0adaa79 - f9b72a376ec9 - fb4975b507c6 - - a287431cdf4f - - a07a2d9ddd42 tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: bowtie2 owner: devteam revisions: - 017aba02828d + - 03e9b2fbc005 + - 09b2cdb7ace5 - 749c918495f7 - c3dd1aeb7d07 - - 09b2cdb7ace5 + - f6877ad76b00 tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: lastz owner: devteam revisions: - 2ff111fac1d7 + - 37b497aa133f + - 3e1ea2facca6 - e7f19d6a9af8 tool_panel_section_id: mapping tool_panel_section_label: Mapping @@ -35,6 +39,7 @@ tools: - 01ac0a5fedc3 - 3fe632431b68 - 64f11cf59c6e + - e188dc7a68e6 tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: star_fusion @@ -73,33 +78,73 @@ tools: owner: iuc revisions: - 29bdbc353f20 - - b4e6819b25ef - - 6da3972210ee - 62f5fab76dfb + - 6da3972210ee + - a6ea26c1f225 + - b4e6819b25ef + - d82648ad25a3 tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: minimap2 owner: iuc revisions: + - 09b53c1d4ab1 + - 11a0d50a54e6 + - 1f06dccdc5d1 - 3f4d6399997b - 53c0b7a1a0c3 + - 77b2770508f6 - 8c6cd2650d1f - b3eab4b67562 - - 77b2770508f6 - - f54f5baedfdd - - 1f06dccdc5d1 - - 09b53c1d4ab1 + - be1d967337e4 - c0c2d0941de8 - - 11a0d50a54e6 + - f54f5baedfdd tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: rna_starsolo owner: iuc revisions: + - 13022c3d3076 - 178bdbdb6d24 + - 42ce70172b72 + - 5ef7ec16b04f + - 79b885ce78d7 + - a6fba3d92531 - e403d27e8f24 - ec9cbd6b9a49 - - a6fba3d92531 - eec9494fdafa tool_panel_section_id: mapping tool_panel_section_label: Mapping +- name: bwa_mem2 + owner: iuc + revisions: + - 88bcfaea2fb6 + - b4a22d90cce9 + - bfaa0d22c2e4 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: pileometh + owner: bgruening + revisions: + - 15df15127c18 + - 183cb55b1729 + - 906db57d5d65 + - d6787bab7b11 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: bbtools_bbmap + owner: iuc + revisions: + - 3171f7f52576 + - 517464809c33 + - 858a65b52cf9 + - 9ed6579f52f3 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: metilene + owner: rnateam + revisions: + - 37abd09a0ae6 + - cd253831a014 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping diff --git a/usegalaxy.org/metagenomic_analysis.yml b/usegalaxy.org/metagenomic_analysis.yml index 40258d49..7197a35a 100644 --- a/usegalaxy.org/metagenomic_analysis.yml +++ b/usegalaxy.org/metagenomic_analysis.yml @@ -94,3 +94,31 @@ tools: owner: iuc - name: staramr owner: nml +- name: vapor + owner: iuc +- name: krakentools_kreport2krona + owner: iuc +- name: humann_regroup_table + owner: iuc +- name: humann + owner: iuc +- name: humann_renorm_table + owner: iuc +- name: metaphlan + owner: iuc +- name: humann_unpack_pathways + owner: iuc +- name: humann_split_stratified_table + owner: iuc +- name: humann_rename_table + owner: iuc +- name: combine_metaphlan2_humann2 + owner: bebatut +- name: mash + owner: iuc +- name: mash_sketch + owner: iuc +- name: metabat2 + owner: iuc +- name: megahit_contig2fastg + owner: iuc diff --git a/usegalaxy.org/metagenomic_analysis.yml.lock b/usegalaxy.org/metagenomic_analysis.yml.lock index 4aefb8a4..7b8cd732 100644 --- a/usegalaxy.org/metagenomic_analysis.yml.lock +++ b/usegalaxy.org/metagenomic_analysis.yml.lock @@ -1,11 +1,12 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Metagenomic Analysis tools: - name: kraken2 owner: iuc revisions: + - 20e2f64aa1fe - 328c607150ff - 4a9da2b6c2e3 - e674066930b2 @@ -14,15 +15,18 @@ tools: - name: diamond owner: bgruening revisions: + - 1e3323a44643 + - 54f751e413f4 - 62c9df8382c2 - 64be1ac21109 + - e8ac2b53f262 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: vsearch owner: iuc revisions: - - b3c7199d8786 - 9495df9dd6ef + - b3c7199d8786 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: vegan_rarefaction @@ -60,8 +64,7 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - - c9f8fef1df74 + - e9005d1f3cfd tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: scikit_bio_diversity_beta_diversity @@ -79,24 +82,35 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: + - 27d65c78863c - b11b3ac48bb9 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: biom_add_metadata owner: iuc revisions: + - 0b3c3ad92827 - 28ad7ac9c193 - - e3cbd2287f63 + - 3b6f97e7094c + - 4a6ee918c13a + - 6ef0b5664c69 - a3b86937ead6 + - dad9da48a09a + - e3cbd2287f63 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: biom_convert owner: iuc revisions: + - 091bb5922a82 - 0de92f0b96ef + - 1b5fc03380d4 + - 54ccb7e1f49a - 584008e574b2 + - 72ed72122deb + - a4db66553a61 - bd46669113b9 - - 54ccb7e1f49a + - e177a8ea0bf1 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: kraken_translate @@ -104,6 +118,7 @@ tools: revisions: - 9a5be5b1a5c9 - 9bdcba262627 + - bc3e90fd13be tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: kraken_filter @@ -116,6 +131,7 @@ tools: - name: kraken2tax owner: devteam revisions: + - 50bd98b3ae5a - f03c7ba8d8bc tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis @@ -128,31 +144,41 @@ tools: - name: cat_add_names owner: iuc revisions: + - 21bf2f07f3f3 - 8dfc90f35aba + - acd9fe45eb81 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: cat_prepare owner: iuc revisions: + - 51906c8c692a - 8315b5cebb82 + - a40bbd70b8b1 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: cat_contigs owner: iuc revisions: + - 7aebc0137f20 - c6c77d840993 + - f41dbb0b9ff8 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: cat_summarise owner: iuc revisions: + - 388e6678fa98 - 7f1aaa1932d8 + - a8216def322b tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: cat_bins owner: iuc revisions: + - 0e63d03c8790 - 18676df0cb3a + - 31853794ace2 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_plotqualityprofile @@ -160,9 +186,11 @@ tools: revisions: - 2a90d2fd3336 - 52a911972c02 - - fa11922f3d91 - - f947b4bb5107 + - 7b8cb2b02978 + - a58e4a43f49c - d60df8727f59 + - f947b4bb5107 + - fa11922f3d91 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_plotcomplexity @@ -170,9 +198,11 @@ tools: revisions: - 1728e5ee871a - 498d57610fcd + - 555ccac8a4c5 + - 78faebd0879c - 806fe614ca46 - - ac72310b038a - 8daf4564ccda + - ac72310b038a tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_assigntaxonomyaddspecies @@ -180,58 +210,70 @@ tools: revisions: - 1c9715cef808 - 4d89978c6188 - - 79212a309499 - 5b5a7af9fbb4 - 63f86089423e + - 76d3d2b10738 + - 79212a309499 + - 7c2100246a2f tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_removebimeradenovo owner: iuc revisions: + - 04144473e59e + - 1bc3657cd694 - 5b752525bd6f + - 7136e9ab70db + - 7f3b59dee073 - 7f8f0e9fcb37 - b6dddf8c2e6f - - 04144473e59e - - 7f3b59dee073 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_filterandtrim owner: iuc revisions: - 23fc35093b11 + - 34e55239e68b - 777f9846c56d + - a9f4a217dcd6 + - addaf9d22850 - ca73bbac615a - f732237754fc - - a9f4a217dcd6 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_dada owner: iuc revisions: + - 18a502a9d287 + - 1c35dadbe76f - 2222f08c8316 - 6b4ddc3b64bd + - 84fd33a60b35 + - 96336c6a2bb7 - f79565b12646 - - 18a502a9d287 - - 1c35dadbe76f tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_learnerrors owner: iuc revisions: + - 04c15826a0b8 + - 0776d824d896 - 39638e0aff59 + - 75403243703a + - 8c202e741d68 - afdfa35a89d9 - c48d42d65d2b - - 8c202e741d68 - - 04c15826a0b8 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_makesequencetable owner: iuc revisions: + - 1c9b3bcd4261 + - 43c99742158b + - 8470de786d47 - 99c6929236fa - 9ccec6ed8e82 - bfd62e881837 - - 1c9b3bcd4261 - e96bbb9e24ea tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis @@ -239,34 +281,38 @@ tools: owner: iuc revisions: - 0b884b080bb6 + - 1d75bd0595e2 + - 306a40d4bb8f + - 5c865a382933 - 69900ffd3b8e + - 84743da21318 - b1e55c248f17 - - 306a40d4bb8f - - 1d75bd0595e2 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: dada2_seqcounts owner: iuc revisions: + - 0a1224c4b781 + - 19299bb1c6af - 4cc834cce4fb - 7d28da5e9e27 - - f74c56549143 + - 9058d8943303 - d943081510da - - 0a1224c4b781 + - f74c56549143 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: bio_hansel owner: iuc revisions: - - e3698ac146d7 - 4deefd708943 + - e3698ac146d7 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: khmer_partition owner: iuc revisions: - - e562293ee5ec - b7429b53be2a + - e562293ee5ec tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: khmer_extract_partitions @@ -279,8 +325,8 @@ tools: - name: khmer_count_median owner: iuc revisions: - - 77410799e8e9 - 06d1d91c67e5 + - 77410799e8e9 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: khmer_filter_below_abundance_cutoff @@ -314,13 +360,16 @@ tools: - name: khmer_abundance_distribution owner: iuc revisions: - - e0de12ae3fc2 - c0caca5af183 + - e0de12ae3fc2 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: maxbin2 owner: mbernt revisions: + - 2bc40bfbcfb4 + - 8a0473eb465e + - 9da9706f7ca9 - cfd50144a871 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis @@ -328,12 +377,14 @@ tools: owner: iuc revisions: - 280386b252a5 + - 45210df786b9 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: plasflow owner: iuc revisions: - bda6012394f7 + - ea270d0ad0e6 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: valet @@ -345,6 +396,106 @@ tools: - name: staramr owner: nml revisions: + - 2fd4d4c9c5c2 + - 3b22de20bd4b - da787fc8b740 tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis +- name: vapor + owner: iuc + revisions: + - 244812f5bd1f + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: krakentools_kreport2krona + owner: iuc + revisions: + - 2deaada69b14 + - 88d274322340 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: humann_regroup_table + owner: iuc + revisions: + - 31c6d107e7a5 + - 79706f10d680 + - e88b731dad59 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: humann + owner: iuc + revisions: + - 95bf7479d53c + - fc6c328c292f + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: humann_renorm_table + owner: iuc + revisions: + - 12fb63b5f63f + - a293a742194f + - d7e9a3c41657 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: metaphlan + owner: iuc + revisions: + - 1a6cdf55390f + - ec368db926f4 + - fd69c607b43f + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: humann_unpack_pathways + owner: iuc + revisions: + - 080ea153677c + - 2d35528d2141 + - 5e5a999ffaa9 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: humann_split_stratified_table + owner: iuc + revisions: + - 64bc7acc22a9 + - 6fcb8ac37a3e + - 97f7bb0851e7 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: humann_rename_table + owner: iuc + revisions: + - 094ad9c068af + - 172920f67a84 + - 714d5a28cc5c + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: combine_metaphlan2_humann2 + owner: bebatut + revisions: + - fdfb35745104 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: mash + owner: iuc + revisions: + - 86dec4abcea8 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: mash_sketch + owner: iuc + revisions: + - 43f9ca23c132 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: metabat2 + owner: iuc + revisions: + - eb50e7eca3dc + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: megahit_contig2fastg + owner: iuc + revisions: + - 4ec5b3777508 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis diff --git a/usegalaxy.org/mimodd.yml.lock b/usegalaxy.org/mimodd.yml.lock index d3a388b6..1fb25ad7 100644 --- a/usegalaxy.org/mimodd.yml.lock +++ b/usegalaxy.org/mimodd.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: MiModD tools: diff --git a/usegalaxy.org/monocle3.yml b/usegalaxy.org/monocle3.yml new file mode 100644 index 00000000..8fcd49bc --- /dev/null +++ b/usegalaxy.org/monocle3.yml @@ -0,0 +1,20 @@ +tool_panel_section_label: Monocle3 +tools: +- name: monocle3_create + owner: ebi-gxa +- name: monocle3_partition + owner: ebi-gxa +- name: monocle3_diffexp + owner: ebi-gxa +- name: monocle3_preprocess + owner: ebi-gxa +- name: monocle3_plotcells + owner: ebi-gxa +- name: monocle3_reducedim + owner: ebi-gxa +- name: monocle3_learngraph + owner: ebi-gxa +- name: monocle3_topmarkers + owner: ebi-gxa +- name: monocle3_ordercells + owner: ebi-gxa diff --git a/usegalaxy.org/monocle3.yml.lock b/usegalaxy.org/monocle3.yml.lock new file mode 100644 index 00000000..2e02da58 --- /dev/null +++ b/usegalaxy.org/monocle3.yml.lock @@ -0,0 +1,59 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Monocle3 +tools: +- name: monocle3_create + owner: ebi-gxa + revisions: + - ada68a9d0aec + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 +- name: monocle3_partition + owner: ebi-gxa + revisions: + - d98b4705eb4c + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 +- name: monocle3_diffexp + owner: ebi-gxa + revisions: + - d43a608d14ac + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 +- name: monocle3_preprocess + owner: ebi-gxa + revisions: + - c150370b514c + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 +- name: monocle3_plotcells + owner: ebi-gxa + revisions: + - 91980addce5e + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 +- name: monocle3_reducedim + owner: ebi-gxa + revisions: + - 8900e2a18603 + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 +- name: monocle3_learngraph + owner: ebi-gxa + revisions: + - 5f877012f7af + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 +- name: monocle3_topmarkers + owner: ebi-gxa + revisions: + - a4ab4af54b1a + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 +- name: monocle3_ordercells + owner: ebi-gxa + revisions: + - 3e77dc421569 + tool_panel_section_id: monocle3 + tool_panel_section_label: Monocle3 diff --git a/usegalaxy.org/mothur.yml.lock b/usegalaxy.org/mothur.yml.lock index a71f3fd5..1efd4b9b 100644 --- a/usegalaxy.org/mothur.yml.lock +++ b/usegalaxy.org/mothur.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Mothur tools: @@ -8,18 +8,18 @@ tools: revisions: - 696ed5c6d1f0 - 71e7d93a593e + - a97107cc4c93 - af3efbe580c0 - ec53d27ee602 - - a97107cc4c93 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_merge_count owner: iuc revisions: + - 6e3d1e4c9786 + - 9696e3b3a098 - ccba5bd49390 - d5610390efaa - - 9696e3b3a098 - - 6e3d1e4c9786 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_chimera_vsearch @@ -36,18 +36,18 @@ tools: owner: iuc revisions: - 03b326e1f6a1 - - ba2b321b6b64 - - ac151f3a8f94 - 583af69719db + - ac151f3a8f94 + - ba2b321b6b64 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_biom_info owner: iuc revisions: - - 3b426f118175 - - 76d968f820ac - 223e748e0268 - 31fa2d557ff2 + - 3b426f118175 + - 76d968f820ac tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_venn @@ -55,9 +55,9 @@ tools: revisions: - 139bdc1c3b48 - 200defe4c42b + - 4db54b1c1d83 - 8df8d8b67b13 - e4f4c1c0d193 - - 4db54b1c1d83 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_unique_seqs @@ -73,75 +73,75 @@ tools: - name: mothur_unifrac_weighted owner: iuc revisions: + - 09f802a2c3fa - 136cb4f4b996 - 7cb9b120fd44 - - 09f802a2c3fa - 88c441e56578 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: 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tool_panel_section_label: Mothur - name: mothur_summary_single owner: iuc revisions: + - 2344ed181ae6 - 2857a688a7e9 - 72be09dfd803 - '782564664543' - de4801f05e5e - - 2344ed181ae6 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_summary_shared owner: iuc revisions: + - 545234c1d925 - 74c8ebee088c - 81df36f90a1b - 8c18ced5e8c3 - - 545234c1d925 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_summary_seqs @@ -150,17 +150,17 @@ tools: - 4041dc69af62 - 411ddfefe041 - 4af62516059b - - d7ea2d0b4917 - 609770e516fa + - d7ea2d0b4917 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_summary_qual owner: iuc revisions: - 11be0e5f3ebb - - d50fdfdc2a0c - 656ffc277a38 - 86a40294e149 + - d50fdfdc2a0c tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_sub_sample @@ -169,34 +169,34 @@ tools: - 0f4dfa0332e8 - 2986f7b01e74 - 34e1fbd32a04 - - 893d9058d563 - 67cb43432196 + - 893d9058d563 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tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_get_label owner: iuc revisions: + - 07d9a6a72e6d - 80b791e2a7bd - bb8b69e90604 - - 07d9a6a72e6d - ee13e5a4f9f3 tool_panel_section_id: mothur tool_panel_section_label: Mothur @@ -809,74 +809,74 @@ tools: owner: iuc revisions: - 081d0fbf9751 - - f2b626fe7082 - - f220bbab51e1 - 65d9f4688890 + - f220bbab51e1 + - f2b626fe7082 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_get_groups owner: iuc revisions: + - 03af14e245fb - b1c35f71607f - cfeef38a433e - dd84e5f5eeaa - e4d70a26c19f - - 03af14e245fb tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_get_dists owner: iuc revisions: + - 10005fd5ad53 - 6936b18e2a9e - c8fbbada97dc - d1fba6b01a90 - - 10005fd5ad53 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_get_coremicrobiome owner: iuc revisions: - 42244e3619cf - - ae1411cffbee - 618612060af3 + - ae1411cffbee - da05ce41f8f0 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_get_communitytype owner: iuc revisions: + - 10c5aa12a1d5 - 4e708ec53432 - - beb4e0832f3b - 79dc573692a4 - - 10c5aa12a1d5 + - beb4e0832f3b tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_filter_shared owner: iuc revisions: - 007311ce6297 - - e44c38a17c7a - - 382b60f3756e - 2d1dbf69f589 + - 382b60f3756e + - e44c38a17c7a tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_filter_seqs owner: iuc revisions: + - 3524ca06478e - 89b9efa3c1f0 - a0ce9fb3f260 - b587a3a485b8 - e71c69acde3f - - 3524ca06478e tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_fastq_info owner: iuc revisions: - 1edab4936153 - - f02f3ca6dfd1 - 25f02dced96c - a630c5167f5d + - f02f3ca6dfd1 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_dist_shared @@ -892,47 +892,47 @@ tools: - name: mothur_dist_seqs owner: iuc revisions: + - 0554c9338ca0 - 10f5ecfab7bb - 502323efbd82 - 57eb5df69242 - dcbf475d7d60 - - 0554c9338ca0 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_deunique_tree owner: iuc revisions: - - 98083c5a4338 - - ec5e03c0f18e - 1ace9d6863aa + - 98083c5a4338 - d247213cebfc + - ec5e03c0f18e tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_deunique_seqs owner: iuc revisions: - 0369aff1be76 - - 73aeeac872d7 - 276c9f17a9a2 + - 73aeeac872d7 - f6c604b2793e tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_degap_seqs owner: iuc revisions: - - 2393ecc7387c - - a7fced14ce99 - 1cbf0af70205 + - 2393ecc7387c - 6f08af23888a + - a7fced14ce99 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_create_database owner: iuc revisions: + - 16f6d606521a - 319884cd49a3 - 34669a26ea47 - 3cd1ccb4d58b - - 16f6d606521a tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_count_seqs @@ -940,64 +940,64 @@ tools: revisions: - 014583f8e83b - 59a962f57cb5 + - 7a6f9c899221 - 9cfefba79f40 - f00841c6fc14 - - 7a6f9c899221 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_count_groups owner: iuc revisions: + - 03c86648a52e - 28867c3771e1 - 7b7f375b9b8d - a0fc4eb349af - dc02f3831a1a - - 03c86648a52e tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_corr_axes owner: iuc revisions: + - 03b02c255008 - 0968daa9b52f - 1ba1fe2a0438 - 9db54b02c49d - - 03b02c255008 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_cooccurrence owner: iuc revisions: - 0e05f58541d0 - - 57fe046c8fbe - 512d7ce50a57 + - 57fe046c8fbe - ffdcb7942343 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_consensus_seqs owner: iuc revisions: + - 6f281dc9d01c - bc2b62823fcc - - e432f17722c8 - e14fb5184328 - - 6f281dc9d01c + - e432f17722c8 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_collect_single owner: iuc revisions: - 7f212a2a4a3b - - d3b196069f6f - acfb60d5d435 - c9d3eed082fc + - d3b196069f6f tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_collect_shared owner: iuc revisions: + - 21a043c3ae00 - 44d5c9ba72e6 - 9c78c5ffa049 - d7de4aa1fdd1 - - 21a043c3ae00 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_cluster @@ -1005,37 +1005,37 @@ tools: revisions: - 1b695ad32179 - 3bb756df109c + - 528f950d1044 - 5ea1f1f9d801 - c31bcc652db3 - - 528f950d1044 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_cluster_split owner: iuc revisions: + - 1b7fd1678230 - 2c02989afecb - a54f91ad1c84 - a9924d4f538f - c697df7d7a48 - - 1b7fd1678230 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_cluster_fragments owner: iuc revisions: + - 08b0e9f01d65 - 5fa9b6d481f6 - 881f9a4013a9 - f49de3951b73 - - 08b0e9f01d65 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_cluster_classic owner: iuc revisions: - 6ba59950d95c - - a649d3ca67b7 - 97ac7726c985 - 9bae6b20ed44 + - a649d3ca67b7 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_clearcut @@ -1050,30 +1050,30 @@ tools: - name: mothur_classify_tree owner: iuc revisions: - - 931e9b25e81d - - fec1c905cb22 - 17081663ab68 - 5d8809423177 + - 931e9b25e81d + - fec1c905cb22 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_classify_seqs owner: iuc revisions: + - 09bf9e496c64 - 2f5d4d86eb9a - 5da484e2c7a4 - 65b370206748 - 8ca80de3f4ef - - 09bf9e496c64 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_classify_otu owner: iuc revisions: + - 02446d12c359 - 29882f4a1ef3 - 86b2201a1f4b - c384c39c9c27 - ec7c3ecca41a - - 02446d12c359 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_chop_seqs @@ -1088,28 +1088,28 @@ tools: - name: mothur_chimera_uchime owner: iuc revisions: + - 0706d327ecae - 4e3780d096af - - f1742cf23d95 - 89ae96c8d333 - - 0706d327ecae + - f1742cf23d95 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_chimera_slayer owner: iuc revisions: + - 0fde524609b1 - 753321ddded9 - a899cc1416bc - - 0fde524609b1 - ab328c924a02 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_chimera_pintail owner: iuc revisions: + - 5f66e6f7f6c0 - 93b61db8bdb6 - cc3eef74fe31 - d06d799b19ae - - 5f66e6f7f6c0 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_chimera_perseus @@ -1126,53 +1126,53 @@ tools: revisions: - 35c91da65b75 - 4b57c3241cbc - - c4572980d8f9 - 74dfe7be1563 + - c4572980d8f9 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_chimera_ccode owner: iuc revisions: + - 751904c1033d - 79255ca0b19a - - b6e0f8a9bc6b - 983b440a26b2 - - 751904c1033d + - b6e0f8a9bc6b tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_chimera_bellerophon owner: iuc revisions: + - 14a7c1eca23d - ad0df6ad0499 - - cf1db89b0fda - b732e27030e8 - - 14a7c1eca23d + - cf1db89b0fda tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_bin_seqs owner: iuc revisions: - 3fc101a0498f - - 4bf939e17fa4 - 49a970c244c2 + - 4bf939e17fa4 - 65000a433c3b tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_anosim owner: iuc revisions: + - 4a283edb151c - 652d2803062c - - 98687b00be79 - 87c5f82dac4c - - 4a283edb151c + - 98687b00be79 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_amova owner: iuc revisions: - - 5aa5d26efeea - - d0074e20ae76 - 389ac95dc2f5 - 58b8ae43d27f + - 5aa5d26efeea + - d0074e20ae76 tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_align_seqs @@ -1189,9 +1189,9 @@ tools: owner: iuc revisions: - 0399e5aeaac6 - - dd533a49feed - - b2bc37b60346 - 2f668a63a256 + - b2bc37b60346 + - dd533a49feed tool_panel_section_id: mothur tool_panel_section_label: Mothur - name: mothur_hcluster diff --git a/usegalaxy.org/motif.yml.lock b/usegalaxy.org/motif.yml.lock index b3f516da..413a30b7 100644 --- a/usegalaxy.org/motif.yml.lock +++ b/usegalaxy.org/motif.yml.lock @@ -1,11 +1,12 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Motif tools: - name: meme_meme owner: iuc revisions: + - 19237efe98d1 - 3f0dd362b755 - 57e5d9382f36 - 9dd5373f6a5a @@ -17,6 +18,7 @@ tools: revisions: - 0c5239d1aa65 - c1a9a297ba8b + - c5209f38700d - d7a6ea1e3b9d tool_panel_section_id: motif tool_panel_section_label: Motif @@ -29,8 +31,9 @@ tools: - name: meme_psp_gen owner: iuc revisions: - - ff2f53a32d0e - 164067a66a5c + - 5f95d385a33c + - ff2f53a32d0e tool_panel_section_id: motif tool_panel_section_label: Motif - name: meme_chip diff --git a/usegalaxy.org/multiple_alignments.yml.lock b/usegalaxy.org/multiple_alignments.yml.lock index 7496c8e0..5fc2d2bf 100644 --- a/usegalaxy.org/multiple_alignments.yml.lock +++ b/usegalaxy.org/multiple_alignments.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Multiple Alignments tools: @@ -7,8 +7,8 @@ tools: owner: iuc revisions: - 020c78e91cc5 - - f24a9ff28d3c - e25ee6bac872 + - f24a9ff28d3c tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: maf_stats @@ -16,11 +16,14 @@ tools: revisions: - 0c84cce7b030 - 5a92f4c476b5 + - 87c1c223c704 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: interval2maf owner: iuc revisions: + - 1080e07a2233 + - 7adddc6015c1 - b79f6002b176 - cfea1d6354db tool_panel_section_id: multiple_alignments @@ -28,6 +31,8 @@ tools: - name: mafft owner: rnateam revisions: + - 6f28e90db932 + - a65296ffb4a0 - aaefa93c2dd2 - c5908940967d - f1a5908ea2cb @@ -36,7 +41,10 @@ tools: - name: clustalw owner: devteam revisions: + - 4daabc25df00 + - 5b097fde95dd - d6694932c5e0 + - d9c2b2fde6a3 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: msaboot @@ -57,45 +65,45 @@ tools: - name: mummer_mummer owner: iuc revisions: - - 48badcd29c5d - - fc143c06a842 - 48823c9635a4 + - 48badcd29c5d - bcd65de9725b + - fc143c06a842 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: mummer_dnadiff owner: iuc revisions: - 315c678562d2 - - deacc6b40cc0 - 60698466facd - c9685bc0407c + - deacc6b40cc0 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: mummer_show_coords owner: iuc revisions: - - b8e2c2f95d26 - - f8734af48332 - 959c1f8dae95 - b4124df98b26 + - b8e2c2f95d26 + - f8734af48332 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: mummer_mummerplot owner: iuc revisions: + - 4fc0cb2ac8ae - c0cedc12fcc5 - e8c60daa41e0 - ebe3b0f84de9 - - 4fc0cb2ac8ae tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: mummer_nucmer owner: iuc revisions: - 5b0b49b5421c - - a18fb4f826fc - 636b049e6141 + - a18fb4f826fc - e18267f90096 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments @@ -108,8 +116,8 @@ tools: - name: sina owner: iuc revisions: - - 49b937f12aa4 - 482052b30b78 + - 49b937f12aa4 - 56d7dc39eec8 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments @@ -117,13 +125,14 @@ tools: owner: iuc revisions: - 0243407479f1 + - 0c0288a9d92c - 13a99f96d6cc + - 1c65ddbaeefa - 1e70671a90c6 - 20bef04b5272 - 60ed1c94f584 - 8dc7708c3266 + - 97476dfde728 - a0ffbc759ad8 - - 1c65ddbaeefa - - 0c0288a9d92c tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments diff --git a/usegalaxy.org/nanopore.yml b/usegalaxy.org/nanopore.yml index b24be946..3f16f3a3 100644 --- a/usegalaxy.org/nanopore.yml +++ b/usegalaxy.org/nanopore.yml @@ -40,3 +40,5 @@ tools: owner: iuc - name: flye owner: bgruening +- name: pycoqc + owner: iuc diff --git a/usegalaxy.org/nanopore.yml.lock b/usegalaxy.org/nanopore.yml.lock index 7725d820..013f4da4 100644 --- a/usegalaxy.org/nanopore.yml.lock +++ b/usegalaxy.org/nanopore.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Nanopore tools: @@ -97,68 +97,94 @@ tools: - name: nanoplot owner: iuc revisions: + - 0f1c34698076 - 645159bcee2d + - a3c4fe6f49ab - edbb6c5028f5 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: porechop owner: iuc revisions: - - 93d623d9979c + - 543cbeef3949 - 5f76b20953e5 + - 93d623d9979c tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: medaka_variant owner: iuc revisions: - - e86fcef8ed91 + - 0f5f4a208660 - 19f3b583a9b3 + - 222669c4afb6 + - 9fb055604648 - aabb4e1c0b7b + - cc36773a3681 + - e86fcef8ed91 + - eb746fa6f514 + - ec699520444c - edf6d4003fad - - 9fb055604648 - - 0f5f4a208660 - - 222669c4afb6 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: medaka_consensus owner: iuc revisions: - - 84dcccebad3d + - 0413e62b757a + - 18505fe2bdb1 - 22f6a0e7424f - - fbf007713188 + - 682d1e2c8be4 + - 84dcccebad3d + - b2aae698b9d3 + - d6cddc06aeae - eb1f4ba66dc6 - - 0413e62b757a - fa11aa8103b2 - - b2aae698b9d3 + - fbf007713188 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: medaka_variant_pipeline owner: iuc revisions: - - 148f32860445 - - efca385ce679 - - ea1833858055 - 1040a307be0c - - 7623e5888be9 - - 597407d61386 + - 148f32860445 + - 1d62240feff3 - 3fbefde449bc + - 597407d61386 + - 7623e5888be9 + - ea1833858055 + - efca385ce679 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: medaka_consensus_pipeline owner: iuc revisions: + - 0e9e7fcdd543 + - 1ca4ce7241fd + - 2c72b8c09a70 - 35666d44fe7a + - 72b5e9dda577 + - 79e9a869f40e - b35de691c42c + - cb34f00cc10f - d915879a88bc - - 2c72b8c09a70 - - 1ca4ce7241fd - - 0e9e7fcdd543 - - 72b5e9dda577 + - fc8804320156 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: flye owner: bgruening revisions: + - 0284be52bfcf + - 276f5d8712d5 - 3ee0ef312022 + - 8d4f03b5fe9d + - cb8dfd28c16f + - de24438c9988 + - e27815e82dd4 + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: pycoqc + owner: iuc + revisions: + - 3a2f2e24c37e + - dc1500f42073 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore diff --git a/usegalaxy.org/ncbi_blast_.yml.lock b/usegalaxy.org/ncbi_blast_.yml.lock index 9e55507f..0158b99e 100644 --- a/usegalaxy.org/ncbi_blast_.yml.lock +++ b/usegalaxy.org/ncbi_blast_.yml.lock @@ -1,19 +1,23 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: NCBI BLAST+ tools: - name: ncbi_blast_plus owner: devteam revisions: + - 0e3cf9594bb7 - 2889433c7ae1 - 5edc472ec434 + - a52d2d93e595 + - d999e774072a - e25d3acf6e68 tool_panel_section_id: ncbi_blast_ tool_panel_section_label: NCBI BLAST+ - name: kraken2 owner: iuc revisions: + - 20e2f64aa1fe - 328c607150ff - 4a9da2b6c2e3 - e674066930b2 diff --git a/usegalaxy.org/operate_on_genomic_intervals.yml.lock b/usegalaxy.org/operate_on_genomic_intervals.yml.lock index e15d6143..c4af2af7 100644 --- a/usegalaxy.org/operate_on_genomic_intervals.yml.lock +++ b/usegalaxy.org/operate_on_genomic_intervals.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Operate on Genomic Intervals tools: @@ -7,23 +7,27 @@ tools: owner: devteam revisions: - 381cd27bf67a + - debffd27642d tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals - name: concat owner: devteam revisions: - 35a89f8cc96e + - 73ca13a7ec5f tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals - name: subtract owner: devteam revisions: - 0145969324c4 + - 0427ca314f3d tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals - name: join owner: devteam revisions: + - 718d04143c31 - a10f49d9218a tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals @@ -31,30 +35,36 @@ tools: owner: devteam revisions: - 33b3f3688db4 + - 5b3c6135a982 + - 69c10b56f46d tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals - name: coverage owner: devteam revisions: - 4ef9819dc7fb + - e3363e087468 tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals - name: complement owner: devteam revisions: - 38c8bb402872 + - 8b6c6ec55c6e tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals - name: cluster owner: devteam revisions: - 05696474ee89 + - a126ec6ea0e4 tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals - name: basecoverage owner: devteam revisions: - 2cedec3759e4 + - 9c5ff4695c97 tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals - name: annotation_profiler @@ -66,6 +76,7 @@ tools: - name: flanking_features owner: devteam revisions: + - 9f12b7e500f1 - a09d13b108fd tool_panel_section_id: operate_on_genomic_intervals tool_panel_section_label: Operate on Genomic Intervals diff --git a/usegalaxy.org/pharmacology.yml.lock b/usegalaxy.org/pharmacology.yml.lock index 3507982b..d9b0ec5f 100644 --- a/usegalaxy.org/pharmacology.yml.lock +++ b/usegalaxy.org/pharmacology.yml.lock @@ -1,11 +1,12 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Pharmacology tools: - name: pharmcat owner: bgruening revisions: + - 891283e0ee89 - d67642a21a1d tool_panel_section_id: pharmacology tool_panel_section_label: Pharmacology diff --git a/usegalaxy.org/phenotype_association.yml b/usegalaxy.org/phenotype_association.yml index a21cf8b0..4a339f21 100644 --- a/usegalaxy.org/phenotype_association.yml +++ b/usegalaxy.org/phenotype_association.yml @@ -10,3 +10,7 @@ tools: owner: devteam - name: hgv_hilbertvis owner: devteam +- name: plink + owner: iuc +- name: qq_manhattan + owner: iuc diff --git a/usegalaxy.org/phenotype_association.yml.lock b/usegalaxy.org/phenotype_association.yml.lock index b42b82bb..d3b4b3e5 100644 --- a/usegalaxy.org/phenotype_association.yml.lock +++ b/usegalaxy.org/phenotype_association.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Phenotype Association tools: @@ -33,3 +33,15 @@ tools: - e1a9ad05dced tool_panel_section_id: phenotype_association tool_panel_section_label: Phenotype Association +- name: plink + owner: iuc + revisions: + - 2c0ac05fe240 + tool_panel_section_id: phenotype_association + tool_panel_section_label: Phenotype Association +- name: qq_manhattan + owner: iuc + revisions: + - 7a8a21c5a57f + tool_panel_section_id: phenotype_association + tool_panel_section_label: Phenotype Association diff --git a/usegalaxy.org/picard.yml.lock b/usegalaxy.org/picard.yml.lock index 46f2ff77..7c796e65 100644 --- a/usegalaxy.org/picard.yml.lock +++ b/usegalaxy.org/picard.yml.lock @@ -1,12 +1,16 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Picard tools: - name: picard owner: devteam revisions: + - 1aac2a13842a + - 585027e65f3b - 7d34178f2812 - a1f0b3f4b781 + - b502c227b5e6 + - f9242e01365a tool_panel_section_id: picard tool_panel_section_label: Picard diff --git a/usegalaxy.org/planttribes.yml.lock b/usegalaxy.org/planttribes.yml.lock index ddc5e4b7..0812f2e3 100644 --- a/usegalaxy.org/planttribes.yml.lock +++ b/usegalaxy.org/planttribes.yml.lock @@ -1,11 +1,12 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: PlantTribes tools: - name: plant_tribes_assembly_post_processor owner: greg revisions: + - 4d73965d99a2 - 9c72c91d291f tool_panel_section_id: planttribes tool_panel_section_label: PlantTribes @@ -30,12 +31,14 @@ tools: - name: plant_tribes_gene_family_phylogeny_builder owner: greg revisions: + - 13d2d138e0e2 - c088c185f63f tool_panel_section_id: planttribes tool_panel_section_label: PlantTribes - name: plant_tribes_kaks_analysis owner: greg revisions: + - 2c46551274d6 - 84615d553d44 tool_panel_section_id: planttribes tool_panel_section_label: PlantTribes diff --git a/usegalaxy.org/presto.yml.lock b/usegalaxy.org/presto.yml.lock index 6946f115..6bc26871 100644 --- a/usegalaxy.org/presto.yml.lock +++ b/usegalaxy.org/presto.yml.lock @@ -1,23 +1,23 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: pRESTO tools: - name: migmap owner: iuc revisions: - - 587fa797ede9 - - 6ad9d48a512e - 29ec7b3a458b - 2c9f2a24f7a4 + - 587fa797ede9 + - 6ad9d48a512e tool_panel_section_id: presto tool_panel_section_label: pRESTO - name: prestor_abseq3 owner: iuc revisions: - 097b44ff88db - - ef917c03493c - 967b96c6005a + - ef917c03493c - faba8f53524e tool_panel_section_id: presto tool_panel_section_label: pRESTO @@ -25,8 +25,8 @@ tools: owner: iuc revisions: - 0b103d43a2c7 - - 824d24bfe8dd - 620f3b0a1430 + - 824d24bfe8dd tool_panel_section_id: presto tool_panel_section_label: pRESTO - name: presto_parselog @@ -40,17 +40,17 @@ tools: - name: presto_parseheaders owner: iuc revisions: - - 90315cb06d06 - 1ed5b0772f98 - 4049467b8bb8 + - 90315cb06d06 tool_panel_section_id: presto tool_panel_section_label: pRESTO - name: presto_pairseq owner: iuc revisions: - - f47efbc66fad - - 7bdff30820bf - 49e7407445c3 + - 7bdff30820bf + - f47efbc66fad tool_panel_section_id: presto tool_panel_section_label: pRESTO - name: presto_maskprimers @@ -64,40 +64,40 @@ tools: - name: presto_filterseq owner: iuc revisions: - - 7b102129b1e8 - - 33a09d40751f - 196b83ac37f2 + - 33a09d40751f + - 7b102129b1e8 tool_panel_section_id: presto tool_panel_section_label: pRESTO - name: presto_collapseseq owner: iuc revisions: - - d1a1b738c119 - 3364fd7073ca - c60bd515e46d + - d1a1b738c119 tool_panel_section_id: presto tool_panel_section_label: pRESTO - name: presto_buildconsensus owner: iuc revisions: - - 7c7df98db5a9 - - 5b059629cce0 - 1844a3d2c887 + - 5b059629cce0 + - 7c7df98db5a9 tool_panel_section_id: presto tool_panel_section_label: pRESTO - name: presto_assemblepairs owner: iuc revisions: - - 44c980933450 - 0af48f0b7eb8 + - 44c980933450 - 540fcbdac82e tool_panel_section_id: presto tool_panel_section_label: pRESTO - name: presto_alignsets owner: iuc revisions: + - 0b4bd722367d - 40102188d44e - fa4cf8d895f4 - - 0b4bd722367d tool_panel_section_id: presto tool_panel_section_label: pRESTO diff --git a/usegalaxy.org/protein_modeling.yml.lock b/usegalaxy.org/protein_modeling.yml.lock index a413ce1c..d652d039 100644 --- a/usegalaxy.org/protein_modeling.yml.lock +++ b/usegalaxy.org/protein_modeling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Protein Modeling tools: diff --git a/usegalaxy.org/proteomics.yml b/usegalaxy.org/proteomics.yml index e450b60f..5323c9d5 100644 --- a/usegalaxy.org/proteomics.yml +++ b/usegalaxy.org/proteomics.yml @@ -12,3 +12,23 @@ tools: owner: galaxyp - name: msstats owner: galaxyp +- name: eggnog_mapper + owner: galaxyp +- name: encyclopedia_quantify + owner: galaxyp +- name: encyclopedia_searchtolib + owner: galaxyp +- name: openms_decoydatabase + owner: galaxyp +- name: openms_featurefindermultiplex + owner: galaxyp +- name: openms_msgfplusadapter + owner: galaxyp +- name: openms_peptideindexer + owner: galaxyp +- name: openms_falsediscoveryrate + owner: galaxyp +- name: openms_idmapper + owner: galaxyp +- name: openms_metaprosip + owner: galaxyp diff --git a/usegalaxy.org/proteomics.yml.lock b/usegalaxy.org/proteomics.yml.lock index 31d50ff7..b7e4ad4c 100644 --- a/usegalaxy.org/proteomics.yml.lock +++ b/usegalaxy.org/proteomics.yml.lock @@ -1,15 +1,16 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Proteomics tools: - name: peptideshaker owner: galaxyp revisions: + - 1beff3ddce58 - 3634c90301af - - f35bb9d0c93e + - 3ec27b4cee7c - 7fdd9119cc4f - - 1beff3ddce58 + - f35bb9d0c93e tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: custom_pro_db @@ -22,23 +23,100 @@ tools: owner: galaxyp revisions: - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: peptide_genomic_coordinate owner: galaxyp revisions: - 5f49ffce52cb + - cb0378d2d487 tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: maxquant owner: galaxyp revisions: + - 163452d1e255 + - 1f39c833f65f + - 4d17fcdeb8ff + - 837224ad1694 + - 8934bc76bb52 - ea0a1d50c83f + - f522c08e900c tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: msstats owner: galaxyp revisions: + - 28434abe6c5c + - 52ac6fde9a5b + - 593839e1f2c3 - 8212e342e482 + - b7034eff0db1 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: eggnog_mapper + owner: galaxyp + revisions: + - 9d1fbff733cf + - d9c3016f7283 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: encyclopedia_quantify + owner: galaxyp + revisions: + - 0fa397f4f40b + - 1c5cbf8f79ce + - 4081e4faa4ab + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: encyclopedia_searchtolib + owner: galaxyp + revisions: + - 36880dfd9fa7 + - 62a718b76f62 + - fb192dd6658a + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_decoydatabase + owner: galaxyp + revisions: + - 25529df60a81 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_featurefindermultiplex + owner: galaxyp + revisions: + - 9876bda3ec53 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_msgfplusadapter + owner: galaxyp + revisions: + - f5ec766d80cf + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_peptideindexer + owner: galaxyp + revisions: + - d6aca689dd48 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_falsediscoveryrate + owner: galaxyp + revisions: + - 6ccbf9a2072c + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_idmapper + owner: galaxyp + revisions: + - adca857b4884 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_metaprosip + owner: galaxyp + revisions: + - 819ed5aae76f tool_panel_section_id: proteomics tool_panel_section_label: Proteomics diff --git 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tool_panel_section_id: qiime2 + tool_panel_section_label: QIIME2 +- name: qiime2__vsearch__uchime_denovo + owner: q2d2 + revisions: + - 2ecd644cdfcf + tool_panel_section_id: qiime2 + tool_panel_section_label: QIIME2 +- name: qiime2__vsearch__uchime_ref + owner: q2d2 + revisions: + - 7dbbd990440e + tool_panel_section_id: qiime2 + tool_panel_section_label: QIIME2 +- name: qiime2_core__tools__export + owner: q2d2 + revisions: + - ddff0f6d5740 + tool_panel_section_id: qiime2 + tool_panel_section_label: QIIME2 +- name: qiime2_core__tools__import + owner: q2d2 + revisions: + - 18c6b2b6740f + tool_panel_section_id: qiime2 + tool_panel_section_label: QIIME2 diff --git a/usegalaxy.org/regional_variation.yml.lock b/usegalaxy.org/regional_variation.yml.lock index 9f60f2c8..76178b00 100644 --- a/usegalaxy.org/regional_variation.yml.lock +++ b/usegalaxy.org/regional_variation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Regional Variation tools: @@ -24,8 +24,8 @@ tools: - name: substitutions owner: devteam revisions: - - c54f5d0bbb58 - aca54f2b2151 + - c54f5d0bbb58 tool_panel_section_id: regional_variation tool_panel_section_label: Regional Variation - name: indels_3way diff --git a/usegalaxy.org/rna_analysis__deprecated_.yml.lock b/usegalaxy.org/rna_analysis__deprecated_.yml.lock index ebb3bf5c..672a4351 100644 --- a/usegalaxy.org/rna_analysis__deprecated_.yml.lock +++ b/usegalaxy.org/rna_analysis__deprecated_.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RNA Analysis (deprecated) tools: @@ -25,35 +25,37 @@ tools: - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - d080005cffe1 + - e04dbae2abe0 tool_panel_section_id: rna_analysis__deprecated_ tool_panel_section_label: RNA Analysis (deprecated) - name: cuffquant owner: devteam revisions: - - 6dc45faebc1d - 679d93c99757 + - 6dc45faebc1d tool_panel_section_id: rna_analysis__deprecated_ tool_panel_section_label: RNA Analysis (deprecated) - name: cuffnorm owner: devteam revisions: - - f5b2ee725d34 - 9a854107dbb2 + - f5b2ee725d34 tool_panel_section_id: rna_analysis__deprecated_ tool_panel_section_label: RNA Analysis (deprecated) - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - 6a6717a5f421 + - 86285ddd4512 + - cf747d1bd79a tool_panel_section_id: rna_analysis__deprecated_ tool_panel_section_label: RNA Analysis (deprecated) - name: cuffdiff owner: devteam revisions: - - d3ae7d9c2202 + - 43221aef70e2 - af3e173cad7f + - d3ae7d9c2202 tool_panel_section_id: rna_analysis__deprecated_ tool_panel_section_label: RNA Analysis (deprecated) diff --git a/usegalaxy.org/rna_seq.yml b/usegalaxy.org/rna_seq.yml index 1f1c856a..651c455c 100644 --- a/usegalaxy.org/rna_seq.yml +++ b/usegalaxy.org/rna_seq.yml @@ -72,6 +72,8 @@ tools: owner: iuc - name: trinity_run_de_analysis owner: iuc +- name: trinity_samples_qccheck + owner: iuc - name: trinity_super_transcripts owner: iuc - name: trinity @@ -84,6 +86,8 @@ tools: owner: iuc - name: trinity_filter_low_expr_transcripts owner: iuc +- name: trinity_gene_to_trans_map + owner: iuc - name: trinotate owner: iuc - name: tximport @@ -94,3 +98,23 @@ tools: owner: rnateam - name: mirdeep2 owner: rnateam +- name: cemitool + owner: iuc +- name: targetfinder + owner: rnateam +- name: chira_collapse + owner: iuc +- name: chira_extract + owner: iuc +- name: chira_map + owner: iuc +- name: chira_merge + owner: iuc +- name: chira_quantify + owner: iuc +- name: blockbuster + owner: rnateam +- name: blockclust + owner: rnateam +- name: isoformswitchanalyzer + owner: iuc diff --git a/usegalaxy.org/rna_seq.yml.lock b/usegalaxy.org/rna_seq.yml.lock index dbe6b9b7..eaca936e 100644 --- a/usegalaxy.org/rna_seq.yml.lock +++ b/usegalaxy.org/rna_seq.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RNA-seq tools: @@ -7,18 +7,25 @@ tools: owner: iuc revisions: - 0921444c832d + - 119b069fc845 - 58c35179ebf0 - 708348a17fa1 + - d6f5fa4ee473 - e827f9aae031 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: edger owner: iuc revisions: + - 070900306913 + - 0cb907a2a810 - 334ce9b1bac5 - 3d89af8a44f0 + - 5bf899c13979 - 6e53e565fc6a + - a8305cf0c951 - df0c8d0a5992 + - f2843df56434 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: hisat2 @@ -27,6 +34,7 @@ tools: - 0c16cad5e03b - 26371a1df031 - 6c19daec423d + - f4af63aaf57a - fbf98f24097b tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq @@ -34,11 +42,13 @@ tools: owner: iuc revisions: - 38b6d12edc68 + - 6f66ae7c5f7a - 90d16db017d7 - a37612abf7f9 - ce44c6f2ba38 - ea04b737afa0 - f3a5f075498f + - f9d49f5cb597 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: dexseq @@ -46,6 +56,8 @@ tools: revisions: - 62adf13b86ea - 9fd8b69e6e68 + - b47c006d90c5 + - df929f257179 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: stringtie @@ -54,30 +66,38 @@ tools: - 1ebd14235b92 - 333a6e13b622 - 76d290331481 + - 914cfcba0ec8 + - ae618321f34a + - cef79931dda5 - eba36e001f45 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: salmon owner: bgruening revisions: + - 15cd64d7c58b - 49121db48873 - 7fdb9d1591e2 - cc05793bb896 - e3d32471da11 + - ebab418107f5 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: diamond owner: bgruening revisions: + - 1e3323a44643 - 54f751e413f4 - 62c9df8382c2 - 64be1ac21109 + - e8ac2b53f262 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: kallisto_quant owner: iuc revisions: - 40985510cd98 + - 4f9c4e6566e5 - 60f888039fb2 - c971db6f0fe5 tool_panel_section_id: rna_seq @@ -88,6 +108,7 @@ tools: - 01247aaf0a10 - 5ae5c312d718 - 87c11c05d238 + - ce5d418183c5 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: sailfish @@ -99,6 +120,8 @@ tools: - name: goseq owner: iuc revisions: + - 43798b4caee0 + - 602de62d995b - 8b3e3657034e - ef2ad746b589 tool_panel_section_id: rna_seq @@ -109,6 +132,8 @@ tools: - 0696db066a5b - 6a3a025714d3 - 71bacea10eee + - 8fe98f7094de + - 9a882d108833 - cd9874cb9019 - d027d1f4984e tool_panel_section_id: rna_seq @@ -116,11 +141,15 @@ tools: - name: rgrnastar owner: iuc revisions: + - 3ea5a2a63fa2 - 4074fc1940e2 - 44959aa06aeb - 5ec75f5dae3c + - 79de45b5069b - 7ed2edc1337f - 850f3679b9b4 + - 980d2a2e1180 + - b0f2be869d6d - b9e04854e2bb - c772497b2c32 - d5659efd66aa @@ -137,6 +166,7 @@ tools: owner: lparsons revisions: - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: gffcompare @@ -144,12 +174,14 @@ tools: revisions: - 0f710191a66d - 3c97c841a443 + - f99dd58de04f tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: cuffmerge owner: devteam revisions: - 6a6717a5f421 + - 86285ddd4512 - cf747d1bd79a tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq @@ -188,6 +220,7 @@ tools: owner: iuc revisions: - 095162ba8e90 + - 55daa4712413 - 67af24676bd6 - 75427ceb32d1 tool_panel_section_id: rna_seq @@ -234,6 +267,7 @@ tools: - name: ruvseq owner: iuc revisions: + - 3a083c78896e - c24765926774 - d1f7fa5bb3cb - fed9d0350d72 @@ -253,10 +287,14 @@ tools: revisions: - 06ed31cf52ed - 4c139a9415d7 + - 56242ff81c84 - 764f076e9d52 - 7a5cd7987b03 - 828324f3292f + - 8c28affc7c48 + - c0fd285eb553 - c4db6ec33fec + - fab6ff46e019 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: slamdunk @@ -280,18 +318,30 @@ tools: owner: iuc revisions: - 04936df18de3 + - 24e94d84adc9 - 55cf05b65ad5 - ab87da55fe61 - bbbb39ad9a7e + - c63338cf419f + - eafea3083352 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: trinity_samples_qccheck + owner: iuc + revisions: + - 04bb8bb7c198 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: trinity_super_transcripts owner: iuc revisions: - 29472bde8854 + - 3064aa8755a0 + - 5c1fc038df6b - 6723249ce1bd - 6f480aee5877 - 9c545f1c1a4e + - bdede464821e tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: trinity @@ -300,6 +350,10 @@ tools: - 26d5493b20b6 - 3772d9a10f27 - 5b60313a6ce7 + - 77cf519a812e + - 8f1c3df4dd49 + - 9fa24d5aac68 + - d2bc35f3d1c5 - d84caa5a98ad - db1f362cca3e tool_panel_section_id: rna_seq @@ -308,17 +362,24 @@ tools: owner: iuc revisions: - 08326e2e82f1 + - 400691c87530 - 442e3696c634 - 59fff1388bc2 - 81a4697677e7 + - a009c96c5c18 + - ba3720d7e68b + - bcc5f03f1900 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: trinity_contig_exn50_statistic owner: iuc revisions: - 3cdcd5753218 + - 41db7569b4ba - 62b05e565a45 + - 870ac06dff8e - b1e9a0355166 + - be3f26533209 - beafdd47f8cf tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq @@ -326,18 +387,33 @@ tools: owner: iuc revisions: - 00719b8004c9 + - 2fb4ee002432 - 56162e446004 + - 75f4e1859ed7 - 893655fa55f9 - 983552d5822d + - b2bbe9a7f1b8 + - c2b82a94493e tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - 1007cdb58d91 + - 1fdb25a8384d - 42c5172815f7 - 42f93482524f + - a35cba31d904 - a5ec0e79a93a + - aa38fa8c5815 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: trinity_gene_to_trans_map + owner: iuc + revisions: + - 7c7fbf13aadd + - 964b7efe2639 + - ba460ccf0006 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: trinotate @@ -358,6 +434,7 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: + - a8d24f4b6d95 - dbbe92348c7a tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq @@ -373,3 +450,70 @@ tools: - 6a17e1229b9f tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq +- name: cemitool + owner: iuc + revisions: + - 3f9ff31c88bb + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: targetfinder + owner: rnateam + revisions: + - c9d56748fbde + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: chira_collapse + owner: iuc + revisions: + - 05996586c8b3 + - 2b2bfeda00d0 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: chira_extract + owner: iuc + revisions: + - 73d2b7a8d94b + - e7ee3aadf1a5 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: chira_map + owner: iuc + revisions: + - 7925dd016f53 + - 95ddee768b61 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: chira_merge + owner: iuc + revisions: + - 6492560fe1b4 + - 9930af9d17f8 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: chira_quantify + owner: iuc + revisions: + - 06ac35533793 + - 38d2b1f38992 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: blockbuster + owner: rnateam + revisions: + - 7c7ff7a3503f + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: blockclust + owner: rnateam + revisions: + - aab6cf87b40a + - dbb6ee3179bc + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: isoformswitchanalyzer + owner: iuc + revisions: + - 298d81e5e138 + - b3f292d9f35d + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq diff --git a/usegalaxy.org/rseqc.yml.lock b/usegalaxy.org/rseqc.yml.lock index 35ccb93a..03c61731 100644 --- a/usegalaxy.org/rseqc.yml.lock +++ b/usegalaxy.org/rseqc.yml.lock @@ -1,11 +1,12 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: RSeQC tools: - name: rseqc owner: nilesh revisions: + - 473382134e56 - f437057e46f1 tool_panel_section_id: rseqc tool_panel_section_label: RSeQC diff --git a/usegalaxy.org/sam_bam.yml b/usegalaxy.org/sam_bam.yml index 736d0240..c0ac1103 100644 --- a/usegalaxy.org/sam_bam.yml +++ b/usegalaxy.org/sam_bam.yml @@ -46,6 +46,14 @@ tools: owner: devteam - name: bamtools_filter owner: devteam +- name: bamtools_split_mapped + owner: iuc +- name: bamtools_split_paired + owner: iuc +- name: bamtools_split_ref + owner: iuc +- name: bamtools_split_tag + owner: iuc - name: samtools_depth owner: iuc - name: samtools_fastx @@ -66,3 +74,7 @@ tools: owner: iuc - name: bamutil_clip_overlap owner: iuc +- name: samtools_ampliconclip + owner: iuc +- name: revertr2orientationinbam + owner: lldelisle diff --git a/usegalaxy.org/sam_bam.yml.lock b/usegalaxy.org/sam_bam.yml.lock index d896a034..3762632e 100644 --- a/usegalaxy.org/sam_bam.yml.lock +++ b/usegalaxy.org/sam_bam.yml.lock @@ -1,17 +1,21 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: SAM/BAM tools: - name: samtools_sort owner: devteam revisions: + - 6c2c1836728b + - a577ea614bed - e613c1ad4c4c tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_mpileup owner: devteam revisions: + - 9da0311ab1dd + - b61f5d6a7f25 - fa7ad9b89f4a tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM @@ -19,6 +23,8 @@ tools: owner: devteam revisions: - 22970df7a40e + - fe34990e5ce7 + - fefd89ab563c tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtool_filter2 @@ -31,18 +37,23 @@ tools: - name: bam_to_sam owner: devteam revisions: + - 10184eaa85fc - 88eedb4abea0 + - a53efedba9e7 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_idxstats owner: devteam revisions: - 7a6034296ae9 + - 7def34e6cf4d + - fa5d3e61e429 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: sam_to_bam owner: devteam revisions: + - 9bd1568619cd - b77f7b516b17 - cf1ffd88f895 tool_panel_section_id: sam_bam @@ -52,11 +63,15 @@ tools: revisions: - 06dc50b7b711 - 3d873744df7e + - 92ec40abcdcf + - c89806670ab9 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_bedcov owner: devteam revisions: + - 46c6639921f1 + - 6856f8a01905 - 9149ad20699a tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM @@ -64,27 +79,36 @@ tools: owner: devteam revisions: - 135c85f4cfaf + - bcedabb53ddf + - bd850490c7f1 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_stats owner: devteam revisions: - 145f6d74ff5e + - 1cc79f49b8d5 - 24c5d43cb545 + - 3a0efe14891f - 47035d167365 + - fed4aa48ba09 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_slice_bam owner: devteam revisions: + - 344fc91e1bfd - a4a10c7924d1 + - b5c88b7b153e tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_reheader owner: devteam revisions: - - db000c6007a0 - 30388d878f81 + - bb8cfc6f6e0c + - d7b4851d1971 + - db000c6007a0 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_rmdup @@ -102,8 +126,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: pileup_parser @@ -135,7 +159,9 @@ tools: - name: bamtools_split owner: devteam revisions: + - 0a7b0989fa09 - 9676127a1ed2 + - 96c9315b0e29 - e2c1b62e1db1 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM @@ -144,66 +170,111 @@ tools: revisions: - 04866f817daa - 4d343c1f606b + - befc9dad4ca8 + - ddb22028b552 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: bamtools_filter owner: devteam revisions: + - 108db6635177 + - 1dfd95ee241e - 4fe8a75334c8 - bd735cae4ce6 - cb20f99fd45b tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM +- name: bamtools_split_mapped + owner: iuc + revisions: + - 6dbef7ea2253 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: bamtools_split_paired + owner: iuc + revisions: + - 5325e44297b9 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: bamtools_split_ref + owner: iuc + revisions: + - 9b520009db81 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: bamtools_split_tag + owner: iuc + revisions: + - e30af4e78cd3 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM - name: samtools_depth owner: iuc revisions: - - 44de678a44c4 - 2ee8dc1aeda9 + - 44de678a44c4 + - 56faa6a57e50 + - 971dc85e9441 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e + - 66e23b11feae - 720217c23995 + - a8d69aee190e + - b3d99709fe1a tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_fixmate owner: iuc revisions: - - bc0cc7bfbfe9 + - 41e36c99a008 - 595ae1ba934a + - bc0cc7bfbfe9 + - e5ece8fa99de tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_markdup owner: iuc revisions: - 83b8e36e9cbe + - 887e02a45734 - a312a0fdaf31 + - a389f74c3630 + - b5527cc104ab + - ce32171c6d44 - d0a568e1904b tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_merge owner: iuc revisions: + - 36677f429310 + - 65a38e8c8e2a - 740ce0a18f0d - 8890e2d4c068 + - b40e2d865d52 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_phase owner: devteam revisions: + - 1e5880498f52 - b5c3b1856370 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_view owner: iuc revisions: + - 0dbf49c414ae + - 5826298f6a73 + - 6be888be75f9 - b01db2684fa5 - - bf328cec6a42 - - ff313de5f7f4 - b72793637686 + - bf328cec6a42 - c370440f901e + - ff313de5f7f4 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: qualimap_multi_bamqc @@ -215,8 +286,8 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - ac607906f10a - 19ece8afbaab + - ac607906f10a - e7fd6754d093 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM @@ -226,3 +297,17 @@ tools: - 047a20d4258f tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM +- name: samtools_ampliconclip + owner: iuc + revisions: + - 5f3ea90dc6ae + - 6a8febad1f6c + - a941babb9268 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: revertr2orientationinbam + owner: lldelisle + revisions: + - 21ddefab2e4f + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM diff --git a/usegalaxy.org/seqtk.yml.lock b/usegalaxy.org/seqtk.yml.lock index f6a459a2..a0c08f61 100644 --- a/usegalaxy.org/seqtk.yml.lock +++ b/usegalaxy.org/seqtk.yml.lock @@ -1,12 +1,13 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Seqtk tools: - name: seqtk owner: iuc revisions: - - 58c8ece95b53 - 3da72230c066 + - 4b494533146a + - 58c8ece95b53 tool_panel_section_id: seqtk tool_panel_section_label: Seqtk diff --git a/usegalaxy.org/sequence_contamination_filtering.yml b/usegalaxy.org/sequence_contamination_filtering.yml new file mode 100644 index 00000000..8724bc3e --- /dev/null +++ b/usegalaxy.org/sequence_contamination_filtering.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: 'Sequence Contamination Filtering' +tools: +- name: ncbi_fcs_gx + owner: iuc diff --git a/usegalaxy.org/sequence_contamination_filtering.yml.lock b/usegalaxy.org/sequence_contamination_filtering.yml.lock new file mode 100644 index 00000000..8a8bafec --- /dev/null +++ b/usegalaxy.org/sequence_contamination_filtering.yml.lock @@ -0,0 +1,11 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Sequence Contamination Filtering +tools: +- name: ncbi_fcs_gx + owner: iuc + revisions: + - 3cdb96f2855d + tool_panel_section_id: sequence_contamination_filtering + tool_panel_section_label: Sequence Contamination Filtering diff --git a/usegalaxy.org/single_cell.yml b/usegalaxy.org/single_cell.yml index 93ec01c0..0c226835 100644 --- a/usegalaxy.org/single_cell.yml +++ b/usegalaxy.org/single_cell.yml @@ -8,8 +8,6 @@ tools: owner: iuc - name: scanpy_normalize owner: iuc -- name: scanpy_plot - owner: iuc - name: scanpy_cluster_reduce_dimension owner: iuc - name: scanpy_remove_confounders @@ -84,3 +82,35 @@ tools: owner: ebi-gxa - name: retrieve_scxa owner: ebi-gxa +- name: scanpy_regress_variable + owner: ebi-gxa +- name: music_construct_eset + owner: bgruening +- name: music_inspect_eset + owner: bgruening +- name: music_manipulate_eset + owner: bgruening +- name: music_deconvolution + owner: bgruening +- name: music_compare + owner: bgruening +- name: episcanpy_build_matrix + owner: iuc +- name: episcanpy_preprocess + owner: iuc +- name: sinto_barcode + owner: iuc +- name: sinto_fragments + owner: iuc +- name: baredsc_1d + owner: iuc +- name: baredsc_2d + owner: iuc +- name: baredsc_combine_1d + owner: iuc +- name: baredsc_combine_2d + owner: iuc +- name: cite_seq_count + owner: iuc +- name: velocyto_cli + owner: iuc diff --git a/usegalaxy.org/single_cell.yml.lock b/usegalaxy.org/single_cell.yml.lock index e891f4e5..b874b4ab 100644 --- a/usegalaxy.org/single_cell.yml.lock +++ b/usegalaxy.org/single_cell.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Single-cell tools: @@ -8,26 +8,32 @@ tools: revisions: - 6adf98e782f3 - 7647e5cd1b8b + - 95777145cb92 - 9a169729c9f9 + - 9b0cdb8cf6be - aa0c474463c2 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_inspect owner: iuc revisions: + - 3081ff5c84a3 + - 6bd82ed14acd - 6c145a6868cc - 9d33775ec67d - - e4c99c83dfbf - c5d3684f7c4c + - e4c99c83dfbf tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_filter owner: iuc revisions: + - 2d02d9702d3a - 3c86f71498bc - 5511647110ff - - f87ed6503715 + - a03ff8633507 - b409c2486353 + - f87ed6503715 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_normalize @@ -35,17 +41,10 @@ tools: revisions: - 51d945eab1e1 - 5342ce58cd1e + - 94c19fb1281c - a407e7f8bdc1 - ab55fe8030b6 - tool_panel_section_id: single_cell - tool_panel_section_label: Single-cell -- name: scanpy_plot - owner: iuc - revisions: - - 6adf98e782f3 - - 7647e5cd1b8b - - 9a169729c9f9 - - aa0c474463c2 + - c9cb76cf8d6c tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_cluster_reduce_dimension @@ -53,34 +52,42 @@ tools: revisions: - 35bc2eb568ed - 3e4e1cf73d98 - - b2df381a6004 + - 6acb08931836 - aaa5da8e73a9 + - b2df381a6004 + - edec35114f72 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_remove_confounders owner: iuc revisions: - 215733a383f2 + - 458e8f43a775 + - 73ab2ac53d06 - 80d4e2cac903 - - c2ef03559dc6 - bf2017df9837 + - c2ef03559dc6 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: anndata_export owner: iuc revisions: + - 0cb889db0910 - 32c5c85cbc12 - c0b037b12765 - c5ac926c838f + - e1c3c2f2a834 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: anndata_import owner: iuc revisions: - 00712416fdaa + - '499059586799' + - 93dd15e13e6a - ae1e5d9d8972 - cfc3f5a57dc6 - - '499059586799' + - fb9e030ffae4 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: anndata_inspect @@ -89,20 +96,26 @@ tools: - 038e32885fec - 383dcb0500f9 - 39e945f0b2c1 + - 6f0d0c784f09 + - ee98d611afc6 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: anndata_manipulate owner: iuc revisions: + - 3d748954434b - 43cb7b5a6fe7 - 8db95f488f0f + - ed4996a16f7f tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: modify_loom owner: iuc revisions: + - 4b0adaa31c95 - 59be31ac9dc3 - 7784821452ac + - e98619de2776 - eeab712b0b99 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -118,6 +131,7 @@ tools: - name: raceid_clustering owner: iuc revisions: + - 0bff0ee0683a - 7e014059a88d - a4b734cd253b - c4f39bf4a068 @@ -128,6 +142,7 @@ tools: revisions: - 43c146e25a43 - 7608d5faee41 + - b83fbc90161e - d45f092caf24 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -137,19 +152,22 @@ tools: - 37a47c4fd84d - 41f34e925bd5 - be4646256624 + - f3eb2291da05 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: raceid_inspecttrajectory owner: iuc revisions: + - 3478133d0f6f - 69018f285aa3 + - a6821f856a1e - c8434a623268 - - 3478133d0f6f tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: raceid_trajectory owner: iuc revisions: + - 2af7c5086a96 - 44b935f2271b - 72979cac22b2 - e93b008c637a @@ -161,14 +179,16 @@ tools: - 7fd39eb52f38 - 8ed4e80e8799 - ba64b91ed2b9 + - e9283529cba1 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_filter_genes owner: ebi-gxa revisions: + - 474a69c47184 - 7143938df06e - - d82d999fa716 - a1698b43abeb + - d82d999fa716 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_normalise_data @@ -176,14 +196,16 @@ tools: revisions: - 1e9616772e16 - 3a4564b9d685 + - 6b97ffba31da tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_find_variable_genes owner: ebi-gxa revisions: + - 2861ca3bfe4d + - 5c62f39aab8f - 82bd7bf93454 - ae467daae2f7 - - 5c62f39aab8f tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_scale_data @@ -191,59 +213,67 @@ tools: revisions: - 22f2957da902 - 2b6913c840bf + - f86b2c3bc459 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_run_pca owner: ebi-gxa revisions: - 04bdc69f00d7 - - c4f7fb2b1f70 + - 59028945c857 - 988edd5fa902 + - c4f7fb2b1f70 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_compute_graph owner: ebi-gxa revisions: + - 3cf0177ed87e - 5ec3b715809c + - 6417cccad133 - fcaa9048cdaf - - 3cf0177ed87e tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_run_tsne owner: ebi-gxa revisions: + - 181d61d2f3cd + - 384cacc40611 - a147dce191e9 - fe727a9496ea - - 384cacc40611 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_run_umap owner: ebi-gxa revisions: + - abae3d11d920 - ad70b3552c99 + - bd4a244faeb8 - e31937baa330 - - abae3d11d920 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_find_cluster owner: ebi-gxa revisions: + - 15e8a4c60418 + - 2ccd9f9e2cd0 - 621d7d7a605f - 8dc3d8941217 - - 15e8a4c60418 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_find_markers owner: ebi-gxa revisions: + - 615a46c220f0 - 7042ce140caa + - 81c34e67f262 - a57c0538e56b - - 615a46c220f0 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_plot_embed owner: ebi-gxa revisions: + - 35f6611fb8c3 - 9fafbfcdee0d - a71086d2e55f tool_panel_section_id: single_cell @@ -253,12 +283,14 @@ tools: revisions: - 31e5e6d606ef - 53a251c6d991 + - 825dfd66e3fb tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - 4e4420ed5292 + - a8c73996ac50 - b9dd12ab0550 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -266,19 +298,22 @@ tools: owner: ebi-gxa revisions: - 4d13979de6ee + - 9afcfcd1d215 - c8391a25dee3 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 5bea4f3c4edf - 2cef3539f420 + - 3111bcf039dd + - 5bea4f3c4edf tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: gtf2gene_list owner: ebi-gxa revisions: + - 14b3f2a4523b - 1a642de6db01 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -286,6 +321,9 @@ tools: owner: bgruening revisions: - 04b494623f8e + - e32b215b7c04 + - e4c01dcece8b + - f2000bc73102 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: droplet_barcode_plot @@ -297,6 +335,7 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: + - 88f5a0a6a818 - e42c217a450f tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -324,3 +363,112 @@ tools: - 72b6e1747e37 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell +- name: scanpy_regress_variable + owner: ebi-gxa + revisions: + - 1200b55768ce + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_construct_eset + owner: bgruening + revisions: + - 282819d09a4f + - 2cfd0db49bbc + - 7ffaa0968da3 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_inspect_eset + owner: bgruening + revisions: + - 7705cc75ac18 + - 8c64a2da3869 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_manipulate_eset + owner: bgruening + revisions: + - 22232092be53 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_deconvolution + owner: bgruening + revisions: + - 2ba99a52bd44 + - 56371b5a2da9 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: music_compare + owner: bgruening + revisions: + - 4447ed460308 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: episcanpy_build_matrix + owner: iuc + revisions: + - 31a21ba2c5ea + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: episcanpy_preprocess + owner: iuc + revisions: + - 29f5f25b9935 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: sinto_barcode + owner: iuc + revisions: + - d1b34ac42b8f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: sinto_fragments + owner: iuc + revisions: + - 29e6bfb2cf49 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: baredsc_1d + owner: iuc + revisions: + - 02b1fe7aed76 + - 0e70b2dfe4be + - 4fff5a293013 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: baredsc_2d + owner: iuc + revisions: + - 344c2af50552 + - aa4a6f0916b4 + - c29e7bb492bf + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: baredsc_combine_1d + owner: iuc + revisions: + - 050cf43887d3 + - b13d3e4c48e1 + - c32347702e12 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: baredsc_combine_2d + owner: iuc + revisions: + - 1d77986f9ddc + - 239193b96d72 + - ae969fdb8442 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: cite_seq_count + owner: iuc + revisions: + - 3df3d1b51110 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: velocyto_cli + owner: iuc + revisions: + - 883c33ef3372 + - 90e95e9ee190 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell diff --git a/usegalaxy.org/statistics.yml b/usegalaxy.org/statistics.yml index 7e4d465b..039d6600 100644 --- a/usegalaxy.org/statistics.yml +++ b/usegalaxy.org/statistics.yml @@ -60,6 +60,8 @@ tools: owner: lecorguille - name: seq_composition owner: peterjc +- name: seqcomplexity + owner: iuc - name: scipy_sparse owner: bgruening - name: create_tool_recommendation_model diff --git a/usegalaxy.org/statistics.yml.lock b/usegalaxy.org/statistics.yml.lock index c069b11f..3fc3b20b 100644 --- a/usegalaxy.org/statistics.yml.lock +++ b/usegalaxy.org/statistics.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Statistics tools: @@ -183,16 +183,31 @@ tools: - 13be788233da tool_panel_section_id: statistics tool_panel_section_label: Statistics +- name: seqcomplexity + owner: iuc + revisions: + - 054c3355458d + - f14a21f3d5b1 + tool_panel_section_id: statistics + tool_panel_section_label: Statistics - name: scipy_sparse owner: bgruening revisions: + - 42b513bed40b + - 4efac966af2a + - 6d1a9fae57eb - 92e09b827300 + - 9f9cf31e3111 + - b7e93c1deb3f + - e6893a4bcb7b tool_panel_section_id: statistics tool_panel_section_label: Statistics - name: create_tool_recommendation_model owner: bgruening revisions: + - 4f7e6612906b - afec8c595124 + - e94dc7945639 tool_panel_section_id: statistics tool_panel_section_label: Statistics - name: pandas_rolling_window diff --git a/usegalaxy.org/str_fm__microsatellite_analysis.yml.lock b/usegalaxy.org/str_fm__microsatellite_analysis.yml.lock index 02252916..2cc65c14 100644 --- a/usegalaxy.org/str_fm__microsatellite_analysis.yml.lock +++ b/usegalaxy.org/str_fm__microsatellite_analysis.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: 'STR-FM: Microsatellite Analysis' tools: diff --git a/usegalaxy.org/text_manipulation.yml b/usegalaxy.org/text_manipulation.yml index acb78b73..78577c00 100644 --- a/usegalaxy.org/text_manipulation.yml +++ b/usegalaxy.org/text_manipulation.yml @@ -12,8 +12,6 @@ tools: owner: bgruening - name: text_processing owner: bgruening -- name: annotatemyids - owner: iuc - name: column_order_header_sort owner: iuc - name: column_remove_by_header @@ -46,3 +44,7 @@ tools: owner: bgruening - name: diff owner: bgruening +- name: add_value + owner: devteam +- name: concatenate_multiple_datasets + owner: artbio diff --git a/usegalaxy.org/text_manipulation.yml.lock b/usegalaxy.org/text_manipulation.yml.lock index be606366..dc5ab390 100644 --- a/usegalaxy.org/text_manipulation.yml.lock +++ b/usegalaxy.org/text_manipulation.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Text Manipulation tools: @@ -10,22 +10,30 @@ tools: - 13b6f0007d9e - 427903d47026 - 464b9305180e + - 6595517c2dd8 - 6e8d94597139 + - be25c075ed54 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: annotatemyids owner: iuc revisions: + - 133f36c29579 - 1aae04680c4b + - 3e1f6f6d557e - 44018dd6b447 - b5d8e5475247 + - cd2480f35935 - f29602ae449e + - fe3ca740a485 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: uniprot_rest_interface owner: bgruening revisions: - 054483e27a35 + - af5eccf83605 + - bfdc6a7ffd3a tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: add_input_name_as_column @@ -38,6 +46,7 @@ tools: - name: replace_column_by_key_value_file owner: bgruening revisions: + - cc18bac5afdb - d533e4b75800 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation @@ -45,20 +54,16 @@ tools: owner: bgruening revisions: - 0a8c6b61f0f4 + - 20344ce0c811 + - 60edf2f8c28f - 9ff72e942410 + - d698c222f354 - ddf54b12c295 + - e39fceb6ab85 + - f46f0e4f75c4 - fb4ff3c42cd3 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation -- name: annotatemyids - owner: iuc - revisions: - - 1aae04680c4b - - 44018dd6b447 - - b5d8e5475247 - - f29602ae449e - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation - name: column_order_header_sort owner: iuc revisions: @@ -68,6 +73,7 @@ tools: - name: column_remove_by_header owner: iuc revisions: + - 2040e4c2750a - 372967836e98 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation @@ -99,6 +105,7 @@ tools: - name: table_compute owner: iuc revisions: + - 3bf5661c0280 - 60ff16842fcd - 93a3ce78ce55 - dddadbbac949 @@ -107,13 +114,18 @@ tools: - name: regex_find_replace owner: galaxyp revisions: + - 209b7c5ee9d7 + - 399da6b5ec21 + - 503bcd6ebe4b - ae8c4b2488e7 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: split_file_on_column owner: bgruening revisions: + - 37a53100b67e - b60f2452580e + - ff2a81aa3f08 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: query_tabular @@ -122,6 +134,7 @@ tools: - 1ea4e668bf73 - 2e8f945f7285 - 33d61c89fb8d + - 3a6b78c39dca - 83069b38aa85 - cf34c344508d tool_panel_section_id: text_manipulation @@ -134,6 +147,7 @@ tools: - c29d2f80a066 - dfe38b7c34ed - f31bb1e5725d + - f768f6183386 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: concatenate_multiple_datasets @@ -145,7 +159,9 @@ tools: - name: filter_tabular owner: iuc revisions: + - 34d29339abab - 4d5aae46f850 + - 557ec8d7087d - 6544e4b87a4f - 9cc411a62277 tool_panel_section_id: text_manipulation @@ -168,3 +184,16 @@ tools: - 156d0908e232 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation +- name: add_value + owner: devteam + revisions: + - 023f0a3760b3 + - 745871c0b055 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: concatenate_multiple_datasets + owner: artbio + revisions: + - 5b2cc63d7a21 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation diff --git a/usegalaxy.org/training_metabolomics.yml b/usegalaxy.org/training_metabolomics.yml new file mode 100644 index 00000000..ee7283a6 --- /dev/null +++ b/usegalaxy.org/training_metabolomics.yml @@ -0,0 +1,42 @@ +tool_panel_section_label: Metabolomics +tools: +- name: msconvert + owner: galaxyp +- name: msnbase_readmsdata + owner: lecorguille +- name: xcms_fillpeaks + owner: lecorguille +- name: xcms_group + owner: lecorguille +- name: xcms_merge + owner: lecorguille +- name: xcms_retcor + owner: lecorguille +- name: xcms_xcmsset + owner: lecorguille +- name: matchms + owner: recetox +- name: matchms_filtering + owner: recetox +- name: matchms_formatter + owner: recetox +- name: ramclustr + owner: recetox +- name: ramclustr_define_experiment + owner: recetox +- name: riassigner + owner: recetox +- name: waveica + owner: recetox +- name: camera_annotate + owner: lecorguille +- name: xcms_export_samplemetadata + owner: lecorguille +- name: xcms_plot_chromatogram + owner: lecorguille +- name: xcms_summary + owner: lecorguille +- name: idchoice + owner: melpetera +- name: intensity_checks + owner: melpetera \ No newline at end of file diff --git a/usegalaxy.org/training_metabolomics.yml.lock b/usegalaxy.org/training_metabolomics.yml.lock new file mode 100644 index 00000000..de6e9bc2 --- /dev/null +++ b/usegalaxy.org/training_metabolomics.yml.lock @@ -0,0 +1,125 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tools: +- name: msconvert + owner: galaxyp + revisions: + - 6153e8ada1ee + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: msnbase_readmsdata + owner: lecorguille + revisions: + - 11ab2081bd4a + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_fillpeaks + owner: lecorguille + revisions: + - 26d77e9ceb49 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_group + owner: lecorguille + revisions: + - d45a786cbc40 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_merge + owner: lecorguille + revisions: + - 5bd125a3f3b0 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_retcor + owner: lecorguille + revisions: + - aa252eec9229 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_xcmsset + owner: lecorguille + revisions: + - b02d1992a43a + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms + owner: recetox + revisions: + - 4015f250a5a1 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_filtering + owner: recetox + revisions: + - 357df6c47d92 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_formatter + owner: recetox + revisions: + - 715fe77be601 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: ramclustr + owner: recetox + revisions: + - 2ec9253a647e + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: ramclustr_define_experiment + owner: recetox + revisions: + - 25625114618e + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: riassigner + owner: recetox + revisions: + - c702620c22b1 + - f6bf8f1f3224 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: waveica + owner: recetox + revisions: + - b77023c41c76 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: camera_annotate + owner: lecorguille + revisions: + - 512c2b701d96 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_export_samplemetadata + owner: lecorguille + revisions: + - 94eb263cfab4 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_plot_chromatogram + owner: lecorguille + revisions: + - 024974037c4e + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_summary + owner: lecorguille + revisions: + - 018a9771de28 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: idchoice + owner: melpetera + revisions: + - bb19b1d15732 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: intensity_checks + owner: melpetera + revisions: + - a31f3f802b2b + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics diff --git a/usegalaxy.org/transposon_insertion_sequencing.yml.lock b/usegalaxy.org/transposon_insertion_sequencing.yml.lock index bef0ed72..ae05391c 100644 --- a/usegalaxy.org/transposon_insertion_sequencing.yml.lock +++ b/usegalaxy.org/transposon_insertion_sequencing.yml.lock @@ -1,28 +1,29 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Transposon Insertion Sequencing tools: - name: biotradis owner: iuc revisions: - - 58234d95978d - 103bd59b3e33 + - 58234d95978d - 625d5ea9f3c7 + - d1855ded740a tool_panel_section_id: transposon_insertion_sequencing tool_panel_section_label: Transposon Insertion Sequencing - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 07d7991bf205 + - 2aea122fbd25 tool_panel_section_id: transposon_insertion_sequencing tool_panel_section_label: Transposon Insertion Sequencing - name: transit_resampling owner: iuc revisions: - - ad4d42fabf32 - 885459e1c83b + - ad4d42fabf32 tool_panel_section_id: transposon_insertion_sequencing tool_panel_section_label: Transposon Insertion Sequencing - name: transit_hmm @@ -35,14 +36,14 @@ tools: - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_id: transposon_insertion_sequencing tool_panel_section_label: Transposon Insertion Sequencing - name: transit_tn5gaps owner: iuc revisions: - - 4aaabd55eab8 - 3f5fc4b09496 + - 4aaabd55eab8 tool_panel_section_id: transposon_insertion_sequencing tool_panel_section_label: Transposon Insertion Sequencing diff --git a/usegalaxy.org/variant_calling.yml b/usegalaxy.org/variant_calling.yml index c58c9dac..b5fe4853 100644 --- a/usegalaxy.org/variant_calling.yml +++ b/usegalaxy.org/variant_calling.yml @@ -46,8 +46,6 @@ tools: owner: crs4 - name: gatk4_mutect2 owner: iuc -- name: mixcr_analyze - owner: iuc - name: ococo owner: iuc - name: varscan_copynumber @@ -63,4 +61,16 @@ tools: - name: sniffles owner: iuc - name: jasminesv - owner: iuc \ No newline at end of file + owner: iuc +- name: strelka_germline + owner: iuc +- name: strelka_somatic + owner: iuc +- name: deepvariant + owner: iuc +- name: ucsc_fatovcf + owner: iuc +- name: snp_dists + owner: iuc +- name: snp_sites + owner: iuc diff --git a/usegalaxy.org/variant_calling.yml.lock b/usegalaxy.org/variant_calling.yml.lock index e5531fb6..d5bd6885 100644 --- a/usegalaxy.org/variant_calling.yml.lock +++ b/usegalaxy.org/variant_calling.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Variant Calling tools: @@ -22,7 +22,10 @@ tools: owner: iuc revisions: - 268d162b9c49 + - 5b80f544c67f + - 5c7b70713fb5 - 74aebe30fb52 + - 9473cd297a76 - cfcf33df7fc0 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling @@ -35,8 +38,8 @@ tools: - name: snpsift owner: iuc revisions: - - 2e497a770bca - 2b3e65a4252f + - 2e497a770bca - 5fab4f81391d tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling @@ -44,13 +47,14 @@ tools: owner: devteam revisions: - 156b60c1530f + - a5937157062f - ef2c525bd8cd tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: table_annovar owner: devteam revisions: - - 08b003ee9db7 + - d4e292ddda05 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: mutate_snp_codon @@ -90,6 +94,7 @@ tools: - 32f2211eeec3 - 3fe8ef358d66 - 5bbf9eada9c2 + - c9a8ef2aa380 - d220115f882b tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling @@ -100,6 +105,7 @@ tools: - 2953c43180c0 - 435b157bed6d - 606542a18f82 + - 791f73caa0c8 - e0e2fd665102 - e61c9ac190ad tool_panel_section_id: variant_calling @@ -111,6 +117,7 @@ tools: - 074d44697036 - 31216d510164 - 3b4b2121842f + - 4805fe3d8fda - 65432c3abf6c - dfadc322b065 - e1461b5c52a0 @@ -134,6 +141,7 @@ tools: - 354b534eeab7 - 426d707dfc47 - 5d6a078d30b0 + - 971e07ca4456 - c27549b9aa1f - f4473557ffc7 tool_panel_section_id: variant_calling @@ -158,17 +166,21 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: + - 36960e552ddc - 71dfde92fd57 - c39113e2ae34 - ebcd8649c621 + - f88f74d5b1e9 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: bcftools_plugin_frameshifts owner: iuc revisions: + - 399b40b2bcab - 48ac4d611e92 - - eb22990a2be9 + - b40213125e88 - c0b17fc737d4 + - eb22990a2be9 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: exomedepth @@ -180,17 +192,12 @@ tools: - name: gatk4_mutect2 owner: iuc revisions: + - 1cea23583655 - 287c4af133e6 - 3be27a9a7313 - - fd2d6e035c3f - - 1cea23583655 - 53ce8be43212 - tool_panel_section_id: variant_calling - tool_panel_section_label: Variant Calling -- name: mixcr_analyze - owner: iuc - revisions: - - d38cfb922f95 + - fb0bb7174530 + - fd2d6e035c3f tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: ococo @@ -209,8 +216,8 @@ tools: - name: varscan_mpileup owner: iuc revisions: - - e3f170cc4f95 - db94eadb92c1 + - e3f170cc4f95 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: varscan_somatic @@ -245,3 +252,41 @@ tools: - 2b62154e39c8 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling +- name: strelka_germline + owner: iuc + revisions: + - 19481653a22f + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: strelka_somatic + owner: iuc + revisions: + - edbdbc64b397 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: deepvariant + owner: iuc + revisions: + - 918c8b94c8d8 + - 98fe794d2ec0 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: ucsc_fatovcf + owner: iuc + revisions: + - 78df8fc2b3ab + - d9965e143053 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: snp_dists + owner: iuc + revisions: + - f78492521996 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: snp_sites + owner: iuc + revisions: + - 5804f786060d + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling diff --git a/usegalaxy.org/vcf_bcf.yml.lock b/usegalaxy.org/vcf_bcf.yml.lock index 0500766e..df550587 100644 --- a/usegalaxy.org/vcf_bcf.yml.lock +++ b/usegalaxy.org/vcf_bcf.yml.lock @@ -1,5 +1,5 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: VCF/BCF tools: @@ -35,6 +35,7 @@ tools: owner: devteam revisions: - 5b7120c66efc + - dd44c3f416c3 - f0580efedada tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -119,6 +120,7 @@ tools: revisions: - 2968c6916579 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: vcfbreakcreatemulti @@ -185,54 +187,66 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: + - 12038f59c0f4 + - 4b796b58938b + - 8aa9d9b14bcd - aa998b9898b1 - - ed3cfc7d2836 - bdfdf5f6e950 - - 8aa9d9b14bcd + - ed3cfc7d2836 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_query owner: iuc revisions: + - 3b1b51e1fcba - 4eb04768cd49 - 5fce85148ed1 + - a850902cac64 - c9c5718edc19 - - 3b1b51e1fcba + - e53501abf992 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_dosage owner: iuc revisions: - 2ee1392161a6 - - d1e4180297b0 - 5c232a738c74 - 84cf4959145a + - 89720ec3d58e + - cc7f9a4e186b + - d1e4180297b0 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_annotate owner: iuc revisions: + - 2436e3bef247 + - 3f62d4939d54 + - 403553ae19f6 - 8a885a1a92ea - 8e01baf41774 - - 403553ae19f6 - - 2436e3bef247 + - b7ea370b8f5d tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_csq owner: iuc revisions: + - 8899a6d50699 + - ae68ceb4cca3 + - f01b2c9506b9 - f10f5b4e7854 - fa67bc6d3b41 - fdd127bd4a32 - - 8899a6d50699 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_filter owner: iuc revisions: - 0117c6d2ab96 - - a892912c09d5 + - 277719af4dd7 + - 656a916779fe - 6ca7c55a27e8 + - a892912c09d5 - abafcb875ba6 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -240,27 +254,33 @@ tools: owner: iuc revisions: - 1262c96a9974 - - c4a9b38b435d + - 1d1762860d7e - 23680a42e149 + - 59fa8742285e - 98d5499ead46 - - 1d1762860d7e + - abc3ced31cd1 + - c4a9b38b435d tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_call owner: iuc revisions: - 01fd33bc2e75 - - 5801eff9ac7e - 072f606e2e69 + - 21687e35f066 + - 5801eff9ac7e - 912a8ff07fc9 + - f0d44631365f tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_roh owner: iuc revisions: + - 1ccf0e7fb4f6 - 427e353bf26f - - cb681f21e670 - b76adb2f1c51 + - bdc67eeb0bc9 + - cb681f21e670 - d80872078a09 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -268,90 +288,110 @@ tools: owner: iuc revisions: - 27026ed52654 + - 3e0e55c628b8 - 9473302f4588 + - af163c712539 + - b931e65638b8 - e03f2f3ac3a9 - - 3e0e55c628b8 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_isec owner: iuc revisions: + - 02f349bdbf96 - 0d7d3de5ef5d - 1fd4fd0c6ee3 - - 02f349bdbf96 + - 63aabc920911 - 9ece72700ca9 + - d7d1663559e9 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_fill_tags owner: iuc revisions: + - 1fd34b10d28e + - 444e6a756c35 - 87d52abd1cb3 - - cbfa272e5a6a - bf7d6acd9884 - - 1fd34b10d28e + - c01be0ab9806 + - cbfa272e5a6a tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - 3bdc901c18e2 - - 645f97008839 - 582f8b13873d + - 645f97008839 - 79064be67dff + - 80e6e399ccd0 + - 99f4a81a47be tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_stats owner: iuc revisions: + - '388983871932' - 9c0028888512 - - ef2cc5ac23bc + - a2f8dc22d7c0 - b17394940c7a - c636e58df612 + - ef2cc5ac23bc tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_reheader owner: iuc revisions: + - 4db0695a6fc7 + - 8057cf55fa41 - 982bc0e518c8 - - d68c43202172 - 9ef52d95114b - b3b3c060962e + - d68c43202172 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_impute_info owner: iuc revisions: - 0c1889b0917b + - 27e2611639a9 - 2c53c8974cb3 - 776ad0b21536 + - 8dbce095986c - dcf130f10ca5 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_convert_from_vcf owner: iuc revisions: + - 348cd212dbad - 7ca6120cb2a4 - - e968db9208a4 - - b8e9da766b0f - 7cea7c7bf203 + - b8e9da766b0f + - cacc9970727a + - e968db9208a4 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_consensus owner: iuc revisions: + - 147de996e34f + - 92182c270ce4 - a87ae767b01d - - e522022137f6 + - d3081540d175 - d6dc477167f8 - - 92182c270ce4 + - e522022137f6 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_concat owner: iuc revisions: + - 08296952d12f + - 5ee777f9db23 - 81426b3cf18b - 874cc12ae316 + - d144af39073a - d40d4bf05718 - - 5ee777f9db23 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_mendelian @@ -359,31 +399,39 @@ tools: revisions: - 98664595dedf - a9547524b473 - - bf235558f2cf - ab7c07ed8726 + - af36eb5418fe + - bf235558f2cf + - e0a856def0b0 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_mpileup owner: iuc revisions: - - a0c219ecb5e7 - - f65383c7ed49 + - 03191140c66a - 0dbff46d5a1b + - 5660b21a0dbd + - a0c219ecb5e7 - ce9396ddcb2b + - f65383c7ed49 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_counts owner: iuc revisions: + - 28b35180900b - 3f7900995059 - - b781fa08aa3c - 4813f99d81b7 - - 28b35180900b + - b781fa08aa3c + - be6b217710af + - c450406f722b tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_setgt owner: iuc revisions: + - 11af7fce71cf + - 262bba5b90ef - 6a5fa818bd0d - 76fe872413c2 - 8abfcd1a6949 @@ -393,19 +441,23 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 635532ff1ac9 - - b2d1b7dda2b7 - 01d6b7d6365e + - 0238f68ad641 - 4891338c6c54 + - 635532ff1ac9 + - 6d35a3780bfd + - b2d1b7dda2b7 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_missing2ref owner: iuc revisions: + - 03e30f06f15f + - 2f4eef1f0d22 - 5d98fe06e4ae - - e09707e8607b - - dfef7a353ed0 - 701e01819e52 + - dfef7a353ed0 + - e09707e8607b tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_query_list_samples @@ -413,43 +465,53 @@ tools: revisions: - 18cf9de1cf73 - 242753783b68 - - ed4ea9de1791 - 77e0bd62b554 + - 8c3ff4ef1190 + - dba06328556a + - ed4ea9de1791 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_norm owner: iuc revisions: + - 6deb4d549bc9 - a62e934346f5 - - da6fc9f4a367 - c077f71d351f + - da6fc9f4a367 + - ebb2e12a6de1 - ff9e769ccd6c tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_convert_to_vcf owner: iuc revisions: + - 4935320a59a8 + - 55c0e906c14c - 7887b9d94c05 - 8bb5efd7a3dd - - fec517907949 - c14b33ab15d8 + - fec517907949 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_fixploidy owner: iuc revisions: - 26b8544f015e - - ceb03be4f31b - '365325116147' + - 68fec03a63b7 + - 7fe09ad6a939 + - ceb03be4f31b - d9f9294ccccc tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_gtcheck owner: iuc revisions: + - 26d97cdd5410 + - 39810174657a + - 3eac729e66c9 + - 672b6c02fbc7 - 9243f0e24906 - fd1030bc93d9 - - 672b6c02fbc7 - - 39810174657a tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF diff --git a/usegalaxy.org/virology.yml.lock b/usegalaxy.org/virology.yml.lock index 013e76ed..37320c75 100644 --- a/usegalaxy.org/virology.yml.lock +++ b/usegalaxy.org/virology.yml.lock @@ -1,26 +1,32 @@ install_repository_dependencies: true -install_resolver_dependencies: true +install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Virology tools: - name: ivar_consensus owner: iuc revisions: - - 7f781286b55f - - 78bbd17d0703 + - 17f911830a8c - 5e668dc9f379 - - d1459d85ff18 - 731182d54f78 + - 78bbd17d0703 + - 7f781286b55f + - d1459d85ff18 + - e319b5b65879 + - ede363a64152 tool_panel_section_id: virology tool_panel_section_label: Virology - name: ivar_filtervariants owner: iuc revisions: + - 0135f1d487a0 + - 096a5b0210cc + - 1ef5b6e3e09d - 2c47c138176e - - 7fe36019c073 - - 51afc8a64951 - - 4abcfbc2e5b6 - 47a27906d750 + - 4abcfbc2e5b6 + - 51afc8a64951 + - 7fe36019c073 tool_panel_section_id: virology tool_panel_section_label: Virology - name: ivar_getmasked @@ -34,31 +40,40 @@ tools: revisions: - 28a6f1908fcc - 3d18f8c3c0f6 - - ee2beb764a7b - - 75c279fa403a - 43aac8d29685 + - 69797fa273c3 + - 75c279fa403a - 8d36959b000d + - ee29337f905c + - ee2beb764a7b + - f57ce5d5c997 tool_panel_section_id: virology tool_panel_section_label: Virology - name: ivar_trim owner: iuc revisions: + - 0893a1dbb807 + - 28e4bcbc86e7 + - 364f4ffec275 - 397e5f0eb3ef + - 5671e1d3d5ee - 5d6ed46cc101 - - db536ad45f28 - - cf65217ad61c - - 364f4ffec275 - c092052ed673 + - cf65217ad61c + - db536ad45f28 tool_panel_section_id: virology tool_panel_section_label: Virology - name: ivar_variants owner: iuc revisions: - - aa9de8f20668 - - f95f403841ad - - 49236b03e4fd + - 045d6d00f606 + - 230b05597996 - 252dfb042563 - 3888bbe7a9ca + - 49236b03e4fd + - 584beffa972b + - aa9de8f20668 + - f95f403841ad tool_panel_section_id: virology tool_panel_section_label: Virology - name: snpeff_sars_cov_2 @@ -70,21 +85,33 @@ tools: - name: pangolin owner: iuc revisions: + - 03ed9524dcd1 + - 14ae456b8cc5 + - 2f1019071464 + - 2fa9d4f1b48f + - 36912871ccdc + - 3a656a4a43ed - 42126b414951 - 42a174224817 - - 3a656a4a43ed - - fe3e8506112c - - 36912871ccdc + - 5f8727ff21e7 + - 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