Mercurial > repos > stemcellcommons > deeptools_bamqc_workflow
view deepTools_BAM_QC.ga @ 0:897b11a77250 draft default tip
planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
author | scottx611x |
---|---|
date | Tue, 04 Sep 2018 13:55:35 -0400 |
parents | |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "{ \n \"description\": \"Compare aligned samples via pairwise correlation heatmap and PCA plot\", \n \"file_relationship\": { \n \"file_relationship\": {}, \n \"value_type\": \"LIST\", \n \"name\": \"List of BAM Files\", \n \"input_files\": [ \n { \n \"allowed_filetypes\": [{\"name\": \"BAM\"}], \n \"name\": \"Input File\", \n \"description\": \"File to run deepTools BAM QC on\" \n } \n ] \n } \n}", "format-version": "0.1", "name": "deepTools BAM QC", "steps": { "0": { "annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [], "label": null, "name": "Input dataset collection", "outputs": [], "position": { "left": 299.5, "top": 287.5 }, "tool_id": null, "tool_state": "{\"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "7e26711f-78ba-4f74-90ea-b30acefcf685", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "ef8c102b-e5a8-4a1e-9bbc-cf875cfcd72e" } ] }, "1": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.3.0", "errors": null, "id": 1, "input_connections": { "bamfiles": { "id": 0, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool multiBamSummary", "name": "bamfiles" } ], "label": null, "name": "multiBamSummary", "outputs": [ { "name": "outFile", "type": "deeptools_coverage_matrix" }, { "name": "outFileRawCounts", "type": "tabular" } ], "position": { "left": 845.5, "top": 356.5 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.3.0", "tool_shed_repository": { "changeset_revision": "87d2c75884d9", "name": "deeptools_multi_bam_summary", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": null, \"bamfiles\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"region\": \"\\\"\\\"\", \"mode\": \"{\\\"binSize\\\": \\\"10000\\\", \\\"distanceBetweenBins\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"modeOpt\\\": \\\"bins\\\"}\", \"advancedOpt\": \"{\\\"showAdvancedOpt\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"outRawCounts\": \"\\\"false\\\"\"}", "tool_version": "2.2.3.0", "type": "tool", "uuid": "b199cca5-5101-4ad0-8f17-aa902c5ece8f", "workflow_outputs": [ { "label": null, "output_name": "outFileRawCounts", "uuid": "90b33467-e9cc-4c8a-8e96-f8c12c1a8daf" }, { "label": null, "output_name": "outFile", "uuid": "fe5ce046-edd4-4953-8b20-4ccabb4d6eb2" } ] }, "2": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0", "errors": null, "id": 2, "input_connections": { "corData": { "id": 1, "output_name": "outFile" } }, "inputs": [ { "description": "runtime parameter for tool plotCorrelation", "name": "corData" } ], "label": null, "name": "plotCorrelation", "outputs": [ { "name": "outFileName", "type": "png" }, { "name": "matrix", "type": "tabular" } ], "position": { "left": 1225, "top": 215.5 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0", "tool_shed_repository": { "changeset_revision": "b3589208f673", "name": "deeptools_plot_correlation", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": null, \"removeOutliers\": \"\\\"false\\\"\", \"outFileFormat\": \"\\\"svg\\\"\", \"outFileCorMatrix\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"corMethod\": \"\\\"spearman\\\"\", \"skipZeros\": \"\\\"false\\\"\", \"plotting_type\": \"{\\\"plotTitle\\\": \\\"\\\", \\\"colorMap\\\": \\\"RdYlBu\\\", \\\"plotNumbers\\\": \\\"false\\\", \\\"zMin\\\": \\\"\\\", \\\"whatToPlot\\\": \\\"heatmap\\\", \\\"__current_case__\\\": 0, \\\"zMax\\\": \\\"\\\"}\", \"corData\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "2.2.3.0", "type": "tool", "uuid": "4cb57832-703a-4af2-a90c-e0ca2b1dafbe", "workflow_outputs": [ { "label": null, "output_name": "outFileName", "uuid": "04d6ff82-6f3c-4bb8-8449-5c212a152aa3" }, { "label": null, "output_name": "matrix", "uuid": "94a22779-d526-4fb0-aae1-ad8c36cb6ffc" } ] }, "3": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.3.0", "errors": null, "id": 3, "input_connections": { "corData": { "id": 1, "output_name": "outFile" } }, "inputs": [ { "description": "runtime parameter for tool plotPCA", "name": "corData" } ], "label": null, "name": "plotPCA", "outputs": [ { "name": "outFileName", "type": "png" }, { "name": "output_outFileNameData", "type": "tabular" } ], "position": { "left": 1232, "top": 520.5 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.3.0", "tool_shed_repository": { "changeset_revision": "610bbc25ed8b", "name": "deeptools_plot_pca", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": null, \"plotTitle\": \"\\\"\\\"\", \"outFileFormat\": \"\\\"png\\\"\", \"__rerun_remap_job_id__\": null, \"outFileNameData\": \"\\\"false\\\"\", \"corData\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "2.2.3.0", "type": "tool", "uuid": "4a7bf483-9e9e-4c4d-bd87-f4b3ddbaa83f", "workflow_outputs": [ { "label": null, "output_name": "outFileName", "uuid": "da87bbce-e727-417f-9fb3-60c46e5d0e6b" }, { "label": null, "output_name": "output_outFileNameData", "uuid": "37629b80-9917-4092-9446-79fe08e99a7e" } ] } }, "uuid": "46c45881-988d-4a31-808a-bc65ff8a212f" }