Mercurial > repos > stemcellcommons > deeptools_bamqc_workflow
diff 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 diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_BAM_QC.ga Tue Sep 04 13:55:35 2018 -0400 @@ -0,0 +1,210 @@ +{ + "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" +} \ No newline at end of file