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Commit message:
planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8 |
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added:
Qualimap_BAM_QC.ga repository_dependencies.xml |
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| diff -r 000000000000 -r 064dbe5f3b2f Qualimap_BAM_QC.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Qualimap_BAM_QC.ga Tue Sep 04 13:53:32 2018 -0400 |
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| @@ -0,0 +1,109 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{ \n \"description\": \"Quality control of mapped reads\", \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 Qualimap BAM QC on\" \n } \n ] \n } \n}", + "format-version": "0.1", + "name": "Qualimap Bam QC", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 494, + "top": 304.5 + }, + "tool_id": null, + "tool_state": "{}", + "tool_version": null, + "type": "data_input", + "uuid": "354d9a2d-aadd-4c58-886f-5cf9659df944", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "6e6fd3a9-4d85-4095-9e25-e868020b97f7" + } + ] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/qualimap2_bamqc/qualimap_bamqc/2.2", + "errors": null, + "id": 1, + "input_connections": { + "input_realigned_bam_file": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool QualiMap BamQC", + "name": "input_realigned_bam_file" + } + ], + "label": null, + "name": "QualiMap BamQC", + "outputs": [ + { + "name": "genome_results", + "type": "txt" + }, + { + "name": "raw_data_qualimapReport", + "type": "zip" + } + ], + "position": { + "left": 872, + "top": 359.5 + }, + "post_job_actions": { + "RenameDatasetActiongenome_results": { + "action_arguments": { + "newname": "genome_results" + }, + "action_type": "RenameDatasetAction", + "output_name": "genome_results" + }, + "RenameDatasetActionraw_data_qualimapReport": { + "action_arguments": { + "newname": "raw_data_qualimapReport" + }, + "action_type": "RenameDatasetAction", + "output_name": "raw_data_qualimapReport" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/qualimap2_bamqc/qualimap_bamqc/2.2", + "tool_shed_repository": { + "changeset_revision": "a2438e0f1bbf", + "name": "qualimap2_bamqc", + "owner": "refinery-platform", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"mem_size\": \"\\\"8G\\\"\", \"__rerun_remap_job_id__\": null, \"input_realigned_bam_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}", + "tool_version": "2.2", + "type": "tool", + "uuid": "8e63fbd9-22df-4b7b-a0d1-88e8be17bf16", + "workflow_outputs": [ + { + "label": null, + "output_name": "raw_data_qualimapReport", + "uuid": "71d23433-f0ef-452d-9c4b-b4376e2665de" + }, + { + "label": null, + "output_name": "genome_results", + "uuid": "d5f56231-b611-425a-b2e1-d2a9072111f9" + } + ] + } + }, + "uuid": "27bccc25-073c-4061-b573-9cfe9ed47324" +} \ No newline at end of file |
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| diff -r 000000000000 -r 064dbe5f3b2f repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue Sep 04 13:53:32 2018 -0400 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Stem Cell Commons Qualimap BAM QC requires qualimap2_bamqc tool."> + <repository toolshed="https://toolshed.g2.bx.psu.edu" name="qualimap2_bamqc" owner="refinery-platform" changeset_revision="a2438e0f1bbf" /> +</repositories> |