Mercurial > repos > stemcellcommons > merging_workflows
changeset 0:5703e64e15e9 draft default tip
Initial upload
| author | stemcellcommons |
|---|---|
| date | Tue, 05 Dec 2017 14:58:39 -0500 (2017-12-05) |
| parents | |
| children | |
| files | Merge_BAM.ga Merge_FASTQ.ga repository_dependencies.xml |
| diffstat | 3 files changed, 186 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Merge_BAM.ga Tue Dec 05 14:58:39 2017 -0500 @@ -0,0 +1,87 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\n \"description\": \"Merge a list of BAM files into a single BAM.\",\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 be merged\"\n }\n ]\n }\n}", + "format-version": "0.1", + "name": "Merge BAM", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset Collection" + } + ], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 200.5, + "top": 284.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "d9e52442-15c8-45ba-a07e-fdf9de76ac43", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "463f98ce-580f-4a70-8d89-1be510478bb9" + } + ] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.126.0", + "id": 1, + "input_connections": { + "inputFile": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "MergeSamFiles", + "outputs": [ + { + "name": "outFile", + "type": "bam" + } + ], + "position": { + "left": 575, + "top": 285 + }, + "post_job_actions": { + "RenameDatasetActionoutFile": { + "action_arguments": { + "newname": "merged" + }, + "action_type": "RenameDatasetAction", + "output_name": "outFile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.126.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"comments\": \"[]\", \"assume_sorted\": \"\\\"False\\\"\", \"merge_sequence_dictionaries\": \"\\\"False\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.126.0", + "type": "tool", + "uuid": "0f22ffbb-d375-4d1f-9b53-0abce7390f66", + "workflow_outputs": [ + { + "label": null, + "output_name": "outFile", + "uuid": "82e3ef46-e532-4e2f-bafb-f0875211282f" + } + ] + } + }, + "uuid": "a920711d-9852-4048-9694-eda710a7513a" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Merge_FASTQ.ga Tue Dec 05 14:58:39 2017 -0500 @@ -0,0 +1,94 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\n \"description\": \"Merges a list of FASTQ files into a single FASTQ.\",\n \"file_relationship\": {\n \"file_relationship\": {},\n \"value_type\": \"LIST\",\n \"name\": \"List of FASTQ Files\",\n \"input_files\": [\n {\n \"allowed_filetypes\": [{\"name\": \"FASTQ\"}],\n \"name\": \"Input File\",\n \"description\": \"File to be merged\"\n }\n ]\n }\n}", + "format-version": "0.1", + "name": "Merge FASTQ", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset Collection" + } + ], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 161.5, + "top": 215.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "38f167a0-9b63-4c15-92b8-15ade85b580b", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "2d4184c2-900b-435f-9850-fdd368909b74" + } + ] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0", + "id": 1, + "input_connections": { + "input_list": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Collapse Collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 488, + "top": 218 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput": { + "action_arguments": { + "newtype": "fastq" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output" + }, + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "merged" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_list\": \"null\", \"one_header\": \"\\\"False\\\"\", \"filename\": \"{\\\"add_name\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}", + "tool_version": "4.0", + "type": "tool", + "uuid": "e0e26825-a370-4e76-ac2f-e7e90d028ff4", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c7b6d000-a300-4dcf-9f8a-bcfd1052a585" + } + ] + } + }, + "uuid": "dd00f51a-b81d-433f-b178-7a02200a0ae4" +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue Dec 05 14:58:39 2017 -0500 @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<repositories description="Stem Cell Commons Merge FASTQ workflow requires Collapse Collections tool. Stem Cell Commons Merge BAM workflow requires picard tool."> + <repository toolshed="https://toolshed.g2.bx.psu.edu" name="collapse_collections" owner="nml" changeset_revision="25136a2b0cfe" /> + <repository toolshed="https://toolshed.g2.bx.psu.edu" name="picard" owner="devteam" changeset_revision="379fdf4c41ac" /> +</repositories>