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Merge pull request #3 from Public-Health-Bioinformatics/update-micall…
…-lite-galaxy Pipeline v0.2.0: Update micall lite galaxy tool to use micall-lite v0.1rc3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <iridaWorkflow> | ||
| <id>d9820957-5ffc-4a25-b98b-c1a655ad39f7</id> | ||
| <name>micall-lite</name> | ||
| <version>0.2.0</version> | ||
| <analysisType>MICALL_LITE</analysisType> | ||
| <inputs> | ||
| <sequenceReadsPaired>sequence_reads_paired</sequenceReadsPaired> | ||
| <requiresSingleSample>true</requiresSingleSample> | ||
| </inputs> | ||
| <parameters> | ||
| <parameter name="micall_lite-1-readlen" defaultValue="251"> | ||
| <toolParameter toolId="toolshed.g2.bx.psu.edu/repos/public-health-bioinformatics/micall_lite/micall_lite/0.1rc3+galaxy0" parameterName="readlen"/> | ||
| </parameter> | ||
| </parameters> | ||
| <outputs> | ||
| <output name="conseq" fileName="conseq.csv"/> | ||
| <output name="nuc" fileName="nuc.csv"/> | ||
| <output name="amino" fileName="amino.csv"/> | ||
| <output name="insert" fileName="insert.csv"/> | ||
| <output name="align" fileName="align.csv"/> | ||
| </outputs> | ||
| <toolRepositories> | ||
| <repository> | ||
| <name>suite_micall_lite</name> | ||
| <owner>public-health-bioinformatics</owner> | ||
| <url>https://toolshed.g2.bx.psu.edu</url> | ||
| <revision>e9618b79c799</revision> | ||
| </repository> | ||
| </toolRepositories> | ||
| </iridaWorkflow> |
159 changes: 159 additions & 0 deletions
159
src/main/resources/workflows/0.2.0/irida_workflow_structure.ga
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| { | ||
| "uuid": "1552e489-4b45-4dc9-932f-cb31a40befa2", | ||
| "tags": [], | ||
| "format-version": "0.1", | ||
| "name": "micall-lite", | ||
| "version": 1, | ||
| "steps": { | ||
| "0": { | ||
| "tool_id": null, | ||
| "tool_version": null, | ||
| "outputs": [], | ||
| "workflow_outputs": [ | ||
| { | ||
| "output_name": "output", | ||
| "uuid": "8ccb8c72-86d4-4c1b-b7ee-3b69cb25640e", | ||
| "label": null | ||
| } | ||
| ], | ||
| "input_connections": {}, | ||
| "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"sequence_reads_paired\"}", | ||
| "id": 0, | ||
| "uuid": "f6b1e09a-6758-4e74-9f8f-4b62d81a21c7", | ||
| "errors": null, | ||
| "name": "Input dataset collection", | ||
| "label": null, | ||
| "inputs": [], | ||
| "position": { | ||
| "top": 323.5, | ||
| "left": 233 | ||
| }, | ||
| "annotation": "", | ||
| "content_id": null, | ||
| "type": "data_collection_input" | ||
| }, | ||
| "1": { | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/public-health-bioinformatics/micall_lite/micall_lite/0.1rc3+galaxy0", | ||
| "tool_version": "0.1rc3+galaxy0", | ||
| "outputs": [ | ||
| { | ||
| "type": "csv", | ||
| "name": "align" | ||
| }, | ||
| { | ||
| "type": "csv", | ||
| "name": "amino" | ||
| }, | ||
| { | ||
| "type": "csv", | ||
| "name": "conseq" | ||
| }, | ||
| { | ||
| "type": "csv", | ||
| "name": "insert" | ||
| }, | ||
| { | ||
| "type": "csv", | ||
| "name": "nuc" | ||
| } | ||
| ], | ||
| "workflow_outputs": [ | ||
| { | ||
| "output_name": "insert", | ||
| "uuid": "180f33c7-e90d-457f-bc38-b4ce5cf62bcf", | ||
| "label": null | ||
| }, | ||
| { | ||
| "output_name": "align", | ||
| "uuid": "ccf56d54-2265-47fc-b05f-2a418944cc2f", | ||
| "label": null | ||
| }, | ||
| { | ||
| "output_name": "amino", | ||
| "uuid": "8edeee38-7a59-474a-87fa-9b60cdfe59c2", | ||
| "label": null | ||
| }, | ||
| { | ||
| "output_name": "nuc", | ||
| "uuid": "9f103353-6fa0-4a96-b62c-f8ce3ae4e8eb", | ||
| "label": null | ||
| }, | ||
| { | ||
| "output_name": "conseq", | ||
| "uuid": "23ec987d-bbee-4e73-9a36-23bfd2a4cd28", | ||
| "label": null | ||
| } | ||
| ], | ||
| "input_connections": { | ||
| "fastq_input|pair": { | ||
| "output_name": "output", | ||
| "id": 0 | ||
| } | ||
| }, | ||
| "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input_selector\\\": \\\"paired_collection\\\", \\\"pair\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"readlen\": \"\\\"251\\\"\"}", | ||
| "id": 1, | ||
| "tool_shed_repository": { | ||
| "owner": "public-health-bioinformatics", | ||
| "changeset_revision": "e5390c4b69e9", | ||
| "name": "micall_lite", | ||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
| }, | ||
| "uuid": "59e6e04d-12e4-4055-854c-69a11d61e020", | ||
| "errors": null, | ||
| "name": "micall_lite", | ||
| "post_job_actions": { | ||
| "RenameDatasetActionnuc": { | ||
| "output_name": "nuc", | ||
| "action_type": "RenameDatasetAction", | ||
| "action_arguments": { | ||
| "newname": "nuc.csv" | ||
| } | ||
| }, | ||
| "RenameDatasetActionconseq": { | ||
| "output_name": "conseq", | ||
| "action_type": "RenameDatasetAction", | ||
| "action_arguments": { | ||
| "newname": "conseq.csv" | ||
| } | ||
| }, | ||
| "RenameDatasetActionamino": { | ||
| "output_name": "amino", | ||
| "action_type": "RenameDatasetAction", | ||
| "action_arguments": { | ||
| "newname": "amino.csv" | ||
| } | ||
| }, | ||
| "RenameDatasetActioninsert": { | ||
| "output_name": "insert", | ||
| "action_type": "RenameDatasetAction", | ||
| "action_arguments": { | ||
| "newname": "insert.csv" | ||
| } | ||
| }, | ||
| "RenameDatasetActionalign": { | ||
| "output_name": "align", | ||
| "action_type": "RenameDatasetAction", | ||
| "action_arguments": { | ||
| "newname": "align.csv" | ||
| } | ||
| } | ||
| }, | ||
| "label": null, | ||
| "inputs": [ | ||
| { | ||
| "name": "fastq_input", | ||
| "description": "runtime parameter for tool micall_lite" | ||
| } | ||
| ], | ||
| "position": { | ||
| "top": 350.5, | ||
| "left": 562.5 | ||
| }, | ||
| "annotation": "", | ||
| "content_id": "toolshed.g2.bx.psu.edu/repos/public-health-bioinformatics/micall_lite/micall_lite/0.1rc3+galaxy0", | ||
| "type": "tool" | ||
| } | ||
| }, | ||
| "annotation": "", | ||
| "a_galaxy_workflow": "true" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| #Pipeline Info Properties | ||
| #Fri Sep 20 17:47:07 PDT 2019 | ||
| workflow.MICALL_LITE.title=MiCall-Lite Pipeline | ||
| workflow.MICALL_LITE.description=Analyze HIV or HCV viral samples against reference genomes. Derived from the 'MiCall' pipeline from the BC Centre for Excellence in HIV/AIDS Research | ||
| workflow.label.share-analysis-samples.MICALL_LITE=Save Results to Project Line List Metadata | ||
| pipeline.parameters.modal-title.micall-lite=MiCall-Lite Pipeline Parameters | ||
| pipeline.h1.micall-lite=MiCall Lite Pipeline | ||
| pipeline.title.micall-lite=Pipelines - MiCall Lite | ||
| #Tool Parameters - Tool: micall_lite - Workflow Step #: 1 | ||
| #Fri Sep 20 17:47:07 PDT 2019 | ||
| pipeline.parameters.micall-lite.micall_lite-1-readlen=Read Length | ||
|
|