Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
diff Kallisto_RNA-seq_(PE)_Quantification_-_Mouse.ga @ 0:ce9f11c6b94b draft
planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
author | scottx611x |
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date | Tue, 04 Sep 2018 13:56:11 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Kallisto_RNA-seq_(PE)_Quantification_-_Mouse.ga Tue Sep 04 13:56:11 2018 -0400 @@ -0,0 +1,108 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{\n \"description\": \"Rapid transcript quantification via pseudoalignment (https://pachterlab.github.io/kallisto/). Paired-end reads are quantified against the mm10 transcriptome.\",\n \"file_relationship\": {\n \"value_type\": \"LIST\",\n \"name\": \"List of Read Pairs\",\n \"file_relationship\": {\n \"file_relationship\": {},\n \"value_type\": \"PAIR\",\n \"name\": \"Read Pair\",\n \"input_files\": [{\n \"allowed_filetypes\": [{\"name\": \"FASTQ\"}],\n \"name\": \"Input File\",\n \"description\": \"Forward Reads\"\n },\n {\n \"allowed_filetypes\": [{\"name\": \"FASTQ\"}],\n \"name\": \"Input File\",\n \"description\": \"Reverse Reads\"\n }\n ]\n }\n }\n}", + "format-version": "0.1", + "name": "Kallisto RNA-seq (PE) Quantification - Mouse", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 577.5, + "top": 309 + }, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list:paired\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "114f35e8-a538-4978-80ad-786750f2e65a", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "8ca3b6da-cc1e-46b3-a475-6abb4230528c" + } + ] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", + "errors": null, + "id": 1, + "input_connections": { + "single_paired|collection|reads": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Kallisto quant", + "outputs": [ + { + "name": "abundance_h5", + "type": "h5" + }, + { + "name": "abundance_tab", + "type": "tabular" + }, + { + "name": "pseudobam_output", + "type": "bam" + }, + { + "name": "fusion_output", + "type": "tabular" + } + ], + "position": { + "left": 964, + "top": 328.5 + }, + "post_job_actions": { + "HideDatasetActionabundance_h5": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "abundance_h5" + }, + "HideDatasetActionfusion_output": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "fusion_output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", + "tool_shed_repository": { + "changeset_revision": "b818b23df1e0", + "name": "kallisto_quant", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": null, \"bootstrap_samples\": \"\\\"0\\\"\", \"single_paired\": \"{\\\"collection\\\": {\\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"collection_selector\\\": \\\"collection\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"single_paired_selector\\\": \\\"paired\\\"}\", \"__rerun_remap_job_id__\": null, \"reference_transcriptome\": \"{\\\"index\\\": \\\"mm10\\\", \\\"reference_transcriptome_source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"fusion\": \"\\\"false\\\"\", \"bias\": \"\\\"false\\\"\", \"pseudobam\": \"\\\"true\\\"\", \"seed\": \"\\\"42\\\"\"}", + "tool_version": "0.43.1.3", + "type": "tool", + "uuid": "42dbc102-33eb-4c40-a927-21d782c98f25", + "workflow_outputs": [ + { + "label": null, + "output_name": "pseudobam_output", + "uuid": "44ce1fa6-a045-4f45-b356-ab65f6ad05c8" + }, + { + "label": null, + "output_name": "abundance_tab", + "uuid": "2136144c-08f2-4fae-8937-b1c99a5d7f52" + } + ] + } + }, + "uuid": "00c71013-84ba-4eb1-b42b-d57dc0dc9dea" +} \ No newline at end of file