Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
diff Kallisto_RNA-seq_(SE)_Quantification_-_Human.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_(SE)_Quantification_-_Human.ga Tue Sep 04 13:56:11 2018 -0400 @@ -0,0 +1,113 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "{ \n \"description\": \"Rapid transcript quantification via pseudoalignment (https://pachterlab.github.io/kallisto/). Single-end reads are quantified against the hg38 transcriptome.\", \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\": \"FASTQ File\" \n } \n ] \n } \n}", + "format-version": "0.1", + "name": "Kallisto RNA-seq (SE) Quantification - Human", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [], + "label": null, + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 371.5, + "top": 214 + }, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "38a1eccd-850d-4b18-876c-097acf776154", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "51e4c27c-9b75-4306-b858-8ea222b2f4d4" + } + ] + }, + "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|reads": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Kallisto quant", + "name": "single_paired" + } + ], + "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": 1008, + "top": 434.5 + }, + "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\": \"{\\\"fragment_length\\\": \\\"200\\\", \\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"single_paired_selector\\\": \\\"single\\\", \\\"sd\\\": \\\"20\\\"}\", \"__rerun_remap_job_id__\": null, \"reference_transcriptome\": \"{\\\"index\\\": \\\"hg38\\\", \\\"reference_transcriptome_source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"fusion\": \"\\\"false\\\"\", \"bias\": \"\\\"false\\\"\", \"pseudobam\": \"\\\"true\\\"\", \"seed\": \"\\\"42\\\"\"}", + "tool_version": "0.43.1.3", + "type": "tool", + "uuid": "068a2827-4c38-4aed-8a76-f1fb5f179e33", + "workflow_outputs": [ + { + "label": null, + "output_name": "pseudobam_output", + "uuid": "1da5bcc0-11bd-4b2e-a625-4141f0ae0be8" + }, + { + "label": null, + "output_name": "abundance_tab", + "uuid": "e61317ef-a90d-4580-9295-47de567a2b3d" + } + ] + } + }, + "uuid": "a1c133f3-2887-4ac7-b66a-c9ce07e74fc6" +} \ No newline at end of file