Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
view Kallisto_RNA-seq_(SE)_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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{ "a_galaxy_workflow": "true", "annotation": "{ \n \"description\": \"Rapid transcript quantification via pseudoalignment (https://pachterlab.github.io/kallisto/). Single-end reads are quantified against the mm10 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 - Mouse", "steps": { "0": { "annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [], "label": null, "name": "Input dataset collection", "outputs": [], "position": { "left": 372.5, "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": "98278f40-220b-4dea-bd35-f95547c253b0" } ] }, "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": 874, "top": 325.5 }, "post_job_actions": { "HideDatasetActionabundance_h5": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "abundance_h5" }, "HideDatasetActionabundance_tab": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "abundance_tab" }, "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\\\": \\\"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": "c124061f-5652-4e12-878b-88ecdaf4cc09", "workflow_outputs": [ { "label": null, "output_name": "pseudobam_output", "uuid": "84016f1d-3195-49ae-8aad-764d3b1d2729" } ] } }, "uuid": "95467aa5-2868-4f50-a026-7f89be4306a8" }