Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
view Kallisto_RNA-seq_(PE)_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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{ "a_galaxy_workflow": "true", "annotation": "{\n \"description\": \"Rapid transcript quantification via pseudoalignment (https://pachterlab.github.io/kallisto/). Paired-end reads are quantified against the hg38 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 - Human", "steps": { "0": { "annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [], "label": null, "name": "Input dataset collection", "outputs": [], "position": { "left": 366.5, "top": 295 }, "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": "f906db26-f882-4e34-a638-74fe8aa56523" } ] }, "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": 796, "top": 327.5 }, "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\\\": \\\"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": "df9dd3c7-028a-4b96-a09c-33bbb14db527", "workflow_outputs": [ { "label": null, "output_name": "pseudobam_output", "uuid": "47d4c13b-218f-4a2b-b116-0516a0a9b109" }, { "label": null, "output_name": "abundance_tab", "uuid": "fe306756-a099-4e50-aa1f-6983dfff2d00" } ] } }, "uuid": "2ec7af1e-4f59-44a8-99d3-28ceda87411d" }