Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
view Kallisto_RNA-seq_(SE)_Quantification_-_Zebrafish.ga @ 1:cbf8233bf744 draft default tip
planemo upload commit dc4a5924dc98d22c14eac246506d13dfc13c3c6d
author | scottx611x |
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date | Tue, 04 Sep 2018 15:12:04 -0400 |
parents | ce9f11c6b94b |
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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 danRer11 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 - Zebrafish", "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" }