Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows

annotate Kallisto_RNA-seq_(SE)_Quantification_-_Mouse.ga @ 1:cbf8233bf744 draft default tip

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author scottx611x
date Tue, 04 Sep 2018 15:12:04 -0400
parents ce9f11c6b94b
children
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1 {
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2 "a_galaxy_workflow": "true",
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3 "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}",
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4 "format-version": "0.1",
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5 "name": "Kallisto RNA-seq (SE) Quantification - Mouse",
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6 "steps": {
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15 "name": "Input dataset collection",
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22 "tool_state": "{\"collection_type\": \"list\"}",
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24 "type": "data_collection_input",
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26 "workflow_outputs": [
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36 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3",
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40 "single_paired|reads": {
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42 "output_name": "output"
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43 }
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44 },
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46 {
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47 "description": "runtime parameter for tool Kallisto quant",
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48 "name": "single_paired"
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52 "name": "Kallisto quant",
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53 "outputs": [
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54 {
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59 "name": "abundance_tab",
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60 "type": "tabular"
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62 {
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63 "name": "pseudobam_output",
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64 "type": "bam"
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68 "type": "tabular"
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78 "action_type": "HideDatasetAction",
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83 "action_type": "HideDatasetAction",
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84 "output_name": "abundance_tab"
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85 },
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86 "HideDatasetActionfusion_output": {
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87 "action_arguments": {},
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88 "action_type": "HideDatasetAction",
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89 "output_name": "fusion_output"
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90 }
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91 },
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92 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3",
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93 "tool_shed_repository": {
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94 "changeset_revision": "b818b23df1e0",
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95 "name": "kallisto_quant",
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96 "owner": "iuc",
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97 "tool_shed": "toolshed.g2.bx.psu.edu"
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98 },
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99 "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\\\"\"}",
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100 "tool_version": "0.43.1.3",
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101 "type": "tool",
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102 "uuid": "c124061f-5652-4e12-878b-88ecdaf4cc09",
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103 "workflow_outputs": [
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104 {
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106 "output_name": "pseudobam_output",
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108 }
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109 ]
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110 }
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111 },
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112 "uuid": "95467aa5-2868-4f50-a026-7f89be4306a8"
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113 }