Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
annotate 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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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 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}", |
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4 "format-version": "0.1", |
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5 "name": "Kallisto RNA-seq (SE) Quantification - Human", |
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6 "steps": { |
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7 "0": { |
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8 "annotation": "", |
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9 "content_id": null, |
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10 "errors": null, |
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11 "id": 0, |
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12 "input_connections": {}, |
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13 "inputs": [], |
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14 "label": null, |
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15 "name": "Input dataset collection", |
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16 "outputs": [], |
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17 "position": { |
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18 "left": 371.5, |
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19 "top": 214 |
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20 }, |
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21 "tool_id": null, |
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22 "tool_state": "{\"collection_type\": \"list\"}", |
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23 "tool_version": null, |
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24 "type": "data_collection_input", |
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25 "uuid": "38a1eccd-850d-4b18-876c-097acf776154", |
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26 "workflow_outputs": [ |
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27 { |
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28 "label": null, |
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29 "output_name": "output", |
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30 "uuid": "51e4c27c-9b75-4306-b858-8ea222b2f4d4" |
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31 } |
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32 ] |
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33 }, |
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34 "1": { |
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35 "annotation": "", |
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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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37 "errors": null, |
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38 "id": 1, |
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39 "input_connections": { |
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40 "single_paired|reads": { |
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41 "id": 0, |
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42 "output_name": "output" |
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43 } |
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44 }, |
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45 "inputs": [ |
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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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49 } |
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50 ], |
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51 "label": null, |
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52 "name": "Kallisto quant", |
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53 "outputs": [ |
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54 { |
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55 "name": "abundance_h5", |
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56 "type": "h5" |
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57 }, |
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58 { |
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59 "name": "abundance_tab", |
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60 "type": "tabular" |
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61 }, |
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62 { |
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63 "name": "pseudobam_output", |
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64 "type": "bam" |
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65 }, |
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66 { |
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67 "name": "fusion_output", |
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68 "type": "tabular" |
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69 } |
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71 "position": { |
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72 "left": 1008, |
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73 "top": 434.5 |
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74 }, |
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75 "post_job_actions": { |
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76 "HideDatasetActionabundance_h5": { |
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77 "action_arguments": {}, |
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78 "action_type": "HideDatasetAction", |
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79 "output_name": "abundance_h5" |
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80 }, |
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81 "HideDatasetActionfusion_output": { |
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82 "action_arguments": {}, |
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83 "action_type": "HideDatasetAction", |
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84 "output_name": "fusion_output" |
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85 } |
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86 }, |
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87 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", |
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88 "tool_shed_repository": { |
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89 "changeset_revision": "b818b23df1e0", |
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90 "name": "kallisto_quant", |
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91 "owner": "iuc", |
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92 "tool_shed": "toolshed.g2.bx.psu.edu" |
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93 }, |
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94 "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\\\"\"}", |
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95 "tool_version": "0.43.1.3", |
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96 "type": "tool", |
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97 "uuid": "068a2827-4c38-4aed-8a76-f1fb5f179e33", |
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98 "workflow_outputs": [ |
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99 { |
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100 "label": null, |
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101 "output_name": "pseudobam_output", |
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102 "uuid": "1da5bcc0-11bd-4b2e-a625-4141f0ae0be8" |
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103 }, |
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104 { |
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105 "label": null, |
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106 "output_name": "abundance_tab", |
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107 "uuid": "e61317ef-a90d-4580-9295-47de567a2b3d" |
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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": "a1c133f3-2887-4ac7-b66a-c9ce07e74fc6" |
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113 } |