Mercurial > repos > stemcellcommons > kallisto_rnaseq_workflows
annotate Kallisto_RNA-seq_(PE)_Quantification_-_Mouse.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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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/). Paired-end reads are quantified against the mm10 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}", |
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4 "format-version": "0.1", |
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5 "name": "Kallisto RNA-seq (PE) Quantification - Mouse", |
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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": 577.5, |
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19 "top": 309 |
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22 "tool_state": "{\"collection_type\": \"list:paired\"}", |
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23 "tool_version": null, |
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24 "type": "data_collection_input", |
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25 "uuid": "114f35e8-a538-4978-80ad-786750f2e65a", |
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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": "8ca3b6da-cc1e-46b3-a475-6abb4230528c" |
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31 } |
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32 ] |
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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|collection|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 "label": null, |
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47 "name": "Kallisto quant", |
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48 "outputs": [ |
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49 { |
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50 "name": "abundance_h5", |
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51 "type": "h5" |
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52 }, |
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53 { |
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54 "name": "abundance_tab", |
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55 "type": "tabular" |
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58 "name": "pseudobam_output", |
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59 "type": "bam" |
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60 }, |
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62 "name": "fusion_output", |
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63 "type": "tabular" |
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64 } |
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66 "position": { |
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67 "left": 964, |
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68 "top": 328.5 |
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70 "post_job_actions": { |
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71 "HideDatasetActionabundance_h5": { |
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72 "action_arguments": {}, |
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73 "action_type": "HideDatasetAction", |
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74 "output_name": "abundance_h5" |
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76 "HideDatasetActionfusion_output": { |
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77 "action_arguments": {}, |
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78 "action_type": "HideDatasetAction", |
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79 "output_name": "fusion_output" |
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80 } |
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81 }, |
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82 "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3", |
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83 "tool_shed_repository": { |
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84 "changeset_revision": "b818b23df1e0", |
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85 "name": "kallisto_quant", |
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86 "owner": "iuc", |
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87 "tool_shed": "toolshed.g2.bx.psu.edu" |
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88 }, |
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89 "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\\\": \\\"mm10\\\", \\\"reference_transcriptome_source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"fusion\": \"\\\"false\\\"\", \"bias\": \"\\\"false\\\"\", \"pseudobam\": \"\\\"true\\\"\", \"seed\": \"\\\"42\\\"\"}", |
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90 "tool_version": "0.43.1.3", |
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91 "type": "tool", |
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92 "uuid": "42dbc102-33eb-4c40-a927-21d782c98f25", |
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93 "workflow_outputs": [ |
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94 { |
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95 "label": null, |
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96 "output_name": "pseudobam_output", |
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98 }, |
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101 "output_name": "abundance_tab", |
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102 "uuid": "2136144c-08f2-4fae-8937-b1c99a5d7f52" |
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103 } |
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104 ] |
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105 } |
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106 }, |
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107 "uuid": "00c71013-84ba-4eb1-b42b-d57dc0dc9dea" |
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108 } |