Mercurial > repos > stemcellcommons > qualimap_bamqc_workflow

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planemo upload commit 96bf4e03fcbbbc1eb0e4b5af12c7da8aa4477fa8
author scottx611x
date Tue, 04 Sep 2018 13:53:32 -0400
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "{ \n \"description\": \"Quality control of mapped reads\", \n \"file_relationship\": { \n \"file_relationship\": {}, \n \"value_type\": \"LIST\", \n \"name\": \"List of BAM Files\", \n \"input_files\": [ \n { \n \"allowed_filetypes\": [{\"name\": \"BAM\"}], \n \"name\": \"Input File\", \n \"description\": \"File to run Qualimap BAM QC on\" \n } \n ] \n } \n}",
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4 "format-version": "0.1",
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5 "name": "Qualimap Bam QC",
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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",
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16 "outputs": [],
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17 "position": {
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18 "left": 494,
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19 "top": 304.5
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20 },
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21 "tool_id": null,
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22 "tool_state": "{}",
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23 "tool_version": null,
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24 "type": "data_input",
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25 "uuid": "354d9a2d-aadd-4c58-886f-5cf9659df944",
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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": "6e6fd3a9-4d85-4095-9e25-e868020b97f7"
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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/refinery-platform/qualimap2_bamqc/qualimap_bamqc/2.2",
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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 "input_realigned_bam_file": {
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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 QualiMap BamQC",
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48 "name": "input_realigned_bam_file"
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49 }
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50 ],
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51 "label": null,
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52 "name": "QualiMap BamQC",
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53 "outputs": [
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54 {
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55 "name": "genome_results",
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56 "type": "txt"
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57 },
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58 {
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59 "name": "raw_data_qualimapReport",
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60 "type": "zip"
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61 }
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62 ],
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63 "position": {
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64 "left": 872,
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65 "top": 359.5
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66 },
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67 "post_job_actions": {
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68 "RenameDatasetActiongenome_results": {
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69 "action_arguments": {
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70 "newname": "genome_results"
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71 },
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72 "action_type": "RenameDatasetAction",
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73 "output_name": "genome_results"
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74 },
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75 "RenameDatasetActionraw_data_qualimapReport": {
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76 "action_arguments": {
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77 "newname": "raw_data_qualimapReport"
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78 },
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79 "action_type": "RenameDatasetAction",
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80 "output_name": "raw_data_qualimapReport"
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81 }
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82 },
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83 "tool_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/qualimap2_bamqc/qualimap_bamqc/2.2",
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84 "tool_shed_repository": {
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85 "changeset_revision": "a2438e0f1bbf",
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86 "name": "qualimap2_bamqc",
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87 "owner": "refinery-platform",
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88 "tool_shed": "toolshed.g2.bx.psu.edu"
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89 },
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90 "tool_state": "{\"mem_size\": \"\\\"8G\\\"\", \"__rerun_remap_job_id__\": null, \"input_realigned_bam_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}",
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91 "tool_version": "2.2",
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92 "type": "tool",
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93 "uuid": "8e63fbd9-22df-4b7b-a0d1-88e8be17bf16",
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94 "workflow_outputs": [
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95 {
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96 "label": null,
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97 "output_name": "raw_data_qualimapReport",
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98 "uuid": "71d23433-f0ef-452d-9c4b-b4376e2665de"
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99 },
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100 {
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101 "label": null,
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102 "output_name": "genome_results",
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103 "uuid": "d5f56231-b611-425a-b2e1-d2a9072111f9"
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104 }
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105 ]
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106 }
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107 },
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108 "uuid": "27bccc25-073c-4061-b573-9cfe9ed47324"
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109 }