Mercurial > repos > dereeper > sniplay3_complete_workflow
annotate Galaxy-Workflow-SNiPlay.ga @ 2:0c7db2dca8b4 draft default tip
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f-dirty
author | dereeper |
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date | Tue, 14 Aug 2018 09:37:46 -0400 |
parents | 0bf2b08766d9 |
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1 { |
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2 "a_galaxy_workflow": "true", |
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3 "annotation": "", |
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4 "format-version": "0.2", |
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5 "name": "SNiPlay Workflow", |
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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": "Input VCF", |
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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": 200, |
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19 "top": 273 |
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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": "1b36351d-d27f-4696-b500-98a27b4d7ea3", |
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26 "workflow_outputs": [] |
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27 }, |
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28 "1": { |
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29 "annotation": "", |
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30 "content_id": null, |
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31 "errors": null, |
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32 "id": 1, |
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33 "input_connections": {}, |
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34 "inputs": [], |
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35 "label": "Input Fasta Reference", |
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36 "name": "Input dataset", |
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37 "outputs": [], |
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38 "position": { |
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39 "left": 201, |
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40 "top": 360 |
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41 }, |
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42 "tool_id": null, |
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43 "tool_state": "{}", |
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44 "tool_version": null, |
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45 "type": "data_input", |
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46 "uuid": "bc1b70d3-0f2e-4f2c-a690-92c1001aed6e", |
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47 "workflow_outputs": [] |
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48 }, |
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49 "2": { |
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50 "annotation": "", |
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51 "content_id": null, |
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52 "errors": null, |
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53 "id": 2, |
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54 "input_connections": {}, |
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55 "inputs": [], |
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56 "label": "Input GFF Annotation", |
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57 "name": "Input dataset", |
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58 "outputs": [], |
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59 "position": { |
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60 "left": 201, |
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61 "top": 458 |
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62 }, |
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63 "tool_id": null, |
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64 "tool_state": "{}", |
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65 "tool_version": null, |
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66 "type": "data_input", |
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67 "uuid": "a4e7ebaf-ce63-4cc1-b516-bafa883ccc81", |
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68 "workflow_outputs": [] |
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69 }, |
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70 "3": { |
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71 "annotation": "", |
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72 "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", |
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73 "errors": null, |
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74 "id": 3, |
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75 "input_connections": { |
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76 "input": { |
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77 "id": 0, |
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78 "output_name": "output" |
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79 } |
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80 }, |
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81 "inputs": [ |
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82 { |
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83 "description": "runtime parameter for tool VCFtools Filter", |
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84 "name": "input" |
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85 } |
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86 ], |
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88 "name": "VCFtools Filter", |
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89 "outputs": [ |
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90 { |
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91 "name": "fileout", |
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92 "type": "vcf" |
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93 }, |
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95 "name": "fileout_map", |
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96 "type": "tabular" |
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97 }, |
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99 "name": "filelog", |
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100 "type": "txt" |
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101 } |
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102 ], |
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103 "position": { |
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107 "post_job_actions": {}, |
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108 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", |
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109 "tool_shed_repository": { |
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111 "name": "vcftools_filter_stats_diversity", |
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112 "owner": "dereeper", |
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113 "tool_shed": "toolshed.g2.bx.psu.edu" |
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114 }, |
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116 "tool_version": "2.0.0", |
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117 "type": "tool", |
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119 "workflow_outputs": [] |
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120 }, |
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121 "4": { |
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122 "annotation": "", |
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123 "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf/snpEff/2.0.0", |
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124 "errors": null, |
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125 "id": 4, |
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126 "input_connections": { |
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127 "genome": { |
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128 "id": 1, |
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129 "output_name": "output" |
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130 }, |
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131 "gff": { |
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132 "id": 2, |
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133 "output_name": "output" |
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135 "vcf": { |
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137 "output_name": "fileout" |
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140 "inputs": [ |
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141 { |
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142 "description": "runtime parameter for tool SnpEff", |
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143 "name": "gff" |
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146 "description": "runtime parameter for tool SnpEff", |
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147 "name": "genome" |
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150 "description": "runtime parameter for tool SnpEff", |
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151 "name": "vcf" |
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155 "name": "SnpEff", |
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156 "outputs": [ |
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158 "name": "output", |
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159 "type": "vcf" |
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162 "name": "statsFile", |
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163 "type": "html" |
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170 "position": { |
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174 "post_job_actions": {}, |
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175 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/snpeff_from_gff_vcf/snpEff/2.0.0", |
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176 "tool_shed_repository": { |
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177 "changeset_revision": null, |
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178 "name": "snpeff_from_gff_vcf", |
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179 "owner": "dereeper", |
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180 "tool_shed": "toolshed.g2.bx.psu.edu" |
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182 "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"gff\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"genome\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"vcf\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", |
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183 "tool_version": "2.0.0", |
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184 "type": "tool", |
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188 "5": { |
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189 "annotation": "", |
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190 "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3.0", |
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191 "errors": null, |
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193 "input_connections": { |
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194 "input": { |
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195 "id": 4, |
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196 "output_name": "output" |
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197 } |
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199 "inputs": [ |
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201 "description": "runtime parameter for tool SnpSift Filter", |
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206 "name": "SnpSift Filter", |
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210 "type": "vcf" |
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866 ], |
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867 "position": { |
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868 "left": 1296, |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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869 "top": 798 |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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870 }, |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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871 "post_job_actions": {}, |
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872 "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/sniplay_rooting/2.0.0", |
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873 "tool_shed_repository": { |
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874 "changeset_revision": null, |
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875 "name": "sniplay", |
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876 "owner": "dereeper", |
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877 "tool_shed": "toolshed.g2.bx.psu.edu" |
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878 }, |
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879 "tool_state": "{\"fileout_label\": \"\\\"out tree\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"filein\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 36319}]}\"}", |
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880 "tool_version": "2.0.0", |
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881 "type": "tool", |
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882 "uuid": "c49727bf-cb46-4cf6-998c-539977b1a419", |
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883 "workflow_outputs": [] |
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884 } |
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885 }, |
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886 "tags": [], |
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887 "uuid": "6cb99c2c-e345-4e5b-b1c3-80172449e6bd" |
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888 } |