annotate finding_orphan_genes.ga @ 0:b92f5ab6d127 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
author earlhaminst
date Mon, 09 Jan 2017 15:06:04 -0500
parents
children 267a94f068d7
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b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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diff changeset
1 {
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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2 "a_galaxy_workflow": "true",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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3 "annotation": "",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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4 "format-version": "0.1",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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5 "name": "Orphan genes",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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6 "steps": {
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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7 "0": {
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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8 "annotation": "Output file from blast_parser of GeneSeqToFamily",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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11 "input_connections": {},
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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12 "inputs": [
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13 {
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14 "description": "Output file from blast_parser of GeneSeqToFamily",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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15 "name": "blast_parser data"
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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16 }
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17 ],
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b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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19 "name": "Input dataset",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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20 "outputs": [],
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24 },
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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27 "tool_state": "{\"name\": \"blast_parser data\"}",
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b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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34 "output_name": "output",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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37 ]
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38 },
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40 "annotation": "Same CDS, used to run BLASTP in GeneSeqToFamily",
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43 "input_connections": {},
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44 "inputs": [
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46 "description": "Same CDS, used to run BLASTP in GeneSeqToFamily",
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47 "name": "CDS"
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48 }
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49 ],
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50 "label": null,
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51 "name": "Input dataset",
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52 "outputs": [],
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56 },
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59 "tool_state": "{\"name\": \"CDS\"}",
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60 "tool_version": null,
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61 "type": "data_input",
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63 "workflow_outputs": [
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64 {
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66 "output_name": "output",
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68 }
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69 ]
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70 },
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71 "2": {
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72 "annotation": "",
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73 "content_id": "Cut1",
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75 "input_connections": {
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76 "input": {
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77 "id": 0,
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122 }
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123 },
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125 {
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128 }
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129 ],
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131 "name": "FASTA-to-Tabular",
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133 {
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135 "type": "tabular"
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141 },
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144 "action_arguments": {},
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145 "action_type": "HideDatasetAction",
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146 "output_name": "output"
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147 }
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148 },
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149 "tool_errors": null,
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151 "tool_shed_repository": {
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152 "changeset_revision": "7e801ab2b70e",
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153 "name": "fasta_to_tabular",
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154 "owner": "devteam",
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155 "tool_shed": "toolshed.g2.bx.psu.edu"
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156 },
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196 }
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197 },
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202 "name": "text_processing",
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203 "owner": "bgruening",
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204 "tool_shed": "toolshed.g2.bx.psu.edu"
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205 },
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206 "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
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207 "tool_version": "1.1.0",
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208 "type": "tool",
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209 "uuid": "55da94d2-b1d9-46ed-9668-db9b7f19a5bb",
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210 "workflow_outputs": []
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211 },
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212 "5": {
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213 "annotation": "",
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214 "content_id": "Cut1",
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215 "id": 5,
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216 "input_connections": {
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217 "input": {
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218 "id": 3,
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219 "output_name": "output"
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220 }
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221 },
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222 "inputs": [
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223 {
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224 "description": "runtime parameter for tool Cut",
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225 "name": "input"
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226 }
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227 ],
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228 "label": null,
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229 "name": "Cut",
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230 "outputs": [
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231 {
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232 "name": "out_file1",
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233 "type": "tabular"
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234 }
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296 "workflow_outputs": []
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297 },
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309 "output_name": "out_file1"
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311 },
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312 "inputs": [
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313 {
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340 },
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342 "tool_id": "comp1",
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345 "type": "tool",
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348 },
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354 "identifiers": {
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357 },
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358 "input": {
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359 "id": 1,
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360 "output_name": "output"
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361 }
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362 },
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364 {
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365 "description": "runtime parameter for tool Filter by FASTA IDs",
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366 "name": "input"
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367 },
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368 {
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369 "description": "runtime parameter for tool Filter by FASTA IDs",
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370 "name": "identifiers"
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371 }
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372 ],
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374 "name": "Filter by FASTA IDs",
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375 "outputs": [
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376 {
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377 "name": "output",
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378 "type": "fasta"
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379 }
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380 ],
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381 "position": {
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384 },
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385 "post_job_actions": {},
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387 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0",
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388 "tool_shed_repository": {
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389 "changeset_revision": "8d15aebf55fd",
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390 "name": "filter_by_fasta_ids",
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391 "owner": "galaxyp",
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392 "tool_shed": "toolshed.g2.bx.psu.edu"
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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393 },
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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394 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"identifiers\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dedup\": \"\\\"true\\\"\", \"__page__\": 0}",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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395 "tool_version": "1.0",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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396 "type": "tool",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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397 "uuid": "5f5fb6ac-f026-41bc-a89c-2d1d882ece85",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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398 "workflow_outputs": [
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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399 {
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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400 "label": null,
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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401 "output_name": "output",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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402 "uuid": "56824bb4-df6b-4ebc-8c89-c6731b5d76f1"
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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403 }
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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404 ]
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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405 }
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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406 },
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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407 "uuid": "23e0aa20-d91a-429e-817c-654a67b0a171"
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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408 }