Mercurial > repos > earlhaminst > geneseqtofamily

annotate finding_orphan_genes.ga @ 2:58c9294400ed draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit d3da4ff3bfb86ce0686a87c4987e94486854d839
author earlhaminst
date Fri, 12 May 2017 11:50:14 -0400
parents 267a94f068d7
children
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b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
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1 {
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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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
earlhaminst
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3 "annotation": "",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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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
earlhaminst
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6 "steps": {
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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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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b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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10 "id": 0,
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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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
earlhaminst
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12 "inputs": [
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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13 {
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
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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
earlhaminst
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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
earlhaminst
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16 }
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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17 ],
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267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
earlhaminst
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18 "label": "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
earlhaminst
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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
earlhaminst
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20 "outputs": [],
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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21 "position": {
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267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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earlhaminst
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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\"}",
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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29 "type": "data_input",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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31 "workflow_outputs": [
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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32 {
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33 "label": null,
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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36 }
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earlhaminst
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37 ]
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earlhaminst
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38 },
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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40 "annotation": "Same CDS, used to run BLASTP in GeneSeqToFamily",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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42 "id": 1,
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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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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earlhaminst
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49 ],
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267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
earlhaminst
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50 "label": "CDS",
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51 "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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52 "outputs": [],
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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56 },
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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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59 "tool_state": "{\"name\": \"CDS\"}",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
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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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earlhaminst
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72 "annotation": "List of IDs discarded from hcluster_sg results",
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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75 "input_connections": {},
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76 "inputs": [
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77 {
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78 "description": "List of IDs discarded from hcluster_sg results",
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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237 },
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320 }
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321 },
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371 }
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372 },
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376 "tool_version": "1.0.2",
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377 "type": "tool",
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379 "workflow_outputs": []
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380 },
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381 "9": {
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382 "annotation": "",
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383 "content_id": "cat1",
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384 "id": 9,
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385 "input_connections": {
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386 "input1": {
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387 "id": 8,
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388 "output_name": "out_file1"
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389 },
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390 "queries_0|input2": {
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391 "id": 2,
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392 "output_name": "output"
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393 }
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394 },
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395 "inputs": [
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396 {
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397 "description": "runtime parameter for tool Concatenate datasets",
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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398 "name": "input1"
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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399 }
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400 ],
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402 "name": "Concatenate datasets",
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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403 "outputs": [
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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405 "name": "out_file1",
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406 "type": "input"
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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407 }
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412 },
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414 "HideDatasetActionout_file1": {
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415 "action_arguments": {},
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416 "action_type": "HideDatasetAction",
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417 "output_name": "out_file1"
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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418 }
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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419 },
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420 "tool_errors": null,
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421 "tool_id": "cat1",
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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423 "tool_version": "1.0.0",
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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424 "type": "tool",
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426 "workflow_outputs": []
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
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427 },
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429 "annotation": "",
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437 "input": {
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439 "output_name": "output"
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440 }
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441 },
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442 "inputs": [
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443 {
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444 "description": "runtime parameter for tool Filter by FASTA IDs",
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445 "name": "input"
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446 },
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447 {
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448 "description": "runtime parameter for tool Filter by FASTA IDs",
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449 "name": "identifiers"
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450 }
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451 ],
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453 "name": "Filter by FASTA IDs",
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454 "outputs": [
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455 {
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456 "name": "output",
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457 "type": "fasta"
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458 }
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459 ],
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460 "position": {
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463 },
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467 "tool_shed_repository": {
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469 "name": "filter_by_fasta_ids",
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470 "owner": "galaxyp",
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472 },
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474 "tool_version": "1.0",
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475 "type": "tool",
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476 "uuid": "5f5fb6ac-f026-41bc-a89c-2d1d882ece85",
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477 "workflow_outputs": [
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
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478 {
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
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479 "label": null,
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
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480 "output_name": "output",
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
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481 "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
parents:
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482 }
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
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483 ]
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
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484 }
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
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485 },
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267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
earlhaminst
parents: 0
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486 "uuid": "cf6b9210-2ed8-46b1-920e-ac6303ed44d5"
267a94f068d7 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
earlhaminst
parents: 0
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487 }