Mercurial > repos > drosofff > metavisitor_workflows
annotate Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga @ 1:3d8eb2c065c7 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit a143c96a3168e4135202479cb58e5a2bcdd153b4
author | drosofff |
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date | Mon, 11 Apr 2016 13:14:14 -0400 |
parents | 4a47903bb4df |
children | 48b020a0d2f7 |
rev | line source |
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0
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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1 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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2 "a_galaxy_workflow": "true", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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3 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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4 "format-version": "0.1", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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5 "name": "Metavisitor: Workflow for Use Case 1-4", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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6 "steps": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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7 "0": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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8 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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9 "content_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
diff
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10 "id": 0, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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11 "input_connections": {}, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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12 "inputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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13 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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14 "description": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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15 "name": "Input Dataset Collection" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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16 } |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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17 ], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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18 "label": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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19 "name": "Input dataset collection", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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20 "outputs": [], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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21 "position": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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22 "left": 211.94445514678955, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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23 "top": 200.00001525878906 |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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24 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
diff
changeset
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25 "tool_errors": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
diff
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26 "tool_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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27 "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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28 "tool_version": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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29 "type": "data_collection_input", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
diff
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30 "uuid": "e60ca12e-15cc-4a01-a912-945af21a5e8e", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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31 "workflow_outputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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32 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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33 "label": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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34 "output_name": "output", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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35 "uuid": "f9af6731-280d-4606-b7c3-ff6e5bc0870e" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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36 } |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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37 ] |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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38 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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39 "1": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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40 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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41 "content_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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42 "id": 1, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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43 "input_connections": {}, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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44 "inputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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45 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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46 "description": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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47 "name": "viral nucleotide BLAST database (NCBI 19-10-2015)" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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48 } |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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49 ], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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50 "label": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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51 "name": "Input dataset", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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52 "outputs": [], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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53 "position": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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54 "left": 1024.9826965332031, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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55 "top": 963.9931259155273 |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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56 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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57 "tool_errors": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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58 "tool_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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59 "tool_state": "{\"name\": \"viral nucleotide BLAST database (NCBI 19-10-2015)\"}", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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60 "tool_version": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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61 "type": "data_input", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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62 "uuid": "462eb78f-9844-42d6-8087-19f2e1e801ca", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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63 "workflow_outputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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64 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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65 "label": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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66 "output_name": "output", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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67 "uuid": "89f3e51c-db84-4ff4-85f3-d3030a160685" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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68 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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69 ] |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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70 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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71 "2": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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72 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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73 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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74 "id": 2, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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75 "input_connections": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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76 "input": { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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77 "id": 0, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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78 "output_name": "output" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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79 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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80 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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81 "inputs": [], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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82 "label": null, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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83 "name": "Clip adapter", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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84 "outputs": [ |
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85 { |
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86 "name": "output", |
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87 "type": "fasta" |
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88 } |
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89 ], |
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90 "position": { |
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91 "left": 420.4861297607422, |
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92 "top": 292.5000228881836 |
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93 }, |
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94 "post_job_actions": {}, |
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95 "tool_errors": null, |
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96 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", |
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97 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"459d9188801e11e5ae6af01fafdfc061\\\"\", \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"CTGTAGGCACCATCAATCGT\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"Nmode\": \"\\\"reject\\\"\"}", |
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98 "tool_version": "1.3.6", |
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99 "type": "tool", |
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100 "uuid": "69611c78-3f25-4471-abf7-426ec35fd2db", |
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101 "workflow_outputs": [ |
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102 { |
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103 "label": null, |
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104 "output_name": "output", |
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105 "uuid": "5d28fac9-5b17-48b1-927d-5ae3fbcd2790" |
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106 } |
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107 ] |
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108 }, |
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109 "3": { |
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110 "annotation": "", |
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111 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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112 "id": 3, |
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113 "input_connections": { |
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114 "input": { |
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115 "id": 2, |
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116 "output_name": "output" |
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117 } |
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118 }, |
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119 "inputs": [], |
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120 "label": null, |
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121 "name": "Concatenate multiple datasets", |
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122 "outputs": [ |
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123 { |
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124 "name": "out_file1", |
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125 "type": "input" |
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126 } |
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127 ], |
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128 "position": { |
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129 "left": 452.50001525878906, |
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130 "top": 463.48961639404297 |
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131 }, |
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132 "post_job_actions": { |
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133 "ChangeDatatypeActionout_file1": { |
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134 "action_arguments": { |
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135 "newtype": "fasta" |
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136 }, |
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137 "action_type": "ChangeDatatypeAction", |
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138 "output_name": "out_file1" |
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139 }, |
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140 "HideDatasetActionout_file1": { |
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141 "action_arguments": {}, |
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142 "action_type": "HideDatasetAction", |
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143 "output_name": "out_file1" |
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144 } |
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145 }, |
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146 "tool_errors": null, |
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147 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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148 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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149 "tool_version": "0.2", |
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150 "type": "tool", |
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151 "uuid": "6be696ec-ca89-4e64-ad39-7d0e7fb4401a", |
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152 "workflow_outputs": [] |
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153 }, |
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154 "4": { |
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155 "annotation": "", |
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156 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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157 "id": 4, |
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158 "input_connections": { |
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159 "switch|input": { |
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160 "id": 3, |
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161 "output_name": "out_file1" |
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162 } |
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163 }, |
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164 "inputs": [], |
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165 "label": null, |
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166 "name": "fasta - tabular", |
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167 "outputs": [ |
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168 { |
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169 "name": "output", |
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170 "type": "fasta" |
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171 } |
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172 ], |
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173 "position": { |
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174 "left": 631.5972595214844, |
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175 "top": 605.5903244018555 |
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176 }, |
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177 "post_job_actions": { |
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178 "HideDatasetActionoutput": { |
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179 "action_arguments": {}, |
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180 "action_type": "HideDatasetAction", |
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181 "output_name": "output" |
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182 } |
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183 }, |
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184 "tool_errors": null, |
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185 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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186 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"fasta2tabular\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null}", |
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187 "tool_version": "1.1.0", |
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188 "type": "tool", |
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189 "uuid": "c700f2a8-231e-4792-a0cc-0e542d36b414", |
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190 "workflow_outputs": [] |
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191 }, |
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192 "5": { |
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193 "annotation": "", |
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194 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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195 "id": 5, |
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196 "input_connections": { |
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197 "switch|input": { |
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198 "id": 4, |
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199 "output_name": "output" |
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200 } |
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201 }, |
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202 "inputs": [], |
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203 "label": null, |
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204 "name": "fasta - tabular", |
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205 "outputs": [ |
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206 { |
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207 "name": "output", |
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208 "type": "fasta" |
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209 } |
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210 ], |
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211 "position": { |
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212 "left": 740.5729675292969, |
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213 "top": 786.5799179077148 |
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214 }, |
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215 "post_job_actions": { |
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216 "RenameDatasetActionoutput": { |
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217 "action_arguments": { |
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218 "newname": "Initial Clipped sequences" |
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219 }, |
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220 "action_type": "RenameDatasetAction", |
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221 "output_name": "output" |
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222 } |
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223 }, |
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224 "tool_errors": null, |
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225 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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226 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"tabular2fastaweight\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null}", |
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227 "tool_version": "1.1.0", |
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228 "type": "tool", |
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229 "uuid": "a51f4a8a-2bea-4fc8-97a5-97af74cd4144", |
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230 "workflow_outputs": [ |
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231 { |
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232 "label": null, |
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233 "output_name": "output", |
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234 "uuid": "28b7e800-5b85-4a42-9af3-7399c7306071" |
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235 } |
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236 ] |
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237 }, |
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238 "6": { |
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239 "annotation": "", |
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240 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", |
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241 "id": 6, |
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242 "input_connections": { |
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243 "input": { |
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244 "id": 5, |
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245 "output_name": "output" |
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246 } |
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247 }, |
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248 "inputs": [], |
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249 "label": null, |
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250 "name": "sRbowtie", |
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251 "outputs": [ |
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252 { |
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253 "name": "output", |
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254 "type": "tabular" |
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255 }, |
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256 { |
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257 "name": "aligned", |
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258 "type": "fasta" |
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259 }, |
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260 { |
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261 "name": "unaligned", |
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262 "type": "fasta" |
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263 } |
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264 ], |
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265 "position": { |
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266 "left": 830.4861755371094, |
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267 "top": 288.4896011352539 |
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268 }, |
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269 "post_job_actions": { |
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270 "HideDatasetActionaligned": { |
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271 "action_arguments": {}, |
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272 "action_type": "HideDatasetAction", |
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273 "output_name": "aligned" |
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274 }, |
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275 "HideDatasetActionoutput": { |
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276 "action_arguments": {}, |
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277 "action_type": "HideDatasetAction", |
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278 "output_name": "output" |
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279 }, |
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280 "RenameDatasetActionunaligned": { |
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281 "action_arguments": { |
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282 "newname": "Non D. melanogaster sequences" |
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283 }, |
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284 "action_type": "RenameDatasetAction", |
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285 "output_name": "unaligned" |
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286 } |
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287 }, |
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288 "tool_errors": null, |
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289 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", |
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290 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm6\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", |
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291 "tool_version": "1.1.2", |
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292 "type": "tool", |
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293 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", |
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294 "workflow_outputs": [ |
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295 { |
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296 "label": null, |
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297 "output_name": "unaligned", |
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298 "uuid": "ffe3bdf3-dea8-420a-8e04-498463c26691" |
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299 } |
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300 ] |
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301 }, |
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302 "7": { |
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303 "annotation": "", |
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304 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", |
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305 "id": 7, |
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306 "input_connections": { |
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307 "inputs_0|input": { |
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308 "id": 6, |
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309 "output_name": "unaligned" |
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310 } |
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311 }, |
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312 "inputs": [], |
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313 "label": null, |
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314 "name": "Oases_optimiser", |
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315 "outputs": [ |
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316 { |
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317 "name": "transcripts", |
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318 "type": "fasta" |
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319 } |
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320 ], |
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321 "position": { |
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322 "left": 1099.4965515136719, |
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323 "top": 509.49654388427734 |
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324 }, |
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325 "post_job_actions": { |
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326 "RenameDatasetActiontranscripts": { |
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327 "action_arguments": { |
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328 "newname": "Oases Contigs" |
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329 }, |
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330 "action_type": "RenameDatasetAction", |
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331 "output_name": "transcripts" |
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332 } |
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333 }, |
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334 "tool_errors": null, |
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335 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", |
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336 "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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337 "tool_version": "1.1.4", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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338 "type": "tool", |
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339 "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c", |
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340 "workflow_outputs": [ |
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341 { |
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342 "label": null, |
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343 "output_name": "transcripts", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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344 "uuid": "f5bf1efc-241a-4b48-8fda-5d83ca3eb956" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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345 } |
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346 ] |
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347 }, |
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348 "8": { |
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349 "annotation": "", |
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350 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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351 "id": 8, |
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352 "input_connections": { |
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353 "db_opts|histdb": { |
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354 "id": 1, |
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355 "output_name": "output" |
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356 }, |
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357 "query": { |
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358 "id": 7, |
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359 "output_name": "transcripts" |
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360 } |
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361 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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362 "inputs": [], |
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363 "label": null, |
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364 "name": "NCBI BLAST+ blastn", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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365 "outputs": [ |
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366 { |
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367 "name": "output1", |
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368 "type": "tabular" |
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369 } |
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370 ], |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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371 "position": { |
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372 "left": 1273.4895935058594, |
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373 "top": 800.4861679077148 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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374 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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375 "post_job_actions": {}, |
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376 "tool_errors": null, |
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377 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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378 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"adv_opts\": \"{\\\"adv_optional_id_files_opts\\\": {\\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\", \\\"__current_case__\\\": 0}, \\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"True\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"qcov_hsp_perc\\\": \\\"0.0\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"5\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"4dd2fde8802311e5bcddf01fafdfc061\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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379 "tool_version": "0.1.06", |
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380 "type": "tool", |
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381 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", |
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382 "workflow_outputs": [ |
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383 { |
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384 "label": null, |
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385 "output_name": "output1", |
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386 "uuid": "c53ba510-461f-4f0d-a075-d8c97924beab" |
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387 } |
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388 ] |
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389 }, |
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390 "9": { |
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391 "annotation": "", |
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392 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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393 "id": 9, |
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394 "input_connections": { |
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395 "blast": { |
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396 "id": 8, |
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397 "output_name": "output1" |
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398 }, |
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399 "sequences": { |
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400 "id": 7, |
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401 "output_name": "transcripts" |
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402 } |
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403 }, |
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404 "inputs": [], |
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405 "label": null, |
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406 "name": "Parse blast output and compile hits", |
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407 "outputs": [ |
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408 { |
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409 "name": "tabularOutput", |
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410 "type": "tabular" |
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411 }, |
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412 { |
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413 "name": "fastaOutput", |
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414 "type": "fasta" |
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415 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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416 { |
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417 "name": "al_sequences", |
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418 "type": "fasta" |
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419 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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420 { |
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421 "name": "un_sequences", |
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422 "type": "fasta" |
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423 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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424 ], |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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425 "position": { |
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426 "left": 1564.9827575683594, |
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427 "top": 513.489616394043 |
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428 }, |
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429 "post_job_actions": { |
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430 "HideDatasetActional_sequences": { |
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431 "action_arguments": {}, |
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432 "action_type": "HideDatasetAction", |
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433 "output_name": "al_sequences" |
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434 }, |
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435 "HideDatasetActionfastaOutput": { |
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436 "action_arguments": {}, |
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437 "action_type": "HideDatasetAction", |
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438 "output_name": "fastaOutput" |
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439 }, |
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440 "HideDatasetActionun_sequences": { |
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441 "action_arguments": {}, |
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442 "action_type": "HideDatasetAction", |
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443 "output_name": "un_sequences" |
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444 } |
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445 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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446 "tool_errors": null, |
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447 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", |
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448 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"use_filters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", |
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449 "tool_version": "2.4.3", |
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450 "type": "tool", |
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451 "uuid": "84989771-81db-4d86-bff6-cfda892b1959", |
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452 "workflow_outputs": [ |
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453 { |
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454 "label": null, |
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455 "output_name": "tabularOutput", |
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456 "uuid": "8b327d4e-27c9-4ec3-a4f7-be8f8ea27452" |
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457 } |
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458 ] |
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459 } |
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460 }, |
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461 "uuid": "50e69b15-e7a2-4e1d-8fc4-47f35223efd4" |
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462 } |