Mercurial > repos > drosofff > metavisitor_workflows
annotate Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga @ 5:26e2d79e4c17 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit aa9e87614903f27fa5359ce8c437eb6961d68c62
author | drosofff |
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date | Mon, 17 Apr 2017 07:57:13 -0400 |
parents | 46614c7dd247 |
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rev | line source |
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4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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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
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8 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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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
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10 "id": 0, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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
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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
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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
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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
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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
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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
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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
drosofff
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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
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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
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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
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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
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54 "left": 1024.9826965332031, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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55 "top": 963.9931259155273 |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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56 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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
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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
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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, |
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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, |
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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": [], |
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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_shed_repository": { |
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98 "changeset_revision": "a18edcf9c7ed", |
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99 "name": "yac_clipper", |
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100 "owner": "drosofff", |
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101 "tool_shed": "toolshed.g2.bx.psu.edu" |
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102 }, |
0
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103 "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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104 "tool_version": "1.3.6", |
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105 "type": "tool", |
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106 "uuid": "69611c78-3f25-4471-abf7-426ec35fd2db", |
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107 "workflow_outputs": [ |
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108 { |
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109 "label": null, |
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110 "output_name": "output", |
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111 "uuid": "5d28fac9-5b17-48b1-927d-5ae3fbcd2790" |
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112 } |
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113 ] |
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114 }, |
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115 "3": { |
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116 "annotation": "", |
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117 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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118 "id": 3, |
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119 "input_connections": { |
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120 "input": { |
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121 "id": 2, |
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122 "output_name": "output" |
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123 } |
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124 }, |
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125 "inputs": [], |
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126 "label": null, |
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127 "name": "Concatenate multiple datasets", |
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128 "outputs": [ |
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129 { |
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130 "name": "out_file1", |
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131 "type": "input" |
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132 } |
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133 ], |
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134 "position": { |
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135 "left": 452.50001525878906, |
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136 "top": 463.48961639404297 |
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137 }, |
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138 "post_job_actions": { |
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139 "ChangeDatatypeActionout_file1": { |
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140 "action_arguments": { |
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141 "newtype": "fasta" |
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142 }, |
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143 "action_type": "ChangeDatatypeAction", |
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144 "output_name": "out_file1" |
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145 }, |
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146 "HideDatasetActionout_file1": { |
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147 "action_arguments": {}, |
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148 "action_type": "HideDatasetAction", |
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149 "output_name": "out_file1" |
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150 } |
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151 }, |
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152 "tool_errors": null, |
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153 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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154 "tool_shed_repository": { |
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155 "changeset_revision": "201c568972c3", |
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156 "name": "concatenate_multiple_datasets", |
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157 "owner": "mvdbeek", |
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158 "tool_shed": "toolshed.g2.bx.psu.edu" |
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159 }, |
0
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160 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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161 "tool_version": "0.2", |
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162 "type": "tool", |
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163 "uuid": "6be696ec-ca89-4e64-ad39-7d0e7fb4401a", |
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164 "workflow_outputs": [] |
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165 }, |
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166 "4": { |
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167 "annotation": "", |
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168 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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169 "id": 4, |
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170 "input_connections": { |
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171 "switch|input": { |
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172 "id": 3, |
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173 "output_name": "out_file1" |
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174 } |
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175 }, |
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176 "inputs": [], |
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177 "label": null, |
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178 "name": "fasta - tabular", |
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179 "outputs": [ |
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180 { |
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181 "name": "output", |
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182 "type": "fasta" |
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183 } |
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184 ], |
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185 "position": { |
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186 "left": 631.5972595214844, |
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187 "top": 605.5903244018555 |
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188 }, |
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189 "post_job_actions": { |
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190 "HideDatasetActionoutput": { |
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191 "action_arguments": {}, |
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192 "action_type": "HideDatasetAction", |
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193 "output_name": "output" |
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194 } |
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195 }, |
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196 "tool_errors": null, |
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197 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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198 "tool_shed_repository": { |
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199 "changeset_revision": "36388b666bfc", |
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200 "name": "msp_fasta_tabular_converter", |
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201 "owner": "drosofff", |
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202 "tool_shed": "toolshed.g2.bx.psu.edu" |
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203 }, |
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204 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", |
0
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205 "tool_version": "1.1.0", |
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206 "type": "tool", |
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207 "uuid": "c700f2a8-231e-4792-a0cc-0e542d36b414", |
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208 "workflow_outputs": [] |
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209 }, |
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210 "5": { |
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211 "annotation": "", |
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212 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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213 "id": 5, |
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214 "input_connections": { |
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215 "switch|input": { |
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216 "id": 4, |
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217 "output_name": "output" |
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218 } |
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219 }, |
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220 "inputs": [], |
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221 "label": null, |
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222 "name": "fasta - tabular", |
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223 "outputs": [ |
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224 { |
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225 "name": "output", |
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226 "type": "fasta" |
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227 } |
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228 ], |
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229 "position": { |
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230 "left": 740.5729675292969, |
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231 "top": 786.5799179077148 |
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232 }, |
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233 "post_job_actions": { |
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234 "RenameDatasetActionoutput": { |
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235 "action_arguments": { |
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236 "newname": "Initial Clipped sequences" |
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237 }, |
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238 "action_type": "RenameDatasetAction", |
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239 "output_name": "output" |
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240 } |
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241 }, |
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242 "tool_errors": null, |
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243 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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244 "tool_shed_repository": { |
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245 "changeset_revision": "36388b666bfc", |
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246 "name": "msp_fasta_tabular_converter", |
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247 "owner": "drosofff", |
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248 "tool_shed": "toolshed.g2.bx.psu.edu" |
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249 }, |
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250 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}", |
0
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251 "tool_version": "1.1.0", |
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252 "type": "tool", |
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253 "uuid": "a51f4a8a-2bea-4fc8-97a5-97af74cd4144", |
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254 "workflow_outputs": [ |
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255 { |
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256 "label": null, |
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257 "output_name": "output", |
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258 "uuid": "28b7e800-5b85-4a42-9af3-7399c7306071" |
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259 } |
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260 ] |
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261 }, |
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262 "6": { |
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263 "annotation": "", |
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264 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", |
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265 "id": 6, |
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266 "input_connections": { |
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267 "input": { |
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268 "id": 5, |
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269 "output_name": "output" |
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270 } |
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271 }, |
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272 "inputs": [], |
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273 "label": null, |
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274 "name": "sRbowtie", |
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275 "outputs": [ |
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276 { |
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277 "name": "output", |
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278 "type": "tabular" |
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279 }, |
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280 { |
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281 "name": "aligned", |
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282 "type": "fasta" |
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283 }, |
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284 { |
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285 "name": "unaligned", |
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286 "type": "fasta" |
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287 } |
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288 ], |
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289 "position": { |
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290 "left": 830.4861755371094, |
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291 "top": 288.4896011352539 |
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292 }, |
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293 "post_job_actions": { |
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294 "HideDatasetActionaligned": { |
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295 "action_arguments": {}, |
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296 "action_type": "HideDatasetAction", |
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297 "output_name": "aligned" |
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298 }, |
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299 "HideDatasetActionoutput": { |
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300 "action_arguments": {}, |
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301 "action_type": "HideDatasetAction", |
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302 "output_name": "output" |
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303 }, |
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304 "RenameDatasetActionunaligned": { |
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305 "action_arguments": { |
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306 "newname": "Non D. melanogaster sequences" |
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307 }, |
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308 "action_type": "RenameDatasetAction", |
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309 "output_name": "unaligned" |
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310 } |
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311 }, |
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312 "tool_errors": null, |
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313 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", |
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314 "tool_shed_repository": { |
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315 "changeset_revision": "615d2550977f", |
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316 "name": "msp_sr_bowtie", |
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317 "owner": "drosofff", |
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318 "tool_shed": "toolshed.g2.bx.psu.edu" |
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319 }, |
0
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320 "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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321 "tool_version": "1.1.2.1", |
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322 "type": "tool", |
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323 "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", |
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324 "workflow_outputs": [ |
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325 { |
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326 "label": null, |
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327 "output_name": "unaligned", |
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328 "uuid": "ffe3bdf3-dea8-420a-8e04-498463c26691" |
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329 } |
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330 ] |
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331 }, |
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332 "7": { |
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333 "annotation": "", |
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334 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.2.1", |
0
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335 "id": 7, |
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336 "input_connections": { |
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337 "inputs_0|input": { |
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338 "id": 6, |
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339 "output_name": "unaligned" |
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340 } |
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341 }, |
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342 "inputs": [], |
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343 "label": null, |
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344 "name": "Oases_optimiser", |
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345 "outputs": [ |
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346 { |
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347 "name": "transcripts", |
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348 "type": "fasta" |
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349 } |
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350 ], |
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351 "position": { |
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352 "left": 1099.4965515136719, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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353 "top": 509.49654388427734 |
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354 }, |
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355 "post_job_actions": { |
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356 "RenameDatasetActiontranscripts": { |
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357 "action_arguments": { |
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358 "newname": "Oases Contigs" |
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359 }, |
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360 "action_type": "RenameDatasetAction", |
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361 "output_name": "transcripts" |
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362 } |
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363 }, |
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364 "tool_errors": null, |
4
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365 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.2.1", |
2
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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366 "tool_shed_repository": { |
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367 "changeset_revision": "68ed36eed6c5", |
2
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368 "name": "msp_oases", |
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369 "owner": "drosofff", |
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370 "tool_shed": "toolshed.g2.bx.psu.edu" |
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371 }, |
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372 "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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373 "tool_version": "1.2.1", |
0
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374 "type": "tool", |
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375 "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c", |
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376 "workflow_outputs": [ |
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377 { |
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378 "label": null, |
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379 "output_name": "transcripts", |
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380 "uuid": "f5bf1efc-241a-4b48-8fda-5d83ca3eb956" |
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381 } |
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382 ] |
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383 }, |
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384 "8": { |
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385 "annotation": "", |
3
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386 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08", |
0
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387 "id": 8, |
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388 "input_connections": { |
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389 "db_opts|histdb": { |
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390 "id": 1, |
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391 "output_name": "output" |
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392 }, |
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393 "query": { |
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394 "id": 7, |
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395 "output_name": "transcripts" |
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396 } |
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397 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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398 "inputs": [], |
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399 "label": null, |
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400 "name": "NCBI BLAST+ blastn", |
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401 "outputs": [ |
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402 { |
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403 "name": "output1", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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404 "type": "tabular" |
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405 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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406 ], |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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407 "position": { |
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408 "left": 1273.4895935058594, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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409 "top": 800.4861679077148 |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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410 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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411 "post_job_actions": {}, |
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412 "tool_errors": null, |
3
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413 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08", |
2
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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414 "tool_shed_repository": { |
3
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415 "changeset_revision": "3034ce97dd33", |
2
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416 "name": "ncbi_blast_plus", |
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417 "owner": "devteam", |
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418 "tool_shed": "toolshed.g2.bx.psu.edu" |
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419 }, |
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420 "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\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"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\\\"\"}", |
3
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421 "tool_version": "0.1.08", |
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422 "type": "tool", |
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423 "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", |
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424 "workflow_outputs": [ |
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425 { |
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426 "label": null, |
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427 "output_name": "output1", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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428 "uuid": "c53ba510-461f-4f0d-a075-d8c97924beab" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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429 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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430 ] |
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431 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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432 "9": { |
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433 "annotation": "", |
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434 "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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435 "id": 9, |
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436 "input_connections": { |
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437 "blast": { |
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438 "id": 8, |
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439 "output_name": "output1" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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440 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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441 "sequences": { |
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442 "id": 7, |
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443 "output_name": "transcripts" |
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444 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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 "inputs": [], |
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447 "label": null, |
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448 "name": "Parse blast output and compile hits", |
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449 "outputs": [ |
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450 { |
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451 "name": "tabularOutput", |
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452 "type": "tabular" |
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453 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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454 { |
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455 "name": "fastaOutput", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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456 "type": "fasta" |
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457 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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458 { |
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459 "name": "al_sequences", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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460 "type": "fasta" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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461 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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462 { |
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463 "name": "un_sequences", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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464 "type": "fasta" |
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465 } |
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466 ], |
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467 "position": { |
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468 "left": 1564.9827575683594, |
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469 "top": 513.489616394043 |
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470 }, |
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471 "post_job_actions": { |
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472 "HideDatasetActional_sequences": { |
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473 "action_arguments": {}, |
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474 "action_type": "HideDatasetAction", |
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475 "output_name": "al_sequences" |
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476 }, |
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477 "HideDatasetActionfastaOutput": { |
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478 "action_arguments": {}, |
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479 "action_type": "HideDatasetAction", |
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480 "output_name": "fastaOutput" |
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481 }, |
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482 "HideDatasetActionun_sequences": { |
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483 "action_arguments": {}, |
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484 "action_type": "HideDatasetAction", |
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485 "output_name": "un_sequences" |
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486 } |
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487 }, |
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488 "tool_errors": null, |
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489 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", |
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490 "tool_shed_repository": { |
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491 "changeset_revision": "1991c830504a", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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492 "name": "msp_blastparser_and_hits", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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493 "owner": "drosofff", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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494 "tool_shed": "toolshed.g2.bx.psu.edu" |
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495 }, |
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496 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", |
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497 "tool_version": "2.4.3", |
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498 "type": "tool", |
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499 "uuid": "84989771-81db-4d86-bff6-cfda892b1959", |
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500 "workflow_outputs": [ |
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501 { |
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502 "label": null, |
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503 "output_name": "tabularOutput", |
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504 "uuid": "8b327d4e-27c9-4ec3-a4f7-be8f8ea27452" |
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505 } |
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506 ] |
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507 } |
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508 }, |
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509 "uuid": "50e69b15-e7a2-4e1d-8fc4-47f35223efd4" |
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510 } |