Mercurial > repos > drosofff > metavisitor_workflows
annotate Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.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 | ba15c770fd40 |
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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 remapping in Use Cases 1-1,2,3", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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
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12 "inputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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13 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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14 "description": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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15 "name": "Read fastq files" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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": 199.53128051757812, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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23 "top": 207.51737213134766 |
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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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\": \"Read fastq files\"}", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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", |
2
48b020a0d2f7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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30 "uuid": "ca202c6a-46b7-4f3a-a2ab-dbc781f331b7", |
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4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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
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35 "uuid": "19eaa717-5b9a-4b27-a1c4-a895fc673970" |
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
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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
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40 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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": "Nora Virus Genomes" |
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
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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 collection", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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": 661.5451812744141, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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55 "top": 554.5312805175781 |
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
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58 "tool_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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59 "tool_state": "{\"collection_type\": \"list\", \"name\": \"Nora Virus Genomes\"}", |
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_collection_input", |
2
48b020a0d2f7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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62 "uuid": "e8e196c7-c854-4bd9-ace2-345a0d797090", |
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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 { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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65 "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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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": "46b1caea-3a7c-4663-b2e1-6536a346567a" |
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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 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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71 "2": { |
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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": { |
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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 }, |
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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": 387.51739501953125, |
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92 "top": 324.53126525878906 |
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93 }, |
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94 "post_job_actions": { |
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95 "HideDatasetActionoutput": { |
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96 "action_arguments": {}, |
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97 "action_type": "HideDatasetAction", |
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98 "output_name": "output" |
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99 } |
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100 }, |
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101 "tool_errors": null, |
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102 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", |
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103 "tool_shed_repository": { |
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104 "changeset_revision": "91cce7c1436d", |
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105 "name": "yac_clipper", |
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106 "owner": "drosofff", |
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107 "tool_shed": "toolshed.g2.bx.psu.edu" |
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108 }, |
0
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109 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"CTGTAGGCACCATCAATCGT\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"Nmode\": \"\\\"reject\\\"\"}", |
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110 "tool_version": "1.3.6", |
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111 "type": "tool", |
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112 "uuid": "afa187ce-544c-4287-8699-a9efe8ce45ab", |
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113 "workflow_outputs": [] |
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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": 1, |
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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": 955.729248046875, |
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136 "top": 691.7187805175781 |
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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": "73d5e37a-8a61-4bab-8bf5-12b12fc45988", |
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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/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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169 "id": 4, |
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170 "input_connections": { |
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171 "input": { |
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172 "id": 2, |
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173 "output_name": "output" |
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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": "Concatenate multiple datasets", |
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179 "outputs": [ |
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180 { |
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181 "name": "out_file1", |
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182 "type": "input" |
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183 } |
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184 ], |
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185 "position": { |
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186 "left": 552.5173950195312, |
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187 "top": 226.54515075683594 |
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188 }, |
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189 "post_job_actions": { |
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190 "ChangeDatatypeActionout_file1": { |
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191 "action_arguments": { |
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192 "newtype": "fasta" |
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193 }, |
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194 "action_type": "ChangeDatatypeAction", |
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195 "output_name": "out_file1" |
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196 }, |
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197 "HideDatasetActionout_file1": { |
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198 "action_arguments": {}, |
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199 "action_type": "HideDatasetAction", |
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200 "output_name": "out_file1" |
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201 }, |
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202 "RenameDatasetActionout_file1": { |
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203 "action_arguments": { |
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204 "newname": "clipped Reads" |
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205 }, |
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206 "action_type": "RenameDatasetAction", |
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207 "output_name": "out_file1" |
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208 } |
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209 }, |
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210 "tool_errors": null, |
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211 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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212 "tool_shed_repository": { |
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213 "changeset_revision": "201c568972c3", |
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214 "name": "concatenate_multiple_datasets", |
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215 "owner": "mvdbeek", |
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216 "tool_shed": "toolshed.g2.bx.psu.edu" |
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217 }, |
0
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218 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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219 "tool_version": "0.2", |
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220 "type": "tool", |
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221 "uuid": "f15e8add-3a18-4607-b5e2-51448dcdeb77", |
0
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222 "workflow_outputs": [] |
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223 }, |
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224 "5": { |
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225 "annotation": "", |
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226 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", |
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227 "id": 5, |
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228 "input_connections": { |
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229 "input": { |
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230 "id": 4, |
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231 "output_name": "out_file1" |
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232 }, |
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233 "refGenomeSource|ownFile": { |
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234 "id": 1, |
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235 "output_name": "output" |
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236 } |
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237 }, |
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238 "inputs": [], |
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239 "label": null, |
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240 "name": "sRbowtie", |
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241 "outputs": [ |
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242 { |
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243 "name": "output", |
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244 "type": "tabular" |
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245 }, |
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246 { |
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247 "name": "aligned", |
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248 "type": "fasta" |
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249 }, |
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250 { |
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251 "name": "unaligned", |
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252 "type": "fasta" |
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253 } |
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254 ], |
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255 "position": { |
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256 "left": 846.5451965332031, |
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257 "top": 264.53126525878906 |
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258 }, |
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259 "post_job_actions": { |
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260 "HideDatasetActionaligned": { |
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261 "action_arguments": {}, |
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262 "action_type": "HideDatasetAction", |
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263 "output_name": "aligned" |
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264 }, |
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265 "HideDatasetActionoutput": { |
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266 "action_arguments": {}, |
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267 "action_type": "HideDatasetAction", |
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268 "output_name": "output" |
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269 }, |
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270 "HideDatasetActionunaligned": { |
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271 "action_arguments": {}, |
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272 "action_type": "HideDatasetAction", |
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273 "output_name": "unaligned" |
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274 } |
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275 }, |
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276 "tool_errors": null, |
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277 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", |
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278 "tool_shed_repository": { |
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279 "changeset_revision": "615d2550977f", |
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280 "name": "msp_sr_bowtie", |
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281 "owner": "drosofff", |
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282 "tool_shed": "toolshed.g2.bx.psu.edu" |
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283 }, |
0
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284 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"No\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"multiple\\\"\"}", |
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285 "tool_version": "1.1.2.1", |
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286 "type": "tool", |
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287 "uuid": "a9880e4e-f47f-4a21-ad20-5aefb83b57ad", |
0
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288 "workflow_outputs": [] |
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289 }, |
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290 "6": { |
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291 "annotation": "", |
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292 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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293 "id": 6, |
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294 "input_connections": { |
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295 "input": { |
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296 "id": 5, |
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297 "output_name": "output" |
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298 } |
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299 }, |
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300 "inputs": [], |
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301 "label": null, |
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302 "name": "Concatenate multiple datasets", |
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303 "outputs": [ |
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304 { |
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305 "name": "out_file1", |
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306 "type": "input" |
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307 } |
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308 ], |
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309 "position": { |
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310 "left": 1188.7500610351562, |
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311 "top": 518.7500305175781 |
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312 }, |
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313 "post_job_actions": { |
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314 "ChangeDatatypeActionout_file1": { |
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315 "action_arguments": { |
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316 "newtype": "tabular" |
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317 }, |
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318 "action_type": "ChangeDatatypeAction", |
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319 "output_name": "out_file1" |
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320 }, |
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321 "HideDatasetActionout_file1": { |
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322 "action_arguments": {}, |
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323 "action_type": "HideDatasetAction", |
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324 "output_name": "out_file1" |
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325 }, |
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326 "RenameDatasetActionout_file1": { |
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327 "action_arguments": { |
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328 "newname": "Read Re-mapping" |
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329 }, |
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330 "action_type": "RenameDatasetAction", |
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331 "output_name": "out_file1" |
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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/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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336 "tool_shed_repository": { |
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337 "changeset_revision": "201c568972c3", |
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338 "name": "concatenate_multiple_datasets", |
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339 "owner": "mvdbeek", |
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340 "tool_shed": "toolshed.g2.bx.psu.edu" |
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341 }, |
0
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342 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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343 "tool_version": "0.2", |
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344 "type": "tool", |
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345 "uuid": "afeb8258-2959-4b81-bec4-aaa342dd930d", |
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346 "workflow_outputs": [] |
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347 }, |
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348 "7": { |
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349 "annotation": "", |
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350 "content_id": "wc_gnu", |
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351 "id": 7, |
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352 "input_connections": { |
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353 "input1": { |
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354 "id": 5, |
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355 "output_name": "output" |
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356 } |
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357 }, |
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358 "inputs": [], |
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359 "label": null, |
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360 "name": "Line/Word/Character count", |
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361 "outputs": [ |
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362 { |
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363 "name": "out_file1", |
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364 "type": "tabular" |
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365 } |
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366 ], |
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367 "position": { |
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368 "left": 1352.5174560546875, |
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369 "top": 307.5173797607422 |
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370 }, |
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371 "post_job_actions": { |
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372 "RenameDatasetActionout_file1": { |
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373 "action_arguments": { |
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374 "newname": "nbre of remapped reads" |
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375 }, |
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376 "action_type": "RenameDatasetAction", |
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377 "output_name": "out_file1" |
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378 } |
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379 }, |
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380 "tool_errors": null, |
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381 "tool_id": "wc_gnu", |
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382 "tool_state": "{\"__page__\": 0, \"include_header\": \"\\\"true\\\"\", \"input1\": \"null\", \"options\": \"[\\\"lines\\\"]\", \"__rerun_remap_job_id__\": null}", |
0
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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383 "tool_version": "1.0.0", |
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384 "type": "tool", |
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385 "uuid": "98092466-d430-48bd-b285-770aeee41153", |
0
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386 "workflow_outputs": [ |
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387 { |
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388 "label": null, |
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389 "output_name": "out_file1", |
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390 "uuid": "cdd91e78-45f2-4ec2-b426-93e20d238c4b" |
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391 } |
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392 ] |
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393 }, |
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394 "8": { |
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395 "annotation": "", |
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396 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.2.0", |
0
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397 "id": 8, |
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398 "input_connections": { |
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399 "refGenomeSource|ownFile": { |
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400 "id": 3, |
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401 "output_name": "out_file1" |
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402 }, |
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403 "refGenomeSource|series_0|input": { |
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404 "id": 6, |
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405 "output_name": "out_file1" |
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406 } |
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407 }, |
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408 "inputs": [], |
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409 "label": null, |
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410 "name": "Generate readmap and histograms from alignment files", |
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411 "outputs": [ |
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412 { |
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413 "name": "readmap_dataframe", |
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414 "type": "tabular" |
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415 }, |
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416 { |
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417 "name": "size_distribution_dataframe", |
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418 "type": "tabular" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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421 "name": "readmap_PDF", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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422 "type": "pdf" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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 "name": "size_PDF", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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426 "type": "pdf" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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427 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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428 { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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429 "name": "combi_PDF", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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430 "type": "pdf" |
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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 ], |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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433 "position": { |
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434 "left": 1562.4827270507812, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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435 "top": 554.982666015625 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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436 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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437 "post_job_actions": { |
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438 "HideDatasetActionreadmap_dataframe": { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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439 "action_arguments": {}, |
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440 "action_type": "HideDatasetAction", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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441 "output_name": "readmap_dataframe" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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442 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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443 "HideDatasetActionsize_distribution_dataframe": { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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444 "action_arguments": {}, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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445 "action_type": "HideDatasetAction", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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446 "output_name": "size_distribution_dataframe" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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447 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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448 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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449 "tool_errors": null, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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450 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.2.0", |
2
48b020a0d2f7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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451 "tool_shed_repository": { |
3
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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452 "changeset_revision": "92898cc3ea19", |
2
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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453 "name": "msp_sr_readmap_and_size_histograms", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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454 "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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455 "tool_shed": "toolshed.g2.bx.psu.edu" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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456 }, |
0
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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457 "tool_state": "{\"minquery\": \"\\\"18\\\"\", \"__page__\": 0, \"rows_per_page\": \"\\\"8\\\"\", \"yrange\": \"\\\"0\\\"\", \"title\": \"\\\"Readmaps and size distributions\\\"\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"series\\\": [{\\\"__index__\\\": 0, \\\"norm\\\": \\\"1.0\\\", \\\"input\\\": null}], \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"maxquery\": \"\\\"30\\\"\", \"xlabel\": \"\\\"Coordinates/read size\\\"\", \"ylabel\": \"\\\"Number of reads\\\"\", \"gff\": \"null\"}", |
3
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458 "tool_version": "1.2.0", |
0
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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459 "type": "tool", |
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460 "uuid": "ebaf90ab-b8ea-428f-876c-8f9fabd1fbf9", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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461 "workflow_outputs": [ |
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462 { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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463 "label": null, |
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464 "output_name": "size_PDF", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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465 "uuid": "51ecda12-a282-4c56-8bd9-66f22742b301" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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466 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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467 { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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468 "label": null, |
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469 "output_name": "combi_PDF", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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470 "uuid": "f9345f64-7f9b-440a-b12a-6d123a46800f" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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471 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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472 { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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473 "label": null, |
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474 "output_name": "readmap_PDF", |
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475 "uuid": "eb151acd-9d6d-4c30-8bc5-9124a9a3d815" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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476 } |
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477 ] |
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478 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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479 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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480 "uuid": "35f7ef15-bb91-4eca-b8a7-345dc5cb3136" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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481 } |