Mercurial > repos > drosofff > metavisitor_workflows
annotate Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.ga @ 1:3d8eb2c065c7 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit a143c96a3168e4135202479cb58e5a2bcdd153b4
author | drosofff |
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date | Mon, 11 Apr 2016 13:14:14 -0400 |
parents | 4a47903bb4df |
children | 48b020a0d2f7 |
rev | line source |
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0
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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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
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
parents:
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9 "content_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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10 "id": 0, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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11 "input_connections": {}, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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12 "inputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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": "Read fastq files" |
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": 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
parents:
diff
changeset
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25 "tool_errors": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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26 "tool_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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27 "tool_state": "{\"collection_type\": \"list\", \"name\": \"Read fastq files\"}", |
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": "None", |
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
drosofff
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38 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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39 "1": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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62 "uuid": "None", |
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" |
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 }, |
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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": "", |
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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", |
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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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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", |
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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_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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104 "tool_version": "1.3.6", |
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105 "type": "tool", |
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106 "uuid": "None", |
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107 "workflow_outputs": [] |
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108 }, |
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109 "3": { |
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110 "annotation": "", |
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111 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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112 "id": 3, |
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113 "input_connections": { |
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114 "input": { |
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115 "id": 1, |
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116 "output_name": "output" |
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117 } |
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118 }, |
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119 "inputs": [], |
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120 "label": null, |
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121 "name": "Concatenate multiple datasets", |
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122 "outputs": [ |
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123 { |
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124 "name": "out_file1", |
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125 "type": "input" |
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126 } |
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127 ], |
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128 "position": { |
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129 "left": 955.729248046875, |
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130 "top": 691.7187805175781 |
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131 }, |
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132 "post_job_actions": { |
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133 "ChangeDatatypeActionout_file1": { |
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134 "action_arguments": { |
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135 "newtype": "fasta" |
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136 }, |
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137 "action_type": "ChangeDatatypeAction", |
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138 "output_name": "out_file1" |
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139 }, |
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140 "HideDatasetActionout_file1": { |
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141 "action_arguments": {}, |
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142 "action_type": "HideDatasetAction", |
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143 "output_name": "out_file1" |
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144 } |
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145 }, |
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146 "tool_errors": null, |
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147 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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148 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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149 "tool_version": "0.2", |
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150 "type": "tool", |
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151 "uuid": "None", |
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152 "workflow_outputs": [] |
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153 }, |
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154 "4": { |
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155 "annotation": "", |
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156 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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157 "id": 4, |
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158 "input_connections": { |
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159 "input": { |
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160 "id": 2, |
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161 "output_name": "output" |
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162 } |
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163 }, |
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164 "inputs": [], |
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165 "label": null, |
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166 "name": "Concatenate multiple datasets", |
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167 "outputs": [ |
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168 { |
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169 "name": "out_file1", |
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170 "type": "input" |
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171 } |
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172 ], |
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173 "position": { |
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174 "left": 552.5173950195312, |
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175 "top": 226.54515075683594 |
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176 }, |
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177 "post_job_actions": { |
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178 "ChangeDatatypeActionout_file1": { |
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179 "action_arguments": { |
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180 "newtype": "fasta" |
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181 }, |
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182 "action_type": "ChangeDatatypeAction", |
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183 "output_name": "out_file1" |
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184 }, |
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185 "HideDatasetActionout_file1": { |
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186 "action_arguments": {}, |
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187 "action_type": "HideDatasetAction", |
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188 "output_name": "out_file1" |
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189 }, |
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190 "RenameDatasetActionout_file1": { |
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191 "action_arguments": { |
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192 "newname": "clipped Reads" |
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193 }, |
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194 "action_type": "RenameDatasetAction", |
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195 "output_name": "out_file1" |
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196 } |
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197 }, |
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198 "tool_errors": null, |
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199 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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200 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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201 "tool_version": "0.2", |
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202 "type": "tool", |
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203 "uuid": "None", |
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204 "workflow_outputs": [] |
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205 }, |
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206 "5": { |
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207 "annotation": "", |
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208 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", |
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209 "id": 5, |
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210 "input_connections": { |
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211 "input": { |
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212 "id": 4, |
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213 "output_name": "out_file1" |
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214 }, |
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215 "refGenomeSource|ownFile": { |
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216 "id": 1, |
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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": "sRbowtie", |
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223 "outputs": [ |
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224 { |
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225 "name": "output", |
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226 "type": "tabular" |
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227 }, |
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228 { |
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229 "name": "aligned", |
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230 "type": "fasta" |
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231 }, |
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232 { |
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233 "name": "unaligned", |
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234 "type": "fasta" |
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235 } |
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236 ], |
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237 "position": { |
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238 "left": 846.5451965332031, |
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239 "top": 264.53126525878906 |
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240 }, |
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241 "post_job_actions": { |
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242 "HideDatasetActionaligned": { |
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243 "action_arguments": {}, |
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244 "action_type": "HideDatasetAction", |
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245 "output_name": "aligned" |
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246 }, |
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247 "HideDatasetActionoutput": { |
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248 "action_arguments": {}, |
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249 "action_type": "HideDatasetAction", |
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250 "output_name": "output" |
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251 }, |
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252 "HideDatasetActionunaligned": { |
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253 "action_arguments": {}, |
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254 "action_type": "HideDatasetAction", |
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255 "output_name": "unaligned" |
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256 } |
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257 }, |
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258 "tool_errors": null, |
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259 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", |
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260 "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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261 "tool_version": "1.1.2", |
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262 "type": "tool", |
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263 "uuid": "None", |
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264 "workflow_outputs": [] |
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265 }, |
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266 "6": { |
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267 "annotation": "", |
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268 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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269 "id": 6, |
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270 "input_connections": { |
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271 "input": { |
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272 "id": 5, |
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273 "output_name": "output" |
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274 } |
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275 }, |
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276 "inputs": [], |
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277 "label": null, |
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278 "name": "Concatenate multiple datasets", |
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279 "outputs": [ |
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280 { |
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281 "name": "out_file1", |
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282 "type": "input" |
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283 } |
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284 ], |
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285 "position": { |
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286 "left": 1188.7500610351562, |
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287 "top": 518.7500305175781 |
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288 }, |
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289 "post_job_actions": { |
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290 "ChangeDatatypeActionout_file1": { |
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291 "action_arguments": { |
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292 "newtype": "tabular" |
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293 }, |
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294 "action_type": "ChangeDatatypeAction", |
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295 "output_name": "out_file1" |
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296 }, |
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297 "HideDatasetActionout_file1": { |
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298 "action_arguments": {}, |
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299 "action_type": "HideDatasetAction", |
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300 "output_name": "out_file1" |
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301 }, |
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302 "RenameDatasetActionout_file1": { |
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303 "action_arguments": { |
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304 "newname": "Read Re-mapping" |
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305 }, |
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306 "action_type": "RenameDatasetAction", |
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307 "output_name": "out_file1" |
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308 } |
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309 }, |
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310 "tool_errors": null, |
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311 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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312 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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313 "tool_version": "0.2", |
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314 "type": "tool", |
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315 "uuid": "None", |
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316 "workflow_outputs": [] |
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317 }, |
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318 "7": { |
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319 "annotation": "", |
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320 "content_id": "wc_gnu", |
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321 "id": 7, |
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322 "input_connections": { |
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323 "input1": { |
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324 "id": 5, |
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325 "output_name": "output" |
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326 } |
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327 }, |
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328 "inputs": [], |
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329 "label": null, |
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330 "name": "Line/Word/Character count", |
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331 "outputs": [ |
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332 { |
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333 "name": "out_file1", |
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334 "type": "tabular" |
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335 } |
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336 ], |
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337 "position": { |
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338 "left": 1352.5174560546875, |
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339 "top": 307.5173797607422 |
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340 }, |
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341 "post_job_actions": { |
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342 "RenameDatasetActionout_file1": { |
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343 "action_arguments": { |
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344 "newname": "nbre of remapped reads" |
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345 }, |
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346 "action_type": "RenameDatasetAction", |
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347 "output_name": "out_file1" |
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348 } |
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349 }, |
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350 "tool_errors": null, |
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351 "tool_id": "wc_gnu", |
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352 "tool_state": "{\"__page__\": 0, \"include_header\": \"\\\"True\\\"\", \"input1\": \"null\", \"options\": \"[\\\"lines\\\"]\", \"__rerun_remap_job_id__\": null}", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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353 "tool_version": "1.0.0", |
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354 "type": "tool", |
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355 "uuid": "None", |
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356 "workflow_outputs": [ |
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357 { |
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358 "label": null, |
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359 "output_name": "out_file1", |
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360 "uuid": "cdd91e78-45f2-4ec2-b426-93e20d238c4b" |
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361 } |
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362 ] |
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363 }, |
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364 "8": { |
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365 "annotation": "", |
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366 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.1.5", |
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367 "id": 8, |
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368 "input_connections": { |
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369 "refGenomeSource|ownFile": { |
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370 "id": 3, |
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371 "output_name": "out_file1" |
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372 }, |
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373 "refGenomeSource|series_0|input": { |
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374 "id": 6, |
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375 "output_name": "out_file1" |
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376 } |
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377 }, |
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378 "inputs": [], |
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379 "label": null, |
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380 "name": "Generate readmap and histograms from alignment files", |
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381 "outputs": [ |
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382 { |
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383 "name": "readmap_dataframe", |
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384 "type": "tabular" |
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385 }, |
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386 { |
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387 "name": "size_distribution_dataframe", |
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388 "type": "tabular" |
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389 }, |
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390 { |
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391 "name": "readmap_PDF", |
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392 "type": "pdf" |
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393 }, |
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394 { |
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395 "name": "size_PDF", |
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396 "type": "pdf" |
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397 }, |
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398 { |
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399 "name": "combi_PDF", |
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400 "type": "pdf" |
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401 } |
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402 ], |
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403 "position": { |
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404 "left": 1562.4827270507812, |
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405 "top": 554.982666015625 |
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406 }, |
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407 "post_job_actions": { |
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408 "HideDatasetActionreadmap_dataframe": { |
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409 "action_arguments": {}, |
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410 "action_type": "HideDatasetAction", |
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411 "output_name": "readmap_dataframe" |
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412 }, |
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413 "HideDatasetActionsize_distribution_dataframe": { |
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414 "action_arguments": {}, |
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415 "action_type": "HideDatasetAction", |
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416 "output_name": "size_distribution_dataframe" |
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417 } |
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418 }, |
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419 "tool_errors": null, |
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420 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.1.5", |
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421 "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\"}", |
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422 "tool_version": "1.1.5", |
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423 "type": "tool", |
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424 "uuid": "ebaf90ab-b8ea-428f-876c-8f9fabd1fbf9", |
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425 "workflow_outputs": [ |
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426 { |
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427 "label": null, |
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428 "output_name": "size_PDF", |
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429 "uuid": "51ecda12-a282-4c56-8bd9-66f22742b301" |
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430 }, |
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431 { |
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432 "label": null, |
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433 "output_name": "combi_PDF", |
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434 "uuid": "f9345f64-7f9b-440a-b12a-6d123a46800f" |
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435 }, |
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436 { |
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437 "label": null, |
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438 "output_name": "readmap_PDF", |
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439 "uuid": "eb151acd-9d6d-4c30-8bc5-9124a9a3d815" |
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440 } |
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441 ] |
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442 } |
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443 }, |
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444 "uuid": "35f7ef15-bb91-4eca-b8a7-345dc5cb3136" |
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445 } |