Mercurial > repos > drosofff > metavisitor_workflows
annotate Galaxy-Workflow-Metavisitor__Spades_test_in_Use_Case_2-2.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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ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
parents:
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1 { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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2 "a_galaxy_workflow": "true", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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3 "annotation": "", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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4 "format-version": "0.1", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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5 "name": "Metavisitor: Spades test in Use Case 2-2", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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6 "steps": { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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7 "0": { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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8 "annotation": "", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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diff
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9 "content_id": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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diff
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10 "id": 0, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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11 "input_connections": {}, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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12 "inputs": [ |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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13 { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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14 "description": "", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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15 "name": "Input Dataset Collection" |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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16 } |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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17 ], |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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18 "label": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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19 "name": "Input dataset collection", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
parents:
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20 "outputs": [], |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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21 "position": { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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22 "left": 199.90625, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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23 "top": 183.59375 |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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24 }, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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25 "tool_errors": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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26 "tool_id": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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27 "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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28 "tool_version": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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29 "type": "data_collection_input", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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30 "uuid": "3b7db228-7d72-4b8a-9296-5e51ceda8cdd", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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31 "workflow_outputs": [ |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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32 { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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33 "label": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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34 "output_name": "output", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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35 "uuid": "dd803215-4fa9-4444-83df-06e42912b545" |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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36 } |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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37 ] |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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38 }, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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39 "1": { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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40 "annotation": "", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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41 "content_id": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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42 "id": 1, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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43 "input_connections": {}, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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44 "inputs": [ |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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45 { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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46 "description": "", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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47 "name": "Protein Blast database" |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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48 } |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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49 ], |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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50 "label": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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51 "name": "Input dataset", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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52 "outputs": [], |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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53 "position": { |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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54 "left": 1355.984375, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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55 "top": 590.5625 |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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56 }, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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57 "tool_errors": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
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58 "tool_id": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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59 "tool_state": "{\"name\": \"Protein Blast database\"}", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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60 "tool_version": null, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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61 "type": "data_input", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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62 "uuid": "9f28fc2b-f552-4021-b6fc-ba95f6f3e8dd", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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63 "workflow_outputs": [ |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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64 { |
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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 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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66 "output_name": "output", |
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67 "uuid": "8d19a7b0-6b52-46ee-be47-cce18eca9453" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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68 } |
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69 ] |
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70 }, |
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71 "2": { |
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72 "annotation": "", |
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73 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", |
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74 "id": 2, |
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75 "input_connections": { |
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76 "library|input_1": { |
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77 "id": 0, |
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78 "output_name": "output" |
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79 } |
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80 }, |
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81 "inputs": [ |
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82 { |
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83 "description": "runtime parameter for tool Bowtie2", |
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84 "name": "library" |
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85 } |
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86 ], |
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87 "label": null, |
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88 "name": "Bowtie2", |
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89 "outputs": [ |
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90 { |
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91 "name": "output_unaligned_reads_l", |
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92 "type": "fastqsanger" |
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93 }, |
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94 { |
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95 "name": "output_aligned_reads_l", |
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96 "type": "fastqsanger" |
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97 }, |
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98 { |
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99 "name": "output_aligned_reads_r", |
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100 "type": "fastqsanger" |
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101 }, |
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102 { |
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103 "name": "output_unaligned_reads_r", |
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104 "type": "fastqsanger" |
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105 }, |
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106 { |
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107 "name": "output", |
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108 "type": "bam" |
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109 }, |
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110 { |
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111 "name": "output_sam", |
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112 "type": "sam" |
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113 }, |
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114 { |
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115 "name": "mapping_stats", |
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116 "type": "txt" |
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117 } |
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118 ], |
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119 "position": { |
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120 "left": 462.484375, |
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121 "top": 214.625 |
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122 }, |
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123 "post_job_actions": { |
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124 "DeleteIntermediatesActionoutput_unaligned_reads_l": { |
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125 "action_arguments": {}, |
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126 "action_type": "DeleteIntermediatesAction", |
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127 "output_name": "output_unaligned_reads_l" |
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128 }, |
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129 "HideDatasetActionmapping_stats": { |
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130 "action_arguments": {}, |
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131 "action_type": "HideDatasetAction", |
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132 "output_name": "mapping_stats" |
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133 }, |
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134 "HideDatasetActionoutput": { |
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135 "action_arguments": {}, |
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136 "action_type": "HideDatasetAction", |
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137 "output_name": "output" |
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138 }, |
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139 "HideDatasetActionoutput_aligned_reads_l": { |
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140 "action_arguments": {}, |
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141 "action_type": "HideDatasetAction", |
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142 "output_name": "output_aligned_reads_l" |
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143 }, |
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144 "HideDatasetActionoutput_aligned_reads_r": { |
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145 "action_arguments": {}, |
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146 "action_type": "HideDatasetAction", |
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147 "output_name": "output_aligned_reads_r" |
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148 }, |
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149 "HideDatasetActionoutput_sam": { |
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150 "action_arguments": {}, |
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151 "action_type": "HideDatasetAction", |
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152 "output_name": "output_sam" |
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153 }, |
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154 "HideDatasetActionoutput_unaligned_reads_l": { |
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155 "action_arguments": {}, |
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156 "action_type": "HideDatasetAction", |
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157 "output_name": "output_unaligned_reads_l" |
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158 }, |
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159 "HideDatasetActionoutput_unaligned_reads_r": { |
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160 "action_arguments": {}, |
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161 "action_type": "HideDatasetAction", |
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162 "output_name": "output_unaligned_reads_r" |
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163 } |
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164 }, |
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165 "tool_errors": null, |
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166 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", |
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167 "tool_shed_repository": { |
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168 "changeset_revision": "a9d4f71dbfb0", |
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169 "name": "bowtie2", |
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170 "owner": "devteam", |
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171 "tool_shed": "toolshed.g2.bx.psu.edu" |
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172 }, |
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173 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"false\\\", \\\"unaligned_file\\\": \\\"true\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"AgamP4\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"true\\\", \\\"input_options\\\": {\\\"int_quals\\\": \\\"false\\\", \\\"solexa_quals\\\": \\\"false\\\", \\\"skip\\\": \\\"0\\\", \\\"input_options_selector\\\": \\\"yes\\\", \\\"qv_encoding\\\": \\\"--phred33\\\", \\\"__current_case__\\\": 0, \\\"trim3\\\": \\\"20\\\", \\\"qupto\\\": \\\"100000000\\\", \\\"trim5\\\": \\\"0\\\"}}\"}", |
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174 "tool_version": "2.2.6.2", |
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175 "type": "tool", |
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176 "uuid": "15edcf5f-9b38-4b7e-ad04-f816d1d4d126", |
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177 "workflow_outputs": [] |
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178 }, |
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179 "3": { |
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180 "annotation": "", |
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181 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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182 "id": 3, |
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183 "input_connections": { |
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184 "input": { |
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185 "id": 2, |
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186 "output_name": "output_unaligned_reads_l" |
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187 } |
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188 }, |
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189 "inputs": [ |
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190 { |
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191 "description": "runtime parameter for tool Concatenate multiple datasets", |
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192 "name": "input" |
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193 } |
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194 ], |
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195 "label": null, |
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196 "name": "Concatenate multiple datasets", |
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197 "outputs": [ |
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198 { |
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199 "name": "out_file1", |
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200 "type": "input" |
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201 } |
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202 ], |
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203 "position": { |
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204 "left": 802.40625, |
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205 "top": 271 |
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206 }, |
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207 "post_job_actions": { |
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208 "ChangeDatatypeActionout_file1": { |
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209 "action_arguments": { |
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210 "newtype": "fasta" |
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211 }, |
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212 "action_type": "ChangeDatatypeAction", |
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213 "output_name": "out_file1" |
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214 }, |
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215 "HideDatasetActionout_file1": { |
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216 "action_arguments": {}, |
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217 "action_type": "HideDatasetAction", |
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218 "output_name": "out_file1" |
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219 } |
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220 }, |
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221 "tool_errors": null, |
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222 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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223 "tool_shed_repository": { |
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224 "changeset_revision": "201c568972c3", |
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225 "name": "concatenate_multiple_datasets", |
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226 "owner": "mvdbeek", |
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227 "tool_shed": "toolshed.g2.bx.psu.edu" |
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228 }, |
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229 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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230 "tool_version": "0.2", |
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231 "type": "tool", |
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232 "uuid": "26ef2a8f-e79e-4e04-92d7-7629b56a3765", |
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233 "workflow_outputs": [] |
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234 }, |
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235 "4": { |
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236 "annotation": "", |
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237 "content_id": "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.4", |
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238 "id": 4, |
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239 "input_connections": { |
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240 "libraries_0|files_0|file_type|unpaired_reads": { |
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241 "id": 3, |
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242 "output_name": "out_file1" |
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243 } |
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244 }, |
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245 "inputs": [], |
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246 "label": null, |
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247 "name": "spades", |
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248 "outputs": [ |
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249 { |
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250 "name": "out_contigs", |
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251 "type": "fasta" |
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252 }, |
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253 { |
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254 "name": "out_contig_stats", |
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255 "type": "tabular" |
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256 }, |
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257 { |
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258 "name": "out_scaffolds", |
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259 "type": "fasta" |
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260 }, |
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261 { |
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262 "name": "out_scaffold_stats", |
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263 "type": "tabular" |
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264 }, |
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265 { |
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266 "name": "out_log", |
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267 "type": "txt" |
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268 } |
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269 ], |
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270 "position": { |
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271 "left": 1084.5, |
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272 "top": 278 |
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273 }, |
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274 "post_job_actions": { |
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275 "HideDatasetActionout_contig_stats": { |
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276 "action_arguments": {}, |
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277 "action_type": "HideDatasetAction", |
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278 "output_name": "out_contig_stats" |
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279 }, |
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280 "HideDatasetActionout_contigs": { |
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281 "action_arguments": {}, |
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282 "action_type": "HideDatasetAction", |
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283 "output_name": "out_contigs" |
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284 }, |
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285 "HideDatasetActionout_log": { |
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286 "action_arguments": {}, |
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287 "action_type": "HideDatasetAction", |
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288 "output_name": "out_log" |
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289 }, |
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290 "HideDatasetActionout_scaffold_stats": { |
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291 "action_arguments": {}, |
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292 "action_type": "HideDatasetAction", |
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293 "output_name": "out_scaffold_stats" |
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294 }, |
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295 "HideDatasetActionout_scaffolds": { |
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296 "action_arguments": {}, |
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297 "action_type": "HideDatasetAction", |
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298 "output_name": "out_scaffolds" |
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299 } |
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300 }, |
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301 "tool_errors": null, |
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302 "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.4", |
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303 "tool_shed_repository": { |
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304 "changeset_revision": "35cb17bd8bf9", |
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305 "name": "spades", |
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306 "owner": "nml", |
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307 "tool_shed": "toolshed.g2.bx.psu.edu" |
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308 }, |
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309 "tool_state": "{\"__page__\": 0, \"iontorrent\": \"\\\"false\\\"\", \"cov\": \"{\\\"state\\\": \\\"auto\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null, \"nanopore\": \"[]\", \"kmer_choice\": \"{\\\"auto_kmer_choice\\\": \\\"true\\\", \\\"__current_case__\\\": 1}\", \"libraries\": \"[{\\\"lib_type\\\": \\\"paired_end\\\", \\\"__index__\\\": 0, \\\"orientation\\\": \\\"fr\\\", \\\"files\\\": [{\\\"file_type\\\": {\\\"type\\\": \\\"unpaired\\\", \\\"unpaired_reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2}, \\\"__index__\\\": 0}]}]\", \"onlyassembler\": \"\\\"true\\\"\", \"trustedcontigs\": \"[]\", \"pacbio\": \"[]\", \"sc\": \"\\\"false\\\"\", \"untrustedcontigs\": \"[]\", \"sanger\": \"[]\", \"careful\": \"\\\"false\\\"\"}", |
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310 "tool_version": "1.4", |
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311 "type": "tool", |
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312 "uuid": "baec2830-d2ae-49d8-b01b-ad7b2c4caec6", |
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313 "workflow_outputs": [] |
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314 }, |
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315 "5": { |
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316 "annotation": "", |
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317 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", |
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318 "id": 5, |
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319 "input_connections": { |
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320 "input": { |
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321 "id": 4, |
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322 "output_name": "out_contigs" |
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323 } |
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324 }, |
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325 "inputs": [ |
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326 { |
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327 "description": "runtime parameter for tool Filter sequences by length", |
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328 "name": "input" |
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329 } |
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330 ], |
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331 "label": null, |
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332 "name": "Filter sequences by length", |
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333 "outputs": [ |
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334 { |
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335 "name": "output", |
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336 "type": "fasta" |
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337 } |
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338 ], |
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339 "position": { |
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340 "left": 1376.421875, |
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341 "top": 271.046875 |
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342 }, |
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343 "post_job_actions": {}, |
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344 "tool_errors": null, |
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345 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", |
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346 "tool_shed_repository": { |
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347 "changeset_revision": "c8cd0a03db49", |
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348 "name": "fasta_filter_by_length", |
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349 "owner": "devteam", |
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350 "tool_shed": "toolshed.g2.bx.psu.edu" |
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351 }, |
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352 "tool_state": "{\"__page__\": 0, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"5000\\\"\"}", |
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353 "tool_version": "1.1", |
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354 "type": "tool", |
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355 "uuid": "db1f7d30-3b47-4030-9724-e371e0ec54a1", |
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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": "output", |
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360 "uuid": "0b517cd3-6991-4968-91e3-894446dd6d8b" |
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361 } |
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362 ] |
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363 }, |
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364 "6": { |
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365 "annotation": "", |
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366 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.08", |
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367 "id": 6, |
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368 "input_connections": { |
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369 "db_opts|histdb": { |
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370 "id": 1, |
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371 "output_name": "output" |
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372 }, |
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373 "query": { |
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374 "id": 5, |
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375 "output_name": "output" |
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376 } |
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377 }, |
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378 "inputs": [ |
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379 { |
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380 "description": "runtime parameter for tool NCBI BLAST+ blastx", |
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381 "name": "db_opts" |
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382 }, |
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383 { |
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384 "description": "runtime parameter for tool NCBI BLAST+ blastx", |
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385 "name": "query" |
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386 } |
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387 ], |
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388 "label": null, |
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389 "name": "NCBI BLAST+ blastx", |
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390 "outputs": [ |
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391 { |
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392 "name": "output1", |
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393 "type": "tabular" |
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394 } |
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395 ], |
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396 "position": { |
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397 "left": 1653.4375, |
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398 "top": 356 |
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399 }, |
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400 "post_job_actions": {}, |
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401 "tool_errors": null, |
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402 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.08", |
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403 "tool_shed_repository": { |
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404 "changeset_revision": "3034ce97dd33", |
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405 "name": "ncbi_blast_plus", |
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406 "owner": "devteam", |
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407 "tool_shed": "toolshed.g2.bx.psu.edu" |
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408 }, |
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409 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", |
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410 "tool_version": "0.1.08", |
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411 "type": "tool", |
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412 "uuid": "b151f8e8-c81b-466a-8a31-d4b42d4b95e9", |
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413 "workflow_outputs": [ |
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414 { |
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415 "label": null, |
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416 "output_name": "output1", |
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417 "uuid": "65223b13-b6fa-45ae-a927-bb96b184bb75" |
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418 } |
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419 ] |
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420 }, |
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421 "7": { |
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422 "annotation": "", |
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423 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", |
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424 "id": 7, |
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425 "input_connections": { |
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426 "blast": { |
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427 "id": 6, |
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428 "output_name": "output1" |
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429 }, |
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430 "sequences": { |
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431 "id": 5, |
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432 "output_name": "output" |
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433 } |
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|
434 }, |
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435 "inputs": [ |
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436 { |
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changeset
|
437 "description": "runtime parameter for tool Parse blast output and compile hits", |
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438 "name": "blast" |
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439 }, |
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|
440 { |
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|
441 "description": "runtime parameter for tool Parse blast output and compile hits", |
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442 "name": "sequences" |
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443 } |
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444 ], |
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445 "label": null, |
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446 "name": "Parse blast output and compile hits", |
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447 "outputs": [ |
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448 { |
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449 "name": "tabularOutput", |
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450 "type": "tabular" |
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451 }, |
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452 { |
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453 "name": "fastaOutput", |
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454 "type": "fasta" |
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455 }, |
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456 { |
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457 "name": "al_sequences", |
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458 "type": "fasta" |
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459 }, |
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460 { |
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461 "name": "un_sequences", |
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462 "type": "fasta" |
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463 } |
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|
464 ], |
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465 "position": { |
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466 "left": 1997.53125, |
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467 "top": 203.5625 |
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468 }, |
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469 "post_job_actions": { |
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470 "HideDatasetActional_sequences": { |
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471 "action_arguments": {}, |
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472 "action_type": "HideDatasetAction", |
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473 "output_name": "al_sequences" |
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474 }, |
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475 "HideDatasetActionfastaOutput": { |
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476 "action_arguments": {}, |
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477 "action_type": "HideDatasetAction", |
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478 "output_name": "fastaOutput" |
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479 }, |
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480 "HideDatasetActionun_sequences": { |
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481 "action_arguments": {}, |
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482 "action_type": "HideDatasetAction", |
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483 "output_name": "un_sequences" |
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484 } |
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485 }, |
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486 "tool_errors": null, |
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487 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", |
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488 "tool_shed_repository": { |
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489 "changeset_revision": "1991c830504a", |
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490 "name": "msp_blastparser_and_hits", |
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491 "owner": "drosofff", |
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492 "tool_shed": "toolshed.g2.bx.psu.edu" |
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493 }, |
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494 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", |
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495 "tool_version": "2.4.3", |
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496 "type": "tool", |
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497 "uuid": "30288e33-ff64-4089-9b45-428027744176", |
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498 "workflow_outputs": [ |
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499 { |
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500 "label": null, |
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501 "output_name": "tabularOutput", |
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502 "uuid": "6b25acfc-474c-4852-b196-a14a4cf619e3" |
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503 } |
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|
504 ] |
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505 } |
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|
506 }, |
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|
507 "uuid": "d0251632-aef7-4c9b-9617-140c9fbab352" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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508 } |