Mercurial > repos > drosofff > metavisitor_workflows
annotate Galaxy-Workflow-Metavisitor__Workflow_for_small_RNA_profiling_of_contigs.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: Workflow for small RNA profiling of contigs", |
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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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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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 of fastq reads" |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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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
parents:
diff
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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
parents:
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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": 136, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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23 "top": 213 |
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 of fastq reads\"}", |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
drosofff
parents:
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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": "95c42be8-325b-48dc-b325-c8e8f9bf8720", |
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": "b0b38a3f-6467-4a79-8e6c-616befcfae74" |
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
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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
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42 "id": 1, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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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": "de novo assembled Oases contigs" |
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": 134.5, |
ba15c770fd40
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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55 "top": 401 |
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
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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\": \"de novo assembled Oases contigs\"}", |
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": "654820a8-188a-4b01-8e7f-4483c8df585f", |
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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66 "output_name": "output", |
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67 "uuid": "4918a4f9-037a-41c8-9881-3f91784b7666" |
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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/drosofff/yac_clipper/yac/1.3.6", |
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74 "id": 2, |
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75 "input_connections": { |
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76 "input": { |
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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 Clip adapter", |
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84 "name": "input" |
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85 } |
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86 ], |
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87 "label": null, |
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88 "name": "Clip adapter", |
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89 "outputs": [ |
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90 { |
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91 "name": "output", |
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92 "type": "fasta" |
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93 } |
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94 ], |
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95 "position": { |
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96 "left": 407.5, |
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97 "top": 239 |
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98 }, |
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99 "post_job_actions": { |
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100 "RenameDatasetActionoutput": { |
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101 "action_arguments": { |
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102 "newname": "Clipped reads" |
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103 }, |
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104 "action_type": "RenameDatasetAction", |
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105 "output_name": "output" |
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106 } |
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107 }, |
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108 "tool_errors": null, |
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109 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", |
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110 "tool_shed_repository": { |
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111 "changeset_revision": "a18edcf9c7ed", |
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112 "name": "yac_clipper", |
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113 "owner": "drosofff", |
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114 "tool_shed": "toolshed.g2.bx.psu.edu" |
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115 }, |
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116 "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"TGGAATTCTCGGGTGCCAAG\\\", \\\"__current_case__\\\": 0}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"Nmode\": \"\\\"reject\\\"\"}", |
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117 "tool_version": "1.3.6", |
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118 "type": "tool", |
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119 "uuid": "98bb84f7-1199-4755-80e8-47e4cd8d7229", |
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120 "workflow_outputs": [ |
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121 { |
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122 "label": null, |
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123 "output_name": "output", |
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124 "uuid": "69ef3522-aeb9-4145-a95b-74154c090d35" |
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125 } |
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126 ] |
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127 }, |
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128 "3": { |
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129 "annotation": "", |
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130 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", |
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131 "id": 3, |
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132 "input_connections": { |
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133 "input": { |
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134 "id": 1, |
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135 "output_name": "output" |
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136 } |
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137 }, |
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138 "inputs": [ |
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139 { |
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140 "description": "runtime parameter for tool Filter sequences by length", |
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141 "name": "input" |
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142 } |
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143 ], |
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144 "label": null, |
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145 "name": "Filter sequences by length", |
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146 "outputs": [ |
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147 { |
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148 "name": "output", |
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149 "type": "fasta" |
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150 } |
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151 ], |
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152 "position": { |
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153 "left": 364, |
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154 "top": 387 |
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155 }, |
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156 "post_job_actions": { |
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157 "RenameDatasetActionoutput": { |
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158 "action_arguments": { |
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159 "newname": "Contig (>300 nt)" |
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160 }, |
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161 "action_type": "RenameDatasetAction", |
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162 "output_name": "output" |
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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/fasta_filter_by_length/fasta_filter_by_length/1.1", |
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167 "tool_shed_repository": { |
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168 "changeset_revision": "c8cd0a03db49", |
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169 "name": "fasta_filter_by_length", |
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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, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"300\\\"\"}", |
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174 "tool_version": "1.1", |
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175 "type": "tool", |
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176 "uuid": "a66d2ce5-bb0a-433c-b8ea-ea612128ee09", |
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177 "workflow_outputs": [ |
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178 { |
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179 "label": null, |
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180 "output_name": "output", |
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181 "uuid": "cfc01174-02dc-457e-a178-493cef1813ea" |
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182 } |
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183 ] |
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184 }, |
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185 "4": { |
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186 "annotation": "", |
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187 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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188 "id": 4, |
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189 "input_connections": { |
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190 "input": { |
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191 "id": 2, |
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192 "output_name": "output" |
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193 } |
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194 }, |
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195 "inputs": [ |
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196 { |
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197 "description": "runtime parameter for tool Concatenate multiple datasets", |
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198 "name": "input" |
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199 } |
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200 ], |
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201 "label": null, |
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202 "name": "Concatenate multiple datasets", |
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203 "outputs": [ |
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204 { |
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205 "name": "out_file1", |
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206 "type": "input" |
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207 } |
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208 ], |
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209 "position": { |
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210 "left": 627, |
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211 "top": 247 |
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212 }, |
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213 "post_job_actions": { |
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214 "RenameDatasetActionout_file1": { |
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215 "action_arguments": { |
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216 "newname": "Merged Clipped Reads" |
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217 }, |
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218 "action_type": "RenameDatasetAction", |
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219 "output_name": "out_file1" |
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220 } |
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221 }, |
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222 "tool_errors": null, |
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223 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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224 "tool_shed_repository": { |
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225 "changeset_revision": "201c568972c3", |
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226 "name": "concatenate_multiple_datasets", |
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227 "owner": "mvdbeek", |
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228 "tool_shed": "toolshed.g2.bx.psu.edu" |
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229 }, |
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230 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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231 "tool_version": "0.2", |
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232 "type": "tool", |
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233 "uuid": "c54ed9da-2b31-413b-94fc-3ebf21295d50", |
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234 "workflow_outputs": [ |
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235 { |
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236 "label": null, |
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237 "output_name": "out_file1", |
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238 "uuid": "308b80b9-5d82-4d46-865b-233498602a8a" |
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239 } |
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240 ] |
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241 }, |
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242 "5": { |
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243 "annotation": "", |
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244 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0", |
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245 "id": 5, |
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246 "input_connections": { |
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247 "input": { |
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248 "id": 3, |
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249 "output_name": "output" |
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250 } |
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251 }, |
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252 "inputs": [ |
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253 { |
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254 "description": "runtime parameter for tool Regex Find And Replace", |
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255 "name": "input" |
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256 } |
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257 ], |
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258 "label": null, |
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259 "name": "Regex Find And Replace", |
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260 "outputs": [ |
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261 { |
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262 "name": "out_file1", |
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263 "type": "input" |
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264 } |
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265 ], |
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266 "position": { |
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267 "left": 649, |
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268 "top": 381 |
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269 }, |
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270 "post_job_actions": { |
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271 "RenameDatasetActionout_file1": { |
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272 "action_arguments": { |
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273 "newname": "contig (>300t, simplified names)" |
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274 }, |
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275 "action_type": "RenameDatasetAction", |
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276 "output_name": "out_file1" |
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277 } |
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278 }, |
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279 "tool_errors": null, |
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280 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0", |
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281 "tool_shed_repository": { |
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282 "changeset_revision": "9ea374bb0350", |
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283 "name": "regex_find_replace", |
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284 "owner": "jjohnson", |
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285 "tool_shed": "toolshed.g2.bx.psu.edu" |
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286 }, |
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287 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\"\\\", \\\"pattern\\\": \\\"_Confidence_.+\\\"}]\", \"__page__\": 0}", |
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288 "tool_version": "0.1.0", |
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289 "type": "tool", |
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290 "uuid": "4fd98d0b-2ffc-4636-b0dc-c52882a0bb70", |
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291 "workflow_outputs": [ |
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292 { |
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293 "label": null, |
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294 "output_name": "out_file1", |
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295 "uuid": "1d62f8d5-96b9-437b-96ef-51c809eeec5c" |
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296 } |
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297 ] |
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298 }, |
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299 "6": { |
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300 "annotation": "", |
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301 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", |
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302 "id": 6, |
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303 "input_connections": { |
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304 "input": { |
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305 "id": 4, |
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306 "output_name": "out_file1" |
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307 }, |
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308 "refGenomeSource|ownFile": { |
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309 "id": 5, |
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310 "output_name": "out_file1" |
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311 } |
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312 }, |
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313 "inputs": [ |
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314 { |
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315 "description": "runtime parameter for tool sRbowtie", |
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316 "name": "input" |
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317 }, |
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318 { |
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319 "description": "runtime parameter for tool sRbowtie", |
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320 "name": "refGenomeSource" |
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321 } |
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322 ], |
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323 "label": null, |
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324 "name": "sRbowtie", |
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325 "outputs": [ |
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326 { |
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327 "name": "output", |
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328 "type": "tabular" |
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329 }, |
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330 { |
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331 "name": "aligned", |
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332 "type": "fasta" |
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333 }, |
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334 { |
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335 "name": "unaligned", |
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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": 942.5, |
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341 "top": 287 |
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342 }, |
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343 "post_job_actions": { |
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344 "HideDatasetActionaligned": { |
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345 "action_arguments": {}, |
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346 "action_type": "HideDatasetAction", |
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347 "output_name": "aligned" |
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348 }, |
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349 "HideDatasetActionunaligned": { |
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350 "action_arguments": {}, |
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351 "action_type": "HideDatasetAction", |
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352 "output_name": "unaligned" |
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353 } |
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354 }, |
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355 "tool_errors": null, |
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356 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", |
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357 "tool_shed_repository": { |
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358 "changeset_revision": "615d2550977f", |
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359 "name": "msp_sr_bowtie", |
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360 "owner": "drosofff", |
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361 "tool_shed": "toolshed.g2.bx.psu.edu" |
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362 }, |
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363 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"No\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"a_option\\\"\"}", |
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364 "tool_version": "1.1.2.1", |
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365 "type": "tool", |
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366 "uuid": "b4d59da2-94c7-4607-8c51-6287b9dd6e6c", |
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367 "workflow_outputs": [ |
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368 { |
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369 "label": null, |
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370 "output_name": "output", |
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371 "uuid": "400d7592-b9b5-4c70-ba7f-058c656bd305" |
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372 } |
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373 ] |
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374 }, |
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375 "7": { |
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376 "annotation": "", |
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377 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.2.0", |
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378 "id": 7, |
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379 "input_connections": { |
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380 "refGenomeSource|ownFile": { |
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381 "id": 5, |
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382 "output_name": "out_file1" |
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383 }, |
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384 "refGenomeSource|series_0|input": { |
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385 "id": 6, |
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386 "output_name": "output" |
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387 } |
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388 }, |
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389 "inputs": [ |
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390 { |
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391 "description": "runtime parameter for tool Generate readmap and histograms from alignment files", |
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392 "name": "gff" |
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393 }, |
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394 { |
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395 "description": "runtime parameter for tool Generate readmap and histograms from alignment files", |
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396 "name": "refGenomeSource" |
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397 } |
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398 ], |
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399 "label": null, |
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400 "name": "Generate readmap and histograms from alignment files", |
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401 "outputs": [ |
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402 { |
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403 "name": "readmap_dataframe", |
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404 "type": "tabular" |
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405 }, |
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406 { |
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407 "name": "size_distribution_dataframe", |
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408 "type": "tabular" |
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409 }, |
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410 { |
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411 "name": "readmap_PDF", |
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412 "type": "pdf" |
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413 }, |
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414 { |
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415 "name": "size_PDF", |
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416 "type": "pdf" |
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417 }, |
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418 { |
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419 "name": "combi_PDF", |
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420 "type": "pdf" |
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421 } |
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422 ], |
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423 "position": { |
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424 "left": 1243.5, |
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425 "top": 273 |
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426 }, |
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427 "post_job_actions": { |
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428 "HideDatasetActionreadmap_dataframe": { |
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429 "action_arguments": {}, |
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430 "action_type": "HideDatasetAction", |
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431 "output_name": "readmap_dataframe" |
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432 }, |
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433 "HideDatasetActionsize_distribution_dataframe": { |
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434 "action_arguments": {}, |
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435 "action_type": "HideDatasetAction", |
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436 "output_name": "size_distribution_dataframe" |
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437 } |
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438 }, |
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439 "tool_errors": null, |
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440 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.2.0", |
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441 "tool_shed_repository": { |
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442 "changeset_revision": "92898cc3ea19", |
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443 "name": "msp_sr_readmap_and_size_histograms", |
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444 "owner": "drosofff", |
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445 "tool_shed": "toolshed.g2.bx.psu.edu" |
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446 }, |
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447 "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}], \\\"ownFile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"maxquery\": \"\\\"30\\\"\", \"xlabel\": \"\\\"Coordinates/read size\\\"\", \"ylabel\": \"\\\"Number of reads\\\"\", \"gff\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", |
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448 "tool_version": "1.2.0", |
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449 "type": "tool", |
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450 "uuid": "87f9f9b5-5c71-465b-9422-c0696a3048a5", |
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451 "workflow_outputs": [ |
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452 { |
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453 "label": null, |
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454 "output_name": "size_PDF", |
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455 "uuid": "91fa9c78-72dd-41e8-9937-c4b44682f79b" |
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456 }, |
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457 { |
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458 "label": null, |
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459 "output_name": "combi_PDF", |
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460 "uuid": "68f021f3-087b-4f77-813f-74fa61877a0e" |
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461 }, |
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462 { |
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463 "label": null, |
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464 "output_name": "readmap_PDF", |
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465 "uuid": "70966192-62e8-4dff-99b1-3f5dc8de8c28" |
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466 } |
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467 ] |
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468 } |
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469 }, |
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470 "uuid": "c3853e65-8d66-47fc-aad9-6a40f5517622" |
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471 } |