Mercurial > repos > drosofff > metavisitor_workflows
annotate Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-2.ga @ 0:4a47903bb4df draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
author | drosofff |
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date | Tue, 05 Apr 2016 06:42:47 -0400 |
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children | 48b020a0d2f7 |
rev | line source |
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0
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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1 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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2 "a_galaxy_workflow": "true", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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3 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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4 "format-version": "0.1", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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5 "name": "Metavisitor: Workflow for Use Case 2-2", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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6 "steps": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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7 "0": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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8 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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9 "content_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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10 "id": 0, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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11 "input_connections": {}, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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12 "inputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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13 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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14 "description": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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15 "name": "Input Dataset Collection" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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16 } |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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17 ], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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18 "label": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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diff
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19 "name": "Input dataset collection", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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20 "outputs": [], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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21 "position": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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22 "left": 199.91314697265625, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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23 "top": 183.5937557220459 |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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24 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
diff
changeset
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25 "tool_errors": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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diff
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26 "tool_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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27 "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
parents:
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28 "tool_version": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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29 "type": "data_collection_input", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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30 "uuid": "3b7db228-7d72-4b8a-9296-5e51ceda8cdd", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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31 "workflow_outputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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32 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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33 "label": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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34 "output_name": "output", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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35 "uuid": "dd803215-4fa9-4444-83df-06e42912b545" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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36 } |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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37 ] |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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38 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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39 "1": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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40 "annotation": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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41 "content_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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42 "id": 1, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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43 "input_connections": {}, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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44 "inputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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45 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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46 "description": "", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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47 "name": "Protein Blast database" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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48 } |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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49 ], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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50 "label": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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51 "name": "Input dataset", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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52 "outputs": [], |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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53 "position": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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54 "left": 1887.9861450195312, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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55 "top": 619.5659847259521 |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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56 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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57 "tool_errors": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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58 "tool_id": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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59 "tool_state": "{\"name\": \"Protein Blast database\"}", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
drosofff
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60 "tool_version": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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61 "type": "data_input", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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62 "uuid": "9f28fc2b-f552-4021-b6fc-ba95f6f3e8dd", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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63 "workflow_outputs": [ |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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64 { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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65 "label": null, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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66 "output_name": "output", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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67 "uuid": "8d19a7b0-6b52-46ee-be47-cce18eca9453" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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68 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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69 ] |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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70 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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71 "2": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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72 "annotation": "", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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73 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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74 "id": 2, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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75 "input_connections": { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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76 "library|input_1": { |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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77 "id": 0, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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78 "output_name": "output" |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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79 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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80 }, |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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81 "inputs": [], |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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82 "label": null, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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83 "name": "Bowtie2", |
4a47903bb4df
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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84 "outputs": [ |
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85 { |
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86 "name": "output_unaligned_reads_l", |
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87 "type": "fastqsanger" |
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88 }, |
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89 { |
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90 "name": "output_aligned_reads_l", |
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91 "type": "fastqsanger" |
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92 }, |
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93 { |
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94 "name": "output_aligned_reads_r", |
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95 "type": "fastqsanger" |
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96 }, |
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97 { |
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98 "name": "output_unaligned_reads_r", |
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99 "type": "fastqsanger" |
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100 }, |
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101 { |
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102 "name": "output", |
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103 "type": "bam" |
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104 }, |
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105 { |
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106 "name": "output_sam", |
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107 "type": "sam" |
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108 }, |
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109 { |
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110 "name": "mapping_stats", |
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111 "type": "txt" |
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112 } |
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113 ], |
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114 "position": { |
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115 "left": 433.48956298828125, |
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116 "top": 367.6389217376709 |
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117 }, |
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118 "post_job_actions": { |
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119 "DeleteIntermediatesActionoutput_unaligned_reads_l": { |
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120 "action_arguments": {}, |
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121 "action_type": "DeleteIntermediatesAction", |
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122 "output_name": "output_unaligned_reads_l" |
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123 }, |
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124 "HideDatasetActionmapping_stats": { |
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125 "action_arguments": {}, |
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126 "action_type": "HideDatasetAction", |
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127 "output_name": "mapping_stats" |
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128 }, |
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129 "HideDatasetActionoutput": { |
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130 "action_arguments": {}, |
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131 "action_type": "HideDatasetAction", |
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132 "output_name": "output" |
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133 }, |
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134 "HideDatasetActionoutput_aligned_reads_l": { |
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135 "action_arguments": {}, |
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136 "action_type": "HideDatasetAction", |
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137 "output_name": "output_aligned_reads_l" |
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138 }, |
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139 "HideDatasetActionoutput_aligned_reads_r": { |
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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_r" |
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143 }, |
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144 "HideDatasetActionoutput_sam": { |
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145 "action_arguments": {}, |
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146 "action_type": "HideDatasetAction", |
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147 "output_name": "output_sam" |
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148 }, |
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149 "HideDatasetActionoutput_unaligned_reads_l": { |
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150 "action_arguments": {}, |
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151 "action_type": "HideDatasetAction", |
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152 "output_name": "output_unaligned_reads_l" |
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153 }, |
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154 "HideDatasetActionoutput_unaligned_reads_r": { |
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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_r" |
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158 } |
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159 }, |
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160 "tool_errors": null, |
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161 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", |
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162 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"False\\\", \\\"unaligned_file\\\": \\\"True\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"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\\\": {\\\"alignment_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"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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163 "tool_version": "2.2.6.2", |
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164 "type": "tool", |
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165 "uuid": "15edcf5f-9b38-4b7e-ad04-f816d1d4d126", |
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166 "workflow_outputs": [] |
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167 }, |
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168 "3": { |
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169 "annotation": "", |
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170 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", |
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171 "id": 3, |
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172 "input_connections": { |
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173 "input": { |
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174 "id": 2, |
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175 "output_name": "output_unaligned_reads_l" |
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176 } |
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177 }, |
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178 "inputs": [], |
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179 "label": null, |
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180 "name": "FASTQ to FASTA", |
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181 "outputs": [ |
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182 { |
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183 "name": "output", |
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184 "type": "fasta" |
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185 } |
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186 ], |
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187 "position": { |
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188 "left": 774.4097290039062, |
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189 "top": 315.97223472595215 |
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190 }, |
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191 "post_job_actions": { |
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192 "HideDatasetActionoutput": { |
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193 "action_arguments": {}, |
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194 "action_type": "HideDatasetAction", |
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195 "output_name": "output" |
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196 } |
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197 }, |
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198 "tool_errors": null, |
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199 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", |
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200 "tool_state": "{\"__page__\": 0, \"RENAMESEQ\": \"\\\"-r\\\"\", \"SKIPN\": \"\\\"\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", |
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201 "tool_version": "1.0.0", |
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202 "type": "tool", |
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203 "uuid": "None", |
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204 "workflow_outputs": [] |
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205 }, |
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206 "4": { |
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207 "annotation": "", |
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208 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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209 "id": 4, |
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210 "input_connections": { |
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211 "input": { |
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212 "id": 3, |
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213 "output_name": "output" |
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214 } |
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215 }, |
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216 "inputs": [], |
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217 "label": null, |
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218 "name": "Concatenate multiple datasets", |
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219 "outputs": [ |
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220 { |
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221 "name": "out_file1", |
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222 "type": "input" |
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223 } |
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224 ], |
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225 "position": { |
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226 "left": 1005.4166717529297, |
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227 "top": 303.00348472595215 |
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228 }, |
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229 "post_job_actions": { |
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230 "ChangeDatatypeActionout_file1": { |
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231 "action_arguments": { |
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232 "newtype": "fasta" |
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233 }, |
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234 "action_type": "ChangeDatatypeAction", |
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235 "output_name": "out_file1" |
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236 }, |
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237 "HideDatasetActionout_file1": { |
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238 "action_arguments": {}, |
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239 "action_type": "HideDatasetAction", |
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240 "output_name": "out_file1" |
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241 } |
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242 }, |
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243 "tool_errors": null, |
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244 "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", |
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245 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", |
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246 "tool_version": "0.2", |
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247 "type": "tool", |
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248 "uuid": "None", |
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249 "workflow_outputs": [] |
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250 }, |
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251 "5": { |
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252 "annotation": "", |
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253 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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254 "id": 5, |
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255 "input_connections": { |
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256 "switch|input": { |
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257 "id": 4, |
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258 "output_name": "out_file1" |
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259 } |
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260 }, |
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261 "inputs": [], |
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262 "label": null, |
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263 "name": "fasta - tabular", |
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264 "outputs": [ |
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265 { |
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266 "name": "output", |
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267 "type": "fasta" |
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268 } |
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269 ], |
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270 "position": { |
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271 "left": 1290.5555725097656, |
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272 "top": 296.59723472595215 |
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273 }, |
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274 "post_job_actions": { |
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275 "HideDatasetActionoutput": { |
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276 "action_arguments": {}, |
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277 "action_type": "HideDatasetAction", |
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278 "output_name": "output" |
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279 } |
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280 }, |
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281 "tool_errors": null, |
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282 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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283 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"fasta2tabular\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null}", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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284 "tool_version": "1.1.0", |
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285 "type": "tool", |
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286 "uuid": "1d78a822-0e08-4e92-a9f7-bc80166e36a1", |
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287 "workflow_outputs": [] |
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288 }, |
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289 "6": { |
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290 "annotation": "", |
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291 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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292 "id": 6, |
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293 "input_connections": { |
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294 "switch|input": { |
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295 "id": 5, |
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296 "output_name": "output" |
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297 } |
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298 }, |
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299 "inputs": [], |
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300 "label": null, |
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301 "name": "fasta - tabular", |
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302 "outputs": [ |
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303 { |
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304 "name": "output", |
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305 "type": "fasta" |
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306 } |
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307 ], |
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308 "position": { |
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309 "left": 1517.5521240234375, |
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310 "top": 302.5868282318115 |
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311 }, |
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312 "post_job_actions": { |
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313 "HideDatasetActionoutput": { |
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314 "action_arguments": {}, |
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315 "action_type": "HideDatasetAction", |
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316 "output_name": "output" |
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317 } |
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318 }, |
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319 "tool_errors": null, |
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320 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", |
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321 "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"tabular2fastaweight\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null}", |
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322 "tool_version": "1.1.0", |
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323 "type": "tool", |
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324 "uuid": "d6d8e36c-641a-4662-b615-0745b9d9fb55", |
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325 "workflow_outputs": [] |
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326 }, |
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327 "7": { |
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328 "annotation": "", |
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329 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", |
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330 "id": 7, |
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331 "input_connections": { |
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332 "inputs_0|input": { |
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333 "id": 6, |
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334 "output_name": "output" |
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335 } |
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336 }, |
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337 "inputs": [], |
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338 "label": null, |
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339 "name": "Oases_optimiser", |
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340 "outputs": [ |
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341 { |
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342 "name": "transcripts", |
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343 "type": "fasta" |
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344 } |
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345 ], |
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346 "position": { |
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347 "left": 1778.4375610351562, |
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348 "top": 339.0625057220459 |
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349 }, |
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350 "post_job_actions": {}, |
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351 "tool_errors": null, |
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352 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", |
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353 "tool_state": "{\"__page__\": 0, \"end_hash_length\": \"\\\"69\\\"\", \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"start_hash_length\": \"\\\"25\\\"\"}", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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354 "tool_version": "1.1.4", |
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355 "type": "tool", |
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356 "uuid": "None", |
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357 "workflow_outputs": [ |
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358 { |
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359 "label": null, |
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360 "output_name": "transcripts", |
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361 "uuid": "e679f97f-a15b-479d-9154-59cd57642674" |
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362 } |
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363 ] |
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364 }, |
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365 "8": { |
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366 "annotation": "", |
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367 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", |
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368 "id": 8, |
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369 "input_connections": { |
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370 "input": { |
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371 "id": 7, |
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372 "output_name": "transcripts" |
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373 } |
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374 }, |
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375 "inputs": [], |
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376 "label": null, |
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377 "name": "Filter sequences by length", |
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378 "outputs": [ |
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379 { |
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380 "name": "output", |
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381 "type": "fasta" |
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382 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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383 ], |
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384 "position": { |
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385 "left": 1956.4236450195312, |
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386 "top": 213.05556297302246 |
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387 }, |
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388 "post_job_actions": {}, |
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389 "tool_errors": null, |
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390 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", |
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391 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"5000\\\"\"}", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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392 "tool_version": "1.1", |
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393 "type": "tool", |
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394 "uuid": "None", |
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395 "workflow_outputs": [ |
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396 { |
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397 "label": null, |
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398 "output_name": "output", |
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399 "uuid": "0b517cd3-6991-4968-91e3-894446dd6d8b" |
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400 } |
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401 ] |
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402 }, |
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403 "9": { |
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404 "annotation": "", |
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405 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", |
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406 "id": 9, |
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407 "input_connections": { |
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408 "db_opts|histdb": { |
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409 "id": 1, |
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410 "output_name": "output" |
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411 }, |
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412 "query": { |
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413 "id": 8, |
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414 "output_name": "output" |
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415 } |
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416 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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417 "inputs": [], |
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418 "label": null, |
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419 "name": "NCBI BLAST+ blastx", |
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420 "outputs": [ |
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421 { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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422 "name": "output1", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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423 "type": "tabular" |
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424 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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425 ], |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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426 "position": { |
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427 "left": 2225.451416015625, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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428 "top": 313.00348472595215 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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429 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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430 "post_job_actions": {}, |
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431 "tool_errors": null, |
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432 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", |
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433 "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\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"query\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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434 "tool_version": "0.1.06", |
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435 "type": "tool", |
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436 "uuid": "None", |
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437 "workflow_outputs": [ |
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438 { |
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439 "label": null, |
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440 "output_name": "output1", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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441 "uuid": "65223b13-b6fa-45ae-a927-bb96b184bb75" |
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442 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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443 ] |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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444 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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445 "10": { |
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446 "annotation": "", |
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447 "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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448 "id": 10, |
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449 "input_connections": { |
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450 "blast": { |
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451 "id": 9, |
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452 "output_name": "output1" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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453 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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454 "sequences": { |
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455 "id": 8, |
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456 "output_name": "output" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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457 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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458 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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459 "inputs": [], |
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460 "label": null, |
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461 "name": "Parse blast output and compile hits", |
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462 "outputs": [ |
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463 { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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464 "name": "tabularOutput", |
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465 "type": "tabular" |
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466 }, |
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467 { |
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468 "name": "fastaOutput", |
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469 "type": "fasta" |
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470 }, |
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471 { |
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472 "name": "al_sequences", |
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473 "type": "fasta" |
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474 }, |
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475 { |
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476 "name": "un_sequences", |
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477 "type": "fasta" |
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478 } |
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479 ], |
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480 "position": { |
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481 "left": 2559.5313720703125, |
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482 "top": 128.57639122009277 |
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483 }, |
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484 "post_job_actions": { |
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485 "HideDatasetActional_sequences": { |
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486 "action_arguments": {}, |
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487 "action_type": "HideDatasetAction", |
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488 "output_name": "al_sequences" |
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489 }, |
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490 "HideDatasetActionfastaOutput": { |
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491 "action_arguments": {}, |
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492 "action_type": "HideDatasetAction", |
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493 "output_name": "fastaOutput" |
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494 }, |
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495 "HideDatasetActionun_sequences": { |
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496 "action_arguments": {}, |
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497 "action_type": "HideDatasetAction", |
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498 "output_name": "un_sequences" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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499 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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500 }, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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501 "tool_errors": null, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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502 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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503 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"use_filters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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504 "tool_version": "2.4.3", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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505 "type": "tool", |
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506 "uuid": "30288e33-ff64-4089-9b45-428027744176", |
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507 "workflow_outputs": [ |
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508 { |
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509 "label": null, |
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510 "output_name": "tabularOutput", |
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511 "uuid": "6b25acfc-474c-4852-b196-a14a4cf619e3" |
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512 } |
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513 ] |
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514 } |
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515 }, |
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516 "uuid": "ea5b1974-4efa-4a30-a29c-4cfa9fd7da83" |
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517 } |