Mercurial > repos > chrisd > amrplusplus_workflow
annotate amrplusplus_workflow.ga @ 5:04f9c20fecf8 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
author | chrisd |
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date | Wed, 22 Jun 2016 00:27:14 -0400 |
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children | 86dc721b6860 |
rev | line source |
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5
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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1 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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2 "a_galaxy_workflow": "true", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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3 "annotation": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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4 "format-version": "0.1", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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5 "name": "aa", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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6 "steps": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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7 "0": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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8 "annotation": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
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9 "content_id": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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10 "id": 0, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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11 "input_connections": {}, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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12 "inputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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13 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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14 "description": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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15 "name": "FASTQ Forward" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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16 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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17 ], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
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18 "label": "FASTQ Forward", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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19 "name": "Input dataset", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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20 "outputs": [], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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21 "position": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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22 "left": 252, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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23 "top": 323 |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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24 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
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25 "tool_errors": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
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26 "tool_id": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
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27 "tool_state": "{\"name\": \"FASTQ Forward\"}", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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28 "tool_version": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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29 "type": "data_input", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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30 "uuid": "9c1f5852-9697-40e2-bc6f-7ac65ad647ce", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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31 "workflow_outputs": [] |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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32 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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33 "1": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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34 "annotation": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
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35 "content_id": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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36 "id": 1, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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37 "input_connections": {}, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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38 "inputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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39 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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40 "description": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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41 "name": "FASTQ Reverse" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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42 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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43 ], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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44 "label": "FASTQ Reverse", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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45 "name": "Input dataset", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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46 "outputs": [], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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47 "position": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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48 "left": 251, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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49 "top": 399 |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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50 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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51 "tool_errors": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
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52 "tool_id": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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53 "tool_state": "{\"name\": \"FASTQ Reverse\"}", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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54 "tool_version": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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55 "type": "data_input", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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56 "uuid": "030bf3fc-ee71-46c4-bfcf-8d963c04a478", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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57 "workflow_outputs": [] |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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58 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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59 "2": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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60 "annotation": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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61 "content_id": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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62 "id": 2, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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63 "input_connections": {}, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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64 "inputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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65 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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66 "description": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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67 "name": "Host Genome" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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68 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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69 ], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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70 "label": "Host Genome", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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71 "name": "Input dataset", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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72 "outputs": [], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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73 "position": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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74 "left": 498, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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75 "top": 200 |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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76 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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77 "tool_errors": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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78 "tool_id": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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79 "tool_state": "{\"name\": \"Host Genome\"}", |
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80 "tool_version": null, |
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81 "type": "data_input", |
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82 "uuid": "95f884fc-215e-4d54-8212-e43be8a779b5", |
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83 "workflow_outputs": [] |
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84 }, |
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85 "3": { |
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86 "annotation": "", |
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87 "content_id": null, |
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88 "id": 3, |
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89 "input_connections": {}, |
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90 "inputs": [ |
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91 { |
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92 "description": "", |
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93 "name": "AMR Database" |
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94 } |
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95 ], |
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96 "label": "AMR Database", |
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97 "name": "Input dataset", |
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98 "outputs": [], |
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99 "position": { |
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100 "left": 1086, |
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101 "top": 560 |
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102 }, |
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103 "tool_errors": null, |
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104 "tool_id": null, |
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105 "tool_state": "{\"name\": \"AMR Database\"}", |
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106 "tool_version": null, |
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107 "type": "data_input", |
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108 "uuid": "8a65e391-b837-41ef-9575-bedf5294da9e", |
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109 "workflow_outputs": [] |
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110 }, |
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111 "4": { |
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112 "annotation": "", |
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113 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", |
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114 "id": 4, |
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115 "input_connections": { |
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116 "paired_end|paired_input_type_conditional|fastq_r1_in": { |
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117 "id": 0, |
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118 "output_name": "output" |
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119 }, |
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120 "paired_end|paired_input_type_conditional|fastq_r2_in": { |
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121 "id": 1, |
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122 "output_name": "output" |
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123 } |
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124 }, |
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125 "inputs": [], |
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126 "label": null, |
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127 "name": "Trimmomatic", |
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128 "outputs": [ |
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129 { |
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130 "name": "fastq_out_paired", |
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131 "type": "input" |
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132 }, |
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133 { |
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134 "name": "fastq_out_unpaired", |
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135 "type": "input" |
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136 }, |
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137 { |
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138 "name": "fastq_out_r1_paired", |
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139 "type": "fastqsanger" |
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140 }, |
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141 { |
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142 "name": "fastq_out_r2_paired", |
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143 "type": "fastqsanger" |
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144 }, |
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145 { |
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146 "name": "fastq_out_r1_unpaired", |
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147 "type": "fastqsanger" |
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148 }, |
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149 { |
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150 "name": "fastq_out_r2_unpaired", |
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151 "type": "fastqsanger" |
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152 }, |
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153 { |
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154 "name": "fastq_out", |
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155 "type": "fastqsanger" |
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156 } |
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157 ], |
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158 "position": { |
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159 "left": 465, |
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160 "top": 303 |
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161 }, |
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162 "post_job_actions": { |
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163 "HideDatasetActionfastq_out": { |
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164 "action_arguments": {}, |
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165 "action_type": "HideDatasetAction", |
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166 "output_name": "fastq_out" |
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167 }, |
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168 "HideDatasetActionfastq_out_paired": { |
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169 "action_arguments": {}, |
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170 "action_type": "HideDatasetAction", |
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171 "output_name": "fastq_out_paired" |
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172 }, |
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173 "HideDatasetActionfastq_out_r1_unpaired": { |
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174 "action_arguments": {}, |
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175 "action_type": "HideDatasetAction", |
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176 "output_name": "fastq_out_r1_unpaired" |
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177 }, |
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178 "HideDatasetActionfastq_out_r2_unpaired": { |
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179 "action_arguments": {}, |
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180 "action_type": "HideDatasetAction", |
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181 "output_name": "fastq_out_r2_unpaired" |
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182 }, |
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183 "HideDatasetActionfastq_out_unpaired": { |
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184 "action_arguments": {}, |
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185 "action_type": "HideDatasetAction", |
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186 "output_name": "fastq_out_unpaired" |
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187 } |
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188 }, |
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189 "tool_errors": null, |
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190 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", |
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191 "tool_shed_repository": { |
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192 "changeset_revision": "f8a9a5eaca8a", |
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193 "name": "trimmomatic", |
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194 "owner": "pjbriggs", |
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195 "tool_shed": "toolshed.g2.bx.psu.edu" |
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196 }, |
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197 "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"true\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\"}", |
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198 "tool_version": "0.32.3", |
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199 "type": "tool", |
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200 "uuid": "0d5a87ee-c6a3-4bd1-b416-226d0e4783ab", |
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201 "workflow_outputs": [ |
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202 { |
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203 "label": null, |
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204 "output_name": "fastq_out_r1_paired", |
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205 "uuid": "6e06861e-a08e-4fbf-bdd6-daa51499d669" |
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206 }, |
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207 { |
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208 "label": null, |
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209 "output_name": "fastq_out_r2_paired", |
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210 "uuid": "1b2d0dd4-d1ce-4886-b300-8df03d3918fa" |
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211 } |
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212 ] |
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213 }, |
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214 "5": { |
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215 "annotation": "", |
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216 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", |
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217 "id": 5, |
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218 "input_connections": { |
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219 "input1": { |
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220 "id": 3, |
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221 "output_name": "output" |
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222 } |
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223 }, |
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224 "inputs": [ |
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225 { |
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226 "description": "runtime parameter for tool Snip Finder", |
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227 "name": "sam_type" |
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228 }, |
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229 { |
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230 "description": "runtime parameter for tool Snip Finder", |
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231 "name": "input1" |
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232 } |
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233 ], |
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234 "label": null, |
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235 "name": "Snip Finder", |
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236 "outputs": [ |
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237 { |
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238 "name": "output1", |
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239 "type": "tabular" |
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240 } |
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241 ], |
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242 "position": { |
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243 "left": 1368, |
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244 "top": 551 |
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245 }, |
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246 "post_job_actions": {}, |
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247 "tool_errors": null, |
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248 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", |
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249 "tool_shed_repository": { |
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250 "changeset_revision": "d9be5a7e70f5", |
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251 "name": "snipfinder", |
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252 "owner": "chrisd", |
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253 "tool_shed": "toolshed.g2.bx.psu.edu" |
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254 }, |
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255 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"false\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", |
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256 "tool_version": "0.1.0", |
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257 "type": "tool", |
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258 "uuid": "e4564c96-a500-4017-a222-fc0e55a23b20", |
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259 "workflow_outputs": [ |
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260 { |
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261 "label": null, |
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262 "output_name": "output1", |
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263 "uuid": "44843c44-7cf5-4738-9b48-60ad16b8d915" |
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264 } |
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265 ] |
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266 }, |
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267 "6": { |
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268 "annotation": "", |
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269 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", |
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270 "id": 6, |
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271 "input_connections": { |
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272 "input_type|fastq_input1": { |
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273 "id": 4, |
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274 "output_name": "fastq_out_r1_paired" |
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275 }, |
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276 "input_type|fastq_input2": { |
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277 "id": 4, |
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278 "output_name": "fastq_out_r2_paired" |
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279 }, |
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280 "reference_source|ref_file": { |
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281 "id": 2, |
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282 "output_name": "output" |
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283 } |
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284 }, |
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285 "inputs": [ |
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286 { |
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287 "description": "runtime parameter for tool Map with BWA", |
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288 "name": "input_type" |
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289 }, |
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290 { |
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291 "description": "runtime parameter for tool Map with BWA", |
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292 "name": "input_type" |
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293 }, |
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294 { |
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295 "description": "runtime parameter for tool Map with BWA", |
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296 "name": "reference_source" |
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297 } |
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298 ], |
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299 "label": null, |
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300 "name": "Map with BWA", |
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301 "outputs": [ |
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302 { |
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303 "name": "bam_output", |
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304 "type": "bam" |
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305 } |
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306 ], |
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307 "position": { |
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308 "left": 772.5, |
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309 "top": 306 |
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310 }, |
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311 "post_job_actions": {}, |
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312 "tool_errors": null, |
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313 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", |
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314 "tool_shed_repository": { |
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315 "changeset_revision": "546ada4a9f43", |
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316 "name": "bwa", |
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317 "owner": "devteam", |
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318 "tool_shed": "toolshed.g2.bx.psu.edu" |
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319 }, |
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320 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"input_type_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", |
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321 "tool_version": "0.7.12.1", |
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322 "type": "tool", |
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323 "uuid": "880e395c-e063-4ae9-803c-b1961ef0a4fd", |
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324 "workflow_outputs": [ |
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325 { |
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326 "label": null, |
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327 "output_name": "bam_output", |
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328 "uuid": "8b9ad567-40bb-4533-9342-ca2c7a57326a" |
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329 } |
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330 ] |
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331 }, |
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332 "7": { |
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333 "annotation": "", |
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334 "content_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1", |
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335 "id": 7, |
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336 "input_connections": { |
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337 "input": { |
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338 "id": 6, |
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339 "output_name": "bam_output" |
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340 } |
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341 }, |
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342 "inputs": [ |
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343 { |
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344 "description": "runtime parameter for tool Samtools flag_filter", |
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345 "name": "input" |
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346 } |
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347 ], |
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348 "label": null, |
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349 "name": "Samtools flag_filter", |
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350 "outputs": [ |
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351 { |
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352 "name": "output", |
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353 "type": "bam" |
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354 } |
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355 ], |
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356 "position": { |
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357 "left": 1004.5, |
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358 "top": 303 |
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359 }, |
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360 "post_job_actions": {}, |
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361 "tool_errors": null, |
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362 "tool_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1", |
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363 "tool_shed_repository": { |
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364 "changeset_revision": "97bb72be07f9", |
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365 "name": "samtools_flag_filter_1_2", |
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366 "owner": "brenninc", |
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367 "tool_shed": "toolshed.g2.bx.psu.edu" |
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368 }, |
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369 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"bits\": \"[{\\\"__index__\\\": 0, \\\"flag\\\": \\\"0x0004\\\", \\\"state\\\": \\\"f\\\"}]\", \"__page__\": 0}", |
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370 "tool_version": "0.1", |
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371 "type": "tool", |
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372 "uuid": "aa177899-8618-4afb-b484-e2a9eb616f04", |
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373 "workflow_outputs": [ |
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374 { |
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375 "label": null, |
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376 "output_name": "output", |
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377 "uuid": "a960b5e7-cb47-4afb-9688-3a787b4813a5" |
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378 } |
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379 ] |
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380 }, |
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381 "8": { |
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382 "annotation": "", |
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383 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", |
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384 "id": 8, |
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385 "input_connections": { |
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386 "input_type|bam_input": { |
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387 "id": 7, |
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388 "output_name": "output" |
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389 }, |
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390 "reference_source|ref_file": { |
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391 "id": 3, |
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392 "output_name": "output" |
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393 } |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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394 }, |
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395 "inputs": [ |
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396 { |
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397 "description": "runtime parameter for tool Map with BWA", |
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398 "name": "input_type" |
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399 }, |
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400 { |
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401 "description": "runtime parameter for tool Map with BWA", |
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402 "name": "reference_source" |
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403 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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404 ], |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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405 "label": null, |
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406 "name": "Map with BWA", |
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407 "outputs": [ |
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408 { |
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409 "name": "bam_output", |
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410 "type": "bam" |
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411 } |
04f9c20fecf8
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412 ], |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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413 "position": { |
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414 "left": 1279.5, |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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415 "top": 305 |
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416 }, |
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417 "post_job_actions": {}, |
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418 "tool_errors": null, |
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419 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", |
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420 "tool_shed_repository": { |
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421 "changeset_revision": "546ada4a9f43", |
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422 "name": "bwa", |
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423 "owner": "devteam", |
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424 "tool_shed": "toolshed.g2.bx.psu.edu" |
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425 }, |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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426 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 3, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"adv_bam_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", |
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427 "tool_version": "0.7.12.1", |
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428 "type": "tool", |
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429 "uuid": "91a7471e-ee8d-4f6f-8002-d0914dd8df57", |
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430 "workflow_outputs": [ |
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431 { |
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432 "label": null, |
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433 "output_name": "bam_output", |
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434 "uuid": "70c657a7-61ce-4c52-a5b4-564eddd9e79e" |
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435 } |
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436 ] |
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437 }, |
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438 "9": { |
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439 "annotation": "", |
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440 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", |
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441 "id": 9, |
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442 "input_connections": { |
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443 "input1": { |
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444 "id": 8, |
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445 "output_name": "bam_output" |
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446 } |
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447 }, |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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448 "inputs": [ |
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449 { |
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450 "description": "runtime parameter for tool Sort", |
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451 "name": "input1" |
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452 } |
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453 ], |
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454 "label": null, |
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455 "name": "Sort", |
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456 "outputs": [ |
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457 { |
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458 "name": "output1", |
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459 "type": "bam" |
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460 } |
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|
461 ], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
462 "position": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff
changeset
|
463 "left": 1506, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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464 "top": 306 |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
465 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
466 "post_job_actions": {}, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff
changeset
|
467 "tool_errors": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
468 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
469 "tool_shed_repository": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
470 "changeset_revision": "a430da4f04cd", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
471 "name": "samtools_sort", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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472 "owner": "devteam", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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473 "tool_shed": "toolshed.g2.bx.psu.edu" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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474 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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475 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sort_mode\": \"\\\"-n\\\"\"}", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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476 "tool_version": "2.0", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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477 "type": "tool", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
478 "uuid": "62d071ac-483d-43d0-a7a2-59cd7c41ee39", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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479 "workflow_outputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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480 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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481 "label": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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482 "output_name": "output1", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
483 "uuid": "b6efbbfd-4e6b-410c-a99d-f8dd4e600ea9" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
484 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
485 ] |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
486 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
487 "10": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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488 "annotation": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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489 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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490 "id": 10, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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491 "input_connections": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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492 "input1": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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493 "id": 9, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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494 "output_name": "output1" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
495 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
496 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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497 "inputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
498 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
499 "description": "runtime parameter for tool BAM-to-SAM", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
500 "name": "input1" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
501 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
502 ], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
503 "label": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
504 "name": "BAM-to-SAM", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
505 "outputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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changeset
|
506 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff
changeset
|
507 "name": "output1", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
508 "type": "sam" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
509 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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changeset
|
510 ], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
511 "position": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
512 "left": 1507.5, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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513 "top": 433 |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
514 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
515 "post_job_actions": {}, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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516 "tool_errors": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
517 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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518 "tool_shed_repository": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
519 "changeset_revision": "af7c50162f0b", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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520 "name": "bam_to_sam", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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521 "owner": "devteam", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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522 "tool_shed": "toolshed.g2.bx.psu.edu" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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523 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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524 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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525 "tool_version": "2.0", |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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526 "type": "tool", |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
527 "uuid": "5076f37b-5da6-44a3-a3b2-f4172d547dc3", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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528 "workflow_outputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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529 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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530 "label": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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531 "output_name": "output1", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
532 "uuid": "4b52f2d0-1a66-408a-bc99-0da79cc8542f" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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533 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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534 ] |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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535 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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536 "11": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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537 "annotation": "", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
538 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
diff
changeset
|
539 "id": 11, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
diff
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|
540 "input_connections": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
541 "input1": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
542 "id": 3, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
543 "output_name": "output" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
544 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
545 "input2": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
546 "id": 10, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
547 "output_name": "output1" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
548 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
|
549 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
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|
550 "inputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
551 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
|
552 "description": "runtime parameter for tool Coverage Sampler", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
|
553 "name": "input2" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
554 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
|
555 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
|
556 "description": "runtime parameter for tool Coverage Sampler", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
|
557 "name": "input1" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
558 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
559 ], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
560 "label": null, |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
561 "name": "Coverage Sampler", |
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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
562 "outputs": [ |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
563 { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
564 "name": "output1", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
565 "type": "tabular" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
566 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
567 ], |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
568 "position": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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changeset
|
569 "left": 1618.5, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
570 "top": 553 |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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|
571 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
|
572 "post_job_actions": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
573 "HideDatasetActionoutput1": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
574 "action_arguments": {}, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
575 "action_type": "HideDatasetAction", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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576 "output_name": "output1" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
577 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
578 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
579 "tool_errors": null, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
580 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
diff
changeset
|
581 "tool_shed_repository": { |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
582 "changeset_revision": "72901052a829", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
583 "name": "coverage_sampler", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
584 "owner": "chrisd", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
diff
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|
585 "tool_shed": "toolshed.g2.bx.psu.edu" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
586 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
587 "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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changeset
|
588 "tool_version": "0.1.0", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
589 "type": "tool", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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|
590 "uuid": "a79d4e7c-dc9c-45fc-bc5f-e07c8289dc6c", |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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|
591 "workflow_outputs": [] |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
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|
592 } |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff
changeset
|
593 }, |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
diff
changeset
|
594 "uuid": "882a41f1-f16c-4e06-a19b-21a5ffc1fd36" |
04f9c20fecf8
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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|
595 } |