Mercurial > repos > chrisd > amrplusplus_workflow

annotate amrplusplus_workflow.ga @ 7:0b7210ad9187 draft

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
author chrisd
date Sat, 25 Jun 2016 17:17:42 -0400
parents 86dc721b6860
children 0eae27b15aa0
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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
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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
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3 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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4 "format-version": "0.1",
6
86dc721b6860 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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5 "name": "amrplusplus workflow",
5
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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6 "steps": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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7 "0": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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8 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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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
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10 "id": 0,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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11 "input_connections": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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12 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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13 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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14 "description": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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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
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16 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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17 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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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
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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
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20 "outputs": [],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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21 "position": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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22 "left": 252,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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23 "top": 323
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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24 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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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
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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
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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
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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
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29 "type": "data_input",
7
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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30 "uuid": "f1e841db-6f7a-4f32-bd87-8d0d934c4cc1",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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31 "workflow_outputs": [
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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32 {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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33 "label": null,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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34 "output_name": "output",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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35 "uuid": "ad47f164-7e7a-4d22-a967-551b2378427a"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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36 }
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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37 ]
5
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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38 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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39 "1": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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40 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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41 "content_id": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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42 "id": 1,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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43 "input_connections": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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44 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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45 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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46 "description": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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47 "name": "FASTQ Reverse"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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48 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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49 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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50 "label": "FASTQ Reverse",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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51 "name": "Input dataset",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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52 "outputs": [],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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53 "position": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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54 "left": 251,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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55 "top": 399
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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56 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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57 "tool_errors": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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58 "tool_id": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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59 "tool_state": "{\"name\": \"FASTQ Reverse\"}",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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60 "tool_version": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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61 "type": "data_input",
7
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62 "uuid": "a24ee7c0-b919-4426-8866-7d9939536e12",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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63 "workflow_outputs": [
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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64 {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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65 "label": null,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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66 "output_name": "output",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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67 "uuid": "edba093d-cdda-4530-916e-a566d94e2040"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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68 }
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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69 ]
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70 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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71 "2": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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72 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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73 "content_id": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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74 "id": 2,
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75 "input_connections": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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76 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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77 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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78 "description": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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79 "name": "Host Genome"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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80 }
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81 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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82 "label": "Host Genome",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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83 "name": "Input dataset",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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84 "outputs": [],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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88 },
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91 "tool_state": "{\"name\": \"Host Genome\"}",
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92 "tool_version": null,
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93 "type": "data_input",
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94 "uuid": "96c8f450-cb64-4641-884a-c1dabceeff5d",
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95 "workflow_outputs": [
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96 {
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97 "label": null,
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98 "output_name": "output",
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100 }
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101 ]
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102 },
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104 "annotation": "",
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106 "id": 3,
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107 "input_connections": {},
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108 "inputs": [
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109 {
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110 "description": "",
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111 "name": "AMR Database"
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112 }
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113 ],
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114 "label": "AMR Database",
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115 "name": "Input dataset",
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116 "outputs": [],
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117 "position": {
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118 "left": 1086,
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119 "top": 560
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120 },
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121 "tool_errors": null,
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122 "tool_id": null,
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123 "tool_state": "{\"name\": \"AMR Database\"}",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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124 "tool_version": null,
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125 "type": "data_input",
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126 "uuid": "2615ede9-3d0a-422b-b04d-829157475d47",
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127 "workflow_outputs": [
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128 {
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129 "label": null,
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130 "output_name": "output",
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131 "uuid": "32fcc9ba-8864-4fa7-a337-917a9612844a"
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132 }
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133 ]
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134 },
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135 "4": {
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136 "annotation": "",
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137 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
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138 "id": 4,
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139 "input_connections": {
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140 "paired_end|paired_input_type_conditional|fastq_r1_in": {
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141 "id": 0,
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142 "output_name": "output"
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143 },
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144 "paired_end|paired_input_type_conditional|fastq_r2_in": {
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145 "id": 1,
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146 "output_name": "output"
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147 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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148 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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149 "inputs": [],
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150 "label": null,
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151 "name": "Trimmomatic",
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152 "outputs": [
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153 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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154 "name": "fastq_out_paired",
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155 "type": "input"
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156 },
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157 {
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158 "name": "fastq_out_unpaired",
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159 "type": "input"
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160 },
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161 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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162 "name": "fastq_out_r1_paired",
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163 "type": "fastqsanger"
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164 },
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165 {
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166 "name": "fastq_out_r2_paired",
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167 "type": "fastqsanger"
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168 },
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169 {
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170 "name": "fastq_out_r1_unpaired",
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171 "type": "fastqsanger"
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172 },
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173 {
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174 "name": "fastq_out_r2_unpaired",
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175 "type": "fastqsanger"
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176 },
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177 {
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178 "name": "fastq_out",
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179 "type": "fastqsanger"
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180 }
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181 ],
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182 "position": {
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183 "left": 465,
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184 "top": 303
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185 },
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186 "post_job_actions": {
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187 "HideDatasetActionfastq_out": {
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188 "action_arguments": {},
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189 "action_type": "HideDatasetAction",
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190 "output_name": "fastq_out"
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191 },
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192 "HideDatasetActionfastq_out_paired": {
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193 "action_arguments": {},
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194 "action_type": "HideDatasetAction",
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195 "output_name": "fastq_out_paired"
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196 },
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197 "HideDatasetActionfastq_out_r1_unpaired": {
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198 "action_arguments": {},
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199 "action_type": "HideDatasetAction",
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200 "output_name": "fastq_out_r1_unpaired"
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201 },
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202 "HideDatasetActionfastq_out_r2_unpaired": {
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203 "action_arguments": {},
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204 "action_type": "HideDatasetAction",
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205 "output_name": "fastq_out_r2_unpaired"
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206 },
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207 "HideDatasetActionfastq_out_unpaired": {
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208 "action_arguments": {},
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209 "action_type": "HideDatasetAction",
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210 "output_name": "fastq_out_unpaired"
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211 }
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212 },
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213 "tool_errors": null,
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214 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
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215 "tool_shed_repository": {
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216 "changeset_revision": "f8a9a5eaca8a",
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217 "name": "trimmomatic",
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218 "owner": "pjbriggs",
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219 "tool_shed": "toolshed.g2.bx.psu.edu"
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220 },
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221 "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}\"}",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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222 "tool_version": "0.32.3",
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223 "type": "tool",
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224 "uuid": "c943ae63-aa6c-4d42-9088-b08335b8b6c6",
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225 "workflow_outputs": [
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226 {
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227 "label": null,
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228 "output_name": "fastq_out_r1_paired",
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229 "uuid": "e5cb04a2-09b6-41e5-b93d-54c4c6c8e488"
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230 },
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231 {
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232 "label": null,
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233 "output_name": "fastq_out_r2_paired",
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234 "uuid": "ada191c5-9f20-4052-aa5e-03f73f9587ad"
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235 }
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236 ]
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237 },
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238 "5": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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239 "annotation": "",
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240 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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241 "id": 5,
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242 "input_connections": {
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243 "input_type|fastq_input1": {
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244 "id": 4,
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245 "output_name": "fastq_out_r1_paired"
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246 },
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247 "input_type|fastq_input2": {
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248 "id": 4,
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249 "output_name": "fastq_out_r2_paired"
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250 },
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251 "reference_source|ref_file": {
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252 "id": 2,
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253 "output_name": "output"
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254 }
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255 },
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256 "inputs": [
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257 {
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258 "description": "runtime parameter for tool Map with BWA",
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259 "name": "input_type"
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260 },
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262 "description": "runtime parameter for tool Map with BWA",
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263 "name": "input_type"
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264 },
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265 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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266 "description": "runtime parameter for tool Map with BWA",
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267 "name": "reference_source"
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268 }
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269 ],
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270 "label": null,
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271 "name": "Map with BWA",
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272 "outputs": [
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273 {
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274 "name": "bam_output",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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275 "type": "bam"
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276 }
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277 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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278 "position": {
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279 "left": 772.5,
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280 "top": 306
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281 },
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282 "post_job_actions": {},
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283 "tool_errors": null,
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284 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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285 "tool_shed_repository": {
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286 "changeset_revision": "546ada4a9f43",
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287 "name": "bwa",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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288 "owner": "devteam",
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289 "tool_shed": "toolshed.g2.bx.psu.edu"
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290 },
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291 "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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292 "tool_version": "0.7.12.1",
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293 "type": "tool",
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294 "uuid": "3c509fb7-aef9-4e6d-bbb7-f6099d71f15e",
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295 "workflow_outputs": [
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296 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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297 "label": null,
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298 "output_name": "bam_output",
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299 "uuid": "d7011177-89c7-48ac-928e-935c6eecf92d"
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300 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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301 ]
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302 },
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303 "6": {
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304 "annotation": "",
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305 "content_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1",
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306 "id": 6,
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307 "input_connections": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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308 "input": {
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309 "id": 5,
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310 "output_name": "bam_output"
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311 }
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312 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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313 "inputs": [
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314 {
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315 "description": "runtime parameter for tool Samtools flag_filter",
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316 "name": "input"
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317 }
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318 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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319 "label": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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320 "name": "Samtools flag_filter",
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321 "outputs": [
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322 {
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323 "name": "output",
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324 "type": "bam"
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325 }
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326 ],
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327 "position": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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328 "left": 1004.5,
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329 "top": 303
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330 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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331 "post_job_actions": {},
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332 "tool_errors": null,
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333 "tool_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1",
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334 "tool_shed_repository": {
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335 "changeset_revision": "97bb72be07f9",
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336 "name": "samtools_flag_filter_1_2",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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337 "owner": "brenninc",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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338 "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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339 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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340 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"bits\": \"[{\\\"__index__\\\": 0, \\\"flag\\\": \\\"0x0004\\\", \\\"state\\\": \\\"f\\\"}]\", \"__page__\": 0}",
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341 "tool_version": "0.1",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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342 "type": "tool",
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343 "uuid": "e31b4dcc-9623-4c50-8139-214e40fe29d0",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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344 "workflow_outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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345 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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346 "label": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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347 "output_name": "output",
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348 "uuid": "c9c36760-d2a9-4c05-808c-05a092260670"
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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349 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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350 ]
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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351 },
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diff changeset
352 "7": {
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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353 "annotation": "",
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354 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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diff changeset
355 "id": 7,
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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356 "input_connections": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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357 "input_type|bam_input": {
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358 "id": 6,
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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359 "output_name": "output"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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360 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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361 "reference_source|ref_file": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
362 "id": 3,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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363 "output_name": "output"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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364 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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365 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
366 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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367 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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368 "description": "runtime parameter for tool Map with BWA",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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369 "name": "input_type"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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370 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
371 {
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diff changeset
372 "description": "runtime parameter for tool Map with BWA",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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373 "name": "reference_source"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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374 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
375 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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376 "label": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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377 "name": "Map with BWA",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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378 "outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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379 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
380 "name": "bam_output",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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381 "type": "bam"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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382 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
383 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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384 "position": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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385 "left": 1279.5,
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386 "top": 305
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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387 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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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/bwa/bwa/0.7.12.1",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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391 "tool_shed_repository": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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392 "changeset_revision": "546ada4a9f43",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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393 "name": "bwa",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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394 "owner": "devteam",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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395 "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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396 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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397 "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\\\"}\"}",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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398 "tool_version": "0.7.12.1",
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399 "type": "tool",
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diff changeset
400 "uuid": "4dff04dd-4331-4390-a21d-64140a177ce4",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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401 "workflow_outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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402 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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403 "label": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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404 "output_name": "bam_output",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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diff changeset
405 "uuid": "341955c7-7ae9-4872-a52a-f6b2f298cba1"
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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406 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
407 ]
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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408 },
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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diff changeset
409 "8": {
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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410 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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411 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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diff changeset
412 "id": 8,
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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413 "input_connections": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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414 "input1": {
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diff changeset
415 "id": 7,
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
416 "output_name": "bam_output"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
417 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
418 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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419 "inputs": [
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chrisd
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diff changeset
420 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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421 "description": "runtime parameter for tool Sort",
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chrisd
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422 "name": "input1"
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423 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
424 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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425 "label": null,
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chrisd
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diff changeset
426 "name": "Sort",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
427 "outputs": [
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chrisd
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diff changeset
428 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
429 "name": "output1",
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chrisd
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diff changeset
430 "type": "bam"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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431 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
432 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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433 "position": {
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chrisd
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434 "left": 1506,
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chrisd
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435 "top": 306
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diff changeset
436 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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437 "post_job_actions": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
438 "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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diff changeset
439 "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
chrisd
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diff changeset
440 "tool_shed_repository": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
441 "changeset_revision": "a430da4f04cd",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
442 "name": "samtools_sort",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
443 "owner": "devteam",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
444 "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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diff changeset
445 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
446 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sort_mode\": \"\\\"-n\\\"\"}",
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diff changeset
447 "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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448 "type": "tool",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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diff changeset
449 "uuid": "97ca7254-d03b-4cf3-810c-7dbaa6f65e72",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
450 "workflow_outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
451 {
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chrisd
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diff changeset
452 "label": null,
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diff changeset
453 "output_name": "output1",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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diff changeset
454 "uuid": "7b4416a5-ff90-4d1a-83c3-24c44e77f640"
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455 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
456 ]
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
457 },
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
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diff changeset
458 "9": {
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
459 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
460 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",
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chrisd
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diff changeset
461 "id": 9,
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chrisd
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diff changeset
462 "input_connections": {
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chrisd
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diff changeset
463 "input1": {
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
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diff changeset
464 "id": 8,
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
465 "output_name": "output1"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
466 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
467 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
468 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
469 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
470 "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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diff changeset
471 "name": "input1"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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472 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
473 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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474 "label": null,
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chrisd
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diff changeset
475 "name": "BAM-to-SAM",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
476 "outputs": [
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chrisd
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diff changeset
477 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
478 "name": "output1",
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diff changeset
479 "type": "sam"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
480 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
481 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
482 "position": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
483 "left": 1507.5,
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chrisd
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diff changeset
484 "top": 433
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
485 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
486 "post_job_actions": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
487 "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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diff changeset
488 "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
chrisd
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diff changeset
489 "tool_shed_repository": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
490 "changeset_revision": "af7c50162f0b",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
491 "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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diff changeset
492 "owner": "devteam",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
493 "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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494 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
495 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}",
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diff changeset
496 "tool_version": "2.0",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
497 "type": "tool",
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diff changeset
498 "uuid": "5196c387-3fad-46dc-9e6f-63af7ffae562",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
499 "workflow_outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
500 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
501 "label": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
502 "output_name": "output1",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
503 "uuid": "a4536845-4aaa-4a65-bc1b-e235f762a742"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
504 }
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
505 ]
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
506 },
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
507 "10": {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
508 "annotation": "",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
509 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
510 "id": 10,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
511 "input_connections": {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
512 "input1": {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
513 "id": 3,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
514 "output_name": "output"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
515 },
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
516 "sam_type|sampe_input2": {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
517 "id": 9,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
518 "output_name": "output1"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
519 }
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
520 },
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
521 "inputs": [
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
522 {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
523 "description": "runtime parameter for tool Snip Finder",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
524 "name": "sam_type"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
525 },
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
526 {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
527 "description": "runtime parameter for tool Snip Finder",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
528 "name": "input1"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
529 }
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
530 ],
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
531 "label": null,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
532 "name": "Snip Finder",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
533 "outputs": [
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
534 {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
535 "name": "output1",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
536 "type": "tabular"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
537 }
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
538 ],
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
539 "position": {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
540 "left": 1368,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
541 "top": 551
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
542 },
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
543 "post_job_actions": {},
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
544 "tool_errors": null,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
545 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
546 "tool_shed_repository": {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
547 "changeset_revision": "d9be5a7e70f5",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
548 "name": "snipfinder",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
549 "owner": "chrisd",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
550 "tool_shed": "toolshed.g2.bx.psu.edu"
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
551 },
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
552 "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\\\"}\"}",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
553 "tool_version": "0.1.0",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
554 "type": "tool",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
555 "uuid": "3c0b1793-8625-4529-a406-6ffa822b38ab",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
556 "workflow_outputs": [
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
557 {
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
558 "label": null,
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
559 "output_name": "output1",
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
560 "uuid": "b58e3331-4b37-49d9-b311-1120ca9606e6"
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
561 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
562 ]
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
563 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
564 "11": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
565 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
566 "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
chrisd
parents:
diff changeset
567 "id": 11,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
568 "input_connections": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
569 "input1": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
570 "id": 3,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
571 "output_name": "output"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
572 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
573 "input2": {
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
parents: 6
diff changeset
574 "id": 9,
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
575 "output_name": "output1"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
576 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
577 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
578 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
579 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
580 "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:
diff changeset
581 "name": "input2"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
582 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
583 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
584 "description": "runtime parameter for tool Coverage Sampler",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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585 "name": "input1"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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586 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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587 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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588 "label": null,
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589 "name": "Coverage Sampler",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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590 "outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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591 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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592 "name": "output1",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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593 "type": "tabular"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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594 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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595 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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596 "position": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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597 "left": 1618.5,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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598 "top": 553
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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599 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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600 "post_job_actions": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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601 "HideDatasetActionoutput1": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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602 "action_arguments": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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603 "action_type": "HideDatasetAction",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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604 "output_name": "output1"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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605 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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606 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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607 "tool_errors": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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608 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
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609 "tool_shed_repository": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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610 "changeset_revision": "72901052a829",
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611 "name": "coverage_sampler",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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612 "owner": "chrisd",
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613 "tool_shed": "toolshed.g2.bx.psu.edu"
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614 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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615 "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
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616 "tool_version": "0.1.0",
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617 "type": "tool",
7
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618 "uuid": "0907193f-3458-40a1-b0ba-beac3998da62",
5
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619 "workflow_outputs": []
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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620 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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621 },
7
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parents: 6
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622 "uuid": "5f790d55-b08b-45e8-8471-005678ec4eef"
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623 }