annotate Galaxy-Workflow-AmrPlusPlus_PE.ga @ 0:834c10340bce draft

planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
author chrisd
date Wed, 23 Mar 2016 21:49:48 -0400
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834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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1 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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2 "a_galaxy_workflow": "true",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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3 "annotation": "",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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4 "format-version": "0.1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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5 "name": "AmrPlusPlus_PE",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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6 "steps": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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7 "0": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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8 "annotation": "The genome to align non-host reads to",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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9 "content_id": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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10 "id": 0,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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11 "input_connections": {},
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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12 "inputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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13 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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14 "description": "The genome to align non-host reads to",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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15 "name": "AMR Database"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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16 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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17 ],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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18 "label": "AMR Database",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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19 "name": "Input dataset",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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20 "outputs": [],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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21 "position": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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22 "left": 391,
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23 "top": 200
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24 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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25 "tool_errors": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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26 "tool_id": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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27 "tool_state": "{\"name\": \"AMR Database\"}",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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28 "tool_version": null,
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29 "type": "data_input",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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30 "uuid": "66a5eb48-4b35-46cc-9b93-fd88d97d2218",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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31 "workflow_outputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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32 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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33 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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34 "output_name": "output",
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35 "uuid": "d30b93c8-aa9f-49eb-801f-5a02e68a876b"
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36 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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37 ]
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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38 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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39 "1": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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40 "annotation": "Genome used to filter reads on",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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41 "content_id": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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42 "id": 1,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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43 "input_connections": {},
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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44 "inputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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45 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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46 "description": "Genome used to filter reads on",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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47 "name": "Host Genome"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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48 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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49 ],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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50 "label": "Host Genome",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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51 "name": "Input dataset",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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52 "outputs": [],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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53 "position": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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54 "left": 391,
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55 "top": 285
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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56 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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57 "tool_errors": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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58 "tool_id": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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59 "tool_state": "{\"name\": \"Host Genome\"}",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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60 "tool_version": null,
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61 "type": "data_input",
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62 "uuid": "02603c1f-b5f0-4121-9b57-005a98411364",
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63 "workflow_outputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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64 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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65 "label": null,
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66 "output_name": "output",
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67 "uuid": "6b4607b2-f4d8-4b24-ade6-30b2a6377017"
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68 }
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69 ]
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70 },
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71 "2": {
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72 "annotation": "Forward reads",
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73 "content_id": null,
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74 "id": 2,
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75 "input_connections": {},
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76 "inputs": [
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77 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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78 "description": "Forward reads",
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79 "name": "FastQ Forward"
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80 }
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81 ],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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82 "label": "FastQ Forward",
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83 "name": "Input dataset",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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84 "outputs": [],
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85 "position": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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86 "left": 391,
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87 "top": 370
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88 },
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89 "tool_errors": null,
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90 "tool_id": null,
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91 "tool_state": "{\"name\": \"FastQ Forward\"}",
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92 "tool_version": null,
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93 "type": "data_input",
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94 "uuid": "f25b69be-a40e-4d89-8535-84e2c3784148",
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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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99 "uuid": "cd11b688-012e-4d6e-bac7-a35c97057e8e"
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100 }
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101 ]
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102 },
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103 "3": {
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104 "annotation": "Reverse reads",
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105 "content_id": null,
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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": "Reverse reads",
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111 "name": "FastQ Reverse"
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112 }
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113 ],
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114 "label": "FastQ Reverse",
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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": 391,
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119 "top": 455
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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\": \"FastQ Reverse\"}",
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124 "tool_version": null,
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125 "type": "data_input",
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126 "uuid": "837dabbc-eec6-4490-8944-ab408d02631e",
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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": "3a4ab0ae-6842-42ce-b41c-0bc02f2f1ea5"
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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": "testtoolshed.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": 2,
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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": 3,
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146 "output_name": "output"
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147 }
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148 },
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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 {
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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 {
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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": 626,
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184 "top": 200
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185 },
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186 "post_job_actions": {
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187 "DeleteIntermediatesActionfastq_out_paired": {
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188 "action_arguments": {},
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189 "action_type": "DeleteIntermediatesAction",
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190 "output_name": "fastq_out_paired"
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191 },
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192 "HideDatasetActionfastq_out": {
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193 "action_arguments": {},
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194 "action_type": "HideDatasetAction",
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195 "output_name": "fastq_out"
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196 },
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197 "HideDatasetActionfastq_out_paired": {
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198 "action_arguments": {},
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199 "action_type": "HideDatasetAction",
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200 "output_name": "fastq_out_paired"
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201 },
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202 "HideDatasetActionfastq_out_r1_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_r1_unpaired"
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206 },
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207 "HideDatasetActionfastq_out_r2_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_r2_unpaired"
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211 },
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212 "HideDatasetActionfastq_out_unpaired": {
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213 "action_arguments": {},
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214 "action_type": "HideDatasetAction",
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215 "output_name": "fastq_out_unpaired"
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216 }
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217 },
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218 "tool_errors": null,
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219 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
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220 "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\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": null}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"False\\\", \\\"__current_case__\\\": 1}\"}",
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221 "tool_version": "0.32.3",
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222 "type": "tool",
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223 "uuid": "fd478986-09be-4758-9360-a4a345f1efc0",
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224 "workflow_outputs": [
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225 {
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226 "label": null,
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227 "output_name": "fastq_out_r1_paired",
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228 "uuid": "955d6928-ebc0-4dc9-be6c-f2f6f888ca45"
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229 },
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230 {
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231 "label": null,
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232 "output_name": "fastq_out_r2_paired",
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233 "uuid": "19e51c6f-b0b7-46d0-9885-a5701938f310"
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234 }
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235 ]
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236 },
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237 "5": {
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238 "annotation": "",
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239 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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240 "id": 5,
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241 "input_connections": {
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242 "input_type|fastq_input1": {
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243 "id": 4,
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244 "output_name": "fastq_out_r1_paired"
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245 },
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246 "input_type|fastq_input2": {
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247 "id": 4,
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248 "output_name": "fastq_out_r2_paired"
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249 },
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250 "reference_source|ref_file": {
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251 "id": 1,
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252 "output_name": "output"
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253 }
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254 },
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255 "inputs": [],
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256 "label": null,
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257 "name": "Map with BWA",
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258 "outputs": [
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259 {
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260 "name": "bam_output",
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261 "type": "bam"
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262 }
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263 ],
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264 "position": {
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267 },
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268 "post_job_actions": {},
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269 "tool_errors": null,
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270 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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272 "tool_version": "0.7.12.1",
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273 "type": "tool",
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274 "uuid": "6d53f77e-8f8a-4b9a-a674-8f7c55824260",
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275 "workflow_outputs": [
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276 {
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278 "output_name": "bam_output",
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279 "uuid": "efa12320-805e-4d96-aa50-2607b1952c6d"
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280 }
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281 ]
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282 },
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834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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284 "annotation": "",
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285 "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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286 "id": 6,
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287 "input_connections": {
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288 "inputFile": {
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289 "id": 5,
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290 "output_name": "bam_output"
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291 }
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292 },
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293 "inputs": [],
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294 "label": null,
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295 "name": "FilterSamReads",
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296 "outputs": [
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297 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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298 "name": "outFile",
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299 "type": "bam"
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300 }
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301 ],
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302 "position": {
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303 "left": 1282,
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304 "top": 200
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305 },
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306 "post_job_actions": {
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307 "DeleteIntermediatesActionoutFile": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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308 "action_arguments": {},
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309 "action_type": "DeleteIntermediatesAction",
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310 "output_name": "outFile"
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311 }
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312 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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313 "tool_errors": null,
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314 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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315 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"null\", \"filter_type\": \"{\\\"filter\\\": \\\"excludeAligned\\\", \\\"__current_case__\\\": 1}\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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316 "tool_version": "1.136.0",
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317 "type": "tool",
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318 "uuid": "031b872f-1554-4a3e-bd3d-bc7a00b009fe",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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319 "workflow_outputs": [
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320 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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321 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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322 "output_name": "outFile",
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323 "uuid": "c74b2b4e-517e-400c-acdf-4360e31e7289"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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324 }
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325 ]
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326 },
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327 "7": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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328 "annotation": "",
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329 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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330 "id": 7,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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331 "input_connections": {
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332 "input_type|bam_input": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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333 "id": 6,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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334 "output_name": "outFile"
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335 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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336 "reference_source|ref_file": {
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337 "id": 0,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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338 "output_name": "output"
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339 }
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340 },
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341 "inputs": [],
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342 "label": null,
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343 "name": "Map with BWA",
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344 "outputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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345 {
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346 "name": "bam_output",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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348 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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349 ],
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353 },
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chrisd
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354 "post_job_actions": {},
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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359 "type": "tool",
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chrisd
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361 "workflow_outputs": [
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362 {
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chrisd
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364 "output_name": "bam_output",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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366 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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367 ]
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368 },
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370 "annotation": "",
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chrisd
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373 "input_connections": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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374 "inputFile": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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chrisd
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376 "output_name": "bam_output"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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377 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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378 },
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chrisd
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diff changeset
379 "inputs": [],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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380 "label": null,
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chrisd
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381 "name": "SortSam",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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382 "outputs": [
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diff changeset
383 {
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chrisd
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384 "name": "outFile",
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385 "type": "bam"
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386 }
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diff changeset
387 ],
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chrisd
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388 "position": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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389 "left": 1938,
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390 "top": 200
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391 },
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chrisd
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392 "post_job_actions": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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393 "DeleteIntermediatesActionoutFile": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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394 "action_arguments": {},
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
395 "action_type": "DeleteIntermediatesAction",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
396 "output_name": "outFile"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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397 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
398 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
399 "tool_errors": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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400 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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401 "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"queryname\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",
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diff changeset
402 "tool_version": "1.136.1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
403 "type": "tool",
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chrisd
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404 "uuid": "efe328ad-11fa-4e3b-9c9f-6037c5ea4262",
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chrisd
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405 "workflow_outputs": [
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chrisd
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406 {
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chrisd
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diff changeset
407 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
408 "output_name": "outFile",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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409 "uuid": "5b0b2f60-116f-40ee-acf8-f5ddacfc4bc7"
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410 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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411 ]
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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412 },
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chrisd
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diff changeset
413 "9": {
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chrisd
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414 "annotation": "",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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415 "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
416 "id": 9,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
417 "input_connections": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
418 "input1": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
419 "id": 8,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
420 "output_name": "outFile"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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421 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
422 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
423 "inputs": [],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
424 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
425 "name": "BAM-to-SAM",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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426 "outputs": [
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chrisd
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427 {
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chrisd
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diff changeset
428 "name": "output1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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diff changeset
429 "type": "sam"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
430 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
431 ],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
432 "position": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
433 "left": 2266,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
434 "top": 200
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
435 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
436 "post_job_actions": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
437 "DeleteIntermediatesActionoutput1": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
438 "action_arguments": {},
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
439 "action_type": "DeleteIntermediatesAction",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
440 "output_name": "output1"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
441 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
442 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
443 "tool_errors": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
444 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
445 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
446 "tool_version": "2.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
447 "type": "tool",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
448 "uuid": "e4900e78-feb5-4cd6-9194-3131e227388e",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
449 "workflow_outputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
450 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
451 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
452 "output_name": "output1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
453 "uuid": "356bdab0-a907-4c07-a096-fab658a794ba"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
454 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
455 ]
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
456 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
457 "10": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
458 "annotation": "",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
459 "content_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
460 "id": 10,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
461 "input_connections": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
462 "input1": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
463 "id": 0,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
464 "output_name": "output"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
465 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
466 "sam_type|sampe_input2": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
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diff changeset
467 "id": 9,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
468 "output_name": "output1"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
469 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
470 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
471 "inputs": [],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
472 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
473 "name": "Snip Finder",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
474 "outputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
475 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
476 "name": "output1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
477 "type": "tabular"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
478 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
479 ],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
480 "position": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
481 "left": 2501,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
482 "top": 200
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
483 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
484 "post_job_actions": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
485 "RenameDatasetActionoutput1": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
486 "action_arguments": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
487 "newname": "Snip Results"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
488 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
489 "action_type": "RenameDatasetAction",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
490 "output_name": "output1"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
491 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
492 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
493 "tool_errors": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
494 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
495 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"False\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": null}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
496 "tool_version": "0.1.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
497 "type": "tool",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
498 "uuid": "197e5f9d-b4e5-449b-9b2d-67c939f34e32",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
499 "workflow_outputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
500 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
501 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
502 "output_name": "output1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
503 "uuid": "768cb726-399b-490e-82c1-8d523f7208ee"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
504 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
505 ]
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
506 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
507 "11": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
508 "annotation": "",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
509 "content_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
510 "id": 11,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
511 "input_connections": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
512 "input1": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
513 "id": 0,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
514 "output_name": "output"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
515 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
516 "input2": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
517 "id": 9,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
518 "output_name": "output1"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
519 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
520 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
521 "inputs": [],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
522 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
523 "name": "Coverage Sampler",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
524 "outputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
525 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
526 "name": "output1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
527 "type": "tabular"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
528 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
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529 ],
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
530 "position": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
531 "left": 2501,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
532 "top": 341
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
533 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
534 "post_job_actions": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
535 "RenameDatasetActionoutput1": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
536 "action_arguments": {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
537 "newname": "Coverage Results"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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parents:
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538 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
539 "action_type": "RenameDatasetAction",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
540 "output_name": "output1"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
541 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
542 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
543 "tool_errors": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
544 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
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545 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
546 "tool_version": "0.1.0",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
547 "type": "tool",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
548 "uuid": "8ffc98a9-82b8-429c-bd1d-fa4f24b22148",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
549 "workflow_outputs": [
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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parents:
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550 {
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
551 "label": null,
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
552 "output_name": "output1",
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
553 "uuid": "207d0359-f140-47bb-9e2c-4882e2697e82"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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554 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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parents:
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555 ]
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
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556 }
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
557 },
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
chrisd
parents:
diff changeset
558 "uuid": "c3b33138-479d-4709-9a3a-8ba49bb06673"
834c10340bce planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 4a836543109b7d5351b194e4cd3d59918086aacf-dirty
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559 }