annotate amrplusplus_wf.ga @ 2:7550d3bc44a4 draft

planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 46308898745b6aed965f5ce7e4375cc422eba902
author chrisd
date Thu, 24 Mar 2016 04:52:42 -0400
parents 11cb57237849
children
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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1 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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2 "a_galaxy_workflow": "true",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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3 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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4 "format-version": "0.1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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5 "name": "amrplusplus_wf_pe",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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6 "steps": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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7 "0": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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8 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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10 "id": 0,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11 "input_connections": {},
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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12 "inputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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13 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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14 "description": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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15 "name": "Input Dataset"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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16 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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17 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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18 "label": "AMR Database",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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19 "name": "Input dataset",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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20 "outputs": [],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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21 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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24 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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27 "tool_state": "{\"name\": \"Input Dataset\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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28 "tool_version": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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29 "type": "data_input",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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31 "workflow_outputs": []
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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32 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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33 "1": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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34 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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37 "input_connections": {},
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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38 "inputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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39 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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40 "description": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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41 "name": "Input Dataset"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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42 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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43 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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44 "label": "Host Genome",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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45 "name": "Input dataset",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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46 "outputs": [],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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47 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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50 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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53 "tool_state": "{\"name\": \"Input Dataset\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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55 "type": "data_input",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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56 "uuid": "828c1738-4db6-4548-89b8-85e68a00491a",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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57 "workflow_outputs": []
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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58 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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59 "2": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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60 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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63 "input_connections": {},
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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64 "inputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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65 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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66 "description": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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67 "name": "Input Dataset"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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68 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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69 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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70 "label": "FastQ Forward",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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71 "name": "Input dataset",
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72 "outputs": [],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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73 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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74 "left": 200,
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75 "top": 370
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76 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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77 "tool_errors": null,
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78 "tool_id": null,
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79 "tool_state": "{\"name\": \"Input Dataset\"}",
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80 "tool_version": null,
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81 "type": "data_input",
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82 "uuid": "1956acf3-af87-497d-bced-1dc18003b4ee",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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83 "workflow_outputs": []
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84 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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85 "3": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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86 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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87 "content_id": null,
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88 "id": 3,
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89 "input_connections": {},
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90 "inputs": [
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91 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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92 "description": "",
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93 "name": "Input Dataset"
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94 }
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95 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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96 "label": "FastQ Reverse",
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97 "name": "Input dataset",
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98 "outputs": [],
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99 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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100 "left": 200,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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101 "top": 455
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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102 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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103 "tool_errors": null,
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104 "tool_id": null,
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105 "tool_state": "{\"name\": \"Input Dataset\"}",
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106 "tool_version": null,
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107 "type": "data_input",
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108 "uuid": "0e020fbd-697d-4ebc-bd3d-0b45d5104b44",
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109 "workflow_outputs": []
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110 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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111 "4": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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112 "annotation": "",
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113 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
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114 "id": 4,
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115 "input_connections": {
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116 "paired_end|paired_input_type_conditional|fastq_r1_in": {
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117 "id": 2,
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118 "output_name": "output"
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119 },
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120 "paired_end|paired_input_type_conditional|fastq_r2_in": {
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121 "id": 3,
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122 "output_name": "output"
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123 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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124 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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125 "inputs": [],
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126 "label": null,
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127 "name": "Trimmomatic",
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128 "outputs": [
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129 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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130 "name": "fastq_out_paired",
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131 "type": "input"
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132 },
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133 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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134 "name": "fastq_out_unpaired",
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135 "type": "input"
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136 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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137 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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138 "name": "fastq_out_r1_paired",
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139 "type": "fastqsanger"
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140 },
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141 {
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142 "name": "fastq_out_r2_paired",
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143 "type": "fastqsanger"
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144 },
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145 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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146 "name": "fastq_out_r1_unpaired",
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147 "type": "fastqsanger"
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148 },
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149 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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150 "name": "fastq_out_r2_unpaired",
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151 "type": "fastqsanger"
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152 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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153 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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154 "name": "fastq_out",
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155 "type": "fastqsanger"
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156 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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157 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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158 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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159 "left": 435,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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160 "top": 200
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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161 },
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162 "post_job_actions": {
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163 "DeleteIntermediatesActionfastq_out_paired": {
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164 "action_arguments": {},
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165 "action_type": "DeleteIntermediatesAction",
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166 "output_name": "fastq_out_paired"
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167 },
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168 "HideDatasetActionfastq_out": {
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169 "action_arguments": {},
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170 "action_type": "HideDatasetAction",
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171 "output_name": "fastq_out"
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172 },
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173 "HideDatasetActionfastq_out_paired": {
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174 "action_arguments": {},
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175 "action_type": "HideDatasetAction",
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176 "output_name": "fastq_out_paired"
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177 },
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178 "HideDatasetActionfastq_out_r1_unpaired": {
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179 "action_arguments": {},
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180 "action_type": "HideDatasetAction",
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181 "output_name": "fastq_out_r1_unpaired"
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182 },
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183 "HideDatasetActionfastq_out_r2_unpaired": {
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184 "action_arguments": {},
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185 "action_type": "HideDatasetAction",
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186 "output_name": "fastq_out_r2_unpaired"
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187 },
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188 "HideDatasetActionfastq_out_unpaired": {
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189 "action_arguments": {},
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190 "action_type": "HideDatasetAction",
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191 "output_name": "fastq_out_unpaired"
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192 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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193 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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194 "tool_errors": null,
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195 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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196 "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}\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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197 "tool_version": "0.32.3",
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198 "type": "tool",
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199 "uuid": "68fbd2ce-d667-4f34-a3e0-4381d93bfbaa",
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200 "workflow_outputs": [
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201 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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202 "label": null,
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203 "output_name": "fastq_out_r1_paired",
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204 "uuid": "59ce771e-1cad-486b-ab2e-3ed1c85a195c"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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205 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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206 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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207 "label": null,
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208 "output_name": "fastq_out_r2_paired",
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209 "uuid": "29696b1d-f675-4255-b902-f7ded1cf6fad"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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210 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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211 ]
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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212 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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213 "5": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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214 "annotation": "",
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215 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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216 "id": 5,
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217 "input_connections": {
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218 "input_type|fastq_input1": {
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219 "id": 4,
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220 "output_name": "fastq_out_r1_paired"
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221 },
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222 "input_type|fastq_input2": {
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223 "id": 4,
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224 "output_name": "fastq_out_r2_paired"
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225 },
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226 "reference_source|ref_file": {
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227 "id": 1,
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228 "output_name": "output"
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229 }
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230 },
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231 "inputs": [],
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232 "label": null,
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233 "name": "Map with BWA",
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234 "outputs": [
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235 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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236 "name": "bam_output",
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237 "type": "bam"
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238 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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239 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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240 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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241 "left": 763,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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242 "top": 200
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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243 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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244 "post_job_actions": {
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245 "DeleteIntermediatesActionbam_output": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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246 "action_arguments": {},
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247 "action_type": "DeleteIntermediatesAction",
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248 "output_name": "bam_output"
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249 }
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250 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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251 "tool_errors": null,
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252 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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253 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"adv_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}, \\\"fastq_input2\\\": null, \\\"input_type_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"__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\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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254 "tool_version": "0.7.12.1",
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255 "type": "tool",
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256 "uuid": "ddf4de24-ceec-4dd7-a4a2-cd91994b4346",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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257 "workflow_outputs": [
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258 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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259 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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260 "output_name": "bam_output",
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261 "uuid": "ad467c2c-4b48-4f06-9c68-ced14296afb8"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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262 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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263 ]
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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264 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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265 "6": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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266 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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267 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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268 "id": 6,
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269 "input_connections": {
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270 "inputFile": {
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271 "id": 5,
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272 "output_name": "bam_output"
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273 }
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274 },
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275 "inputs": [],
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276 "label": null,
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277 "name": "FilterSamReads",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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278 "outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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279 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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280 "name": "outFile",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
281 "type": "bam"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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282 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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283 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
284 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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285 "left": 1028,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
286 "top": 200
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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287 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
288 "post_job_actions": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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289 "DeleteIntermediatesActionoutFile": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
290 "action_arguments": {},
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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291 "action_type": "DeleteIntermediatesAction",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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292 "output_name": "outFile"
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293 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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294 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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295 "tool_errors": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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296 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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297 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"null\", \"filter_type\": \"{\\\"filter\\\": \\\"excludeAligned\\\", \\\"__current_case__\\\": 1}\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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298 "tool_version": "1.136.0",
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299 "type": "tool",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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300 "uuid": "bf824957-0907-4c1f-983d-f26a88826253",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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301 "workflow_outputs": [
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302 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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303 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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304 "output_name": "outFile",
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diff changeset
305 "uuid": "7aeb6a2f-a869-44df-bb2a-188e44036d1e"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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306 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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307 ]
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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308 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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309 "7": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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310 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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311 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
312 "id": 7,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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313 "input_connections": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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314 "input_type|bam_input": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
315 "id": 6,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
316 "output_name": "outFile"
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317 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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318 "reference_source|ref_file": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
319 "id": 0,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
320 "output_name": "output"
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321 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
322 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
323 "inputs": [],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
324 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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325 "name": "Map with BWA",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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326 "outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
327 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
328 "name": "bam_output",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
329 "type": "bam"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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330 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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331 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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332 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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333 "left": 1356,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
334 "top": 200
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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335 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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336 "post_job_actions": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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337 "DeleteIntermediatesActionbam_output": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
338 "action_arguments": {},
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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339 "action_type": "DeleteIntermediatesAction",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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340 "output_name": "bam_output"
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341 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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342 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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343 "tool_errors": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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344 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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345 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": null, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"__current_case__\\\": 3, \\\"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\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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346 "tool_version": "0.7.12.1",
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347 "type": "tool",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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348 "uuid": "9d1d2fe9-c3c6-4a34-a28d-50b2f7a06e11",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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349 "workflow_outputs": [
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350 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
351 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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352 "output_name": "bam_output",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
353 "uuid": "981cdac9-e993-471c-87c2-c667431ed47f"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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354 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
355 ]
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
356 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
357 "8": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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358 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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359 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
360 "id": 8,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
361 "input_connections": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
362 "inputFile": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
363 "id": 7,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
364 "output_name": "bam_output"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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365 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
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diff changeset
366 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
367 "inputs": [],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
368 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
369 "name": "SortSam",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
370 "outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
371 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
372 "name": "outFile",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
373 "type": "bam"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
374 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
375 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
376 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
377 "left": 1621,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
378 "top": 200
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
379 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
380 "post_job_actions": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
381 "DeleteIntermediatesActionoutFile": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
382 "action_arguments": {},
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
383 "action_type": "DeleteIntermediatesAction",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
384 "output_name": "outFile"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
385 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
386 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
387 "tool_errors": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
388 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
389 "tool_state": "{\"inputFile\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sort_order\": \"\\\"queryname\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
390 "tool_version": "1.136.1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
391 "type": "tool",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
392 "uuid": "42d32394-d968-4cb0-ae06-69e551a8d328",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
393 "workflow_outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
394 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
395 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
396 "output_name": "outFile",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
397 "uuid": "30ae35f3-4cda-4feb-bfbe-6005ea4dcd22"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
398 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
399 ]
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
400 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
401 "9": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
402 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
403 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
404 "id": 9,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
405 "input_connections": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
406 "input1": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
407 "id": 8,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
408 "output_name": "outFile"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
409 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
410 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
411 "inputs": [],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
412 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
413 "name": "BAM-to-SAM",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
414 "outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
415 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
416 "name": "output1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
417 "type": "sam"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
418 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
419 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
420 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
421 "left": 1949,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
422 "top": 200
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
423 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
424 "post_job_actions": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
425 "DeleteIntermediatesActionoutput1": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
426 "action_arguments": {},
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
427 "action_type": "DeleteIntermediatesAction",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
428 "output_name": "output1"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
429 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
430 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
431 "tool_errors": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
432 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
433 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"__page__\": 0}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
434 "tool_version": "2.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
435 "type": "tool",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
436 "uuid": "9fe23b03-b221-4007-a406-44b05be85066",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
437 "workflow_outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
438 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
439 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
440 "output_name": "output1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
441 "uuid": "c34f9ca8-8d2d-4d8a-bb24-c3a030ff45af"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
442 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
443 ]
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
444 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
445 "10": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
446 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
447 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
448 "id": 10,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
449 "input_connections": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
450 "input1": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
451 "id": 0,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
452 "output_name": "output"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
453 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
454 "input2": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
455 "id": 9,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
456 "output_name": "output1"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
457 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
458 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
459 "inputs": [],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
460 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
461 "name": "Coverage Sampler",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
462 "outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
463 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
464 "name": "output1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
465 "type": "tabular"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
466 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
467 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
468 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
469 "left": 2184,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
470 "top": 200
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
471 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
472 "post_job_actions": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
473 "RenameDatasetActionoutput1": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
474 "action_arguments": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
475 "newname": "Coverage Results"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
476 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
477 "action_type": "RenameDatasetAction",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
478 "output_name": "output1"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
479 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
480 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
481 "tool_errors": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
482 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
483 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
484 "tool_version": "0.1.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
485 "type": "tool",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
486 "uuid": "8305b84c-ceb2-41bb-9f07-4c7bedff5d0a",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
487 "workflow_outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
488 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
489 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
490 "output_name": "output1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
491 "uuid": "1db38476-e927-44aa-bac5-0ff46b81a2b7"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
492 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
493 ]
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
494 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
495 "11": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
496 "annotation": "",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
497 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
498 "id": 11,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
499 "input_connections": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
500 "input1": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
501 "id": 0,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
502 "output_name": "output"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
503 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
504 "sam_type|sampe_input2": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
505 "id": 9,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
506 "output_name": "output1"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
507 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
508 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
509 "inputs": [],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
510 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
511 "name": "Snip Finder",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
512 "outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
513 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
514 "name": "output1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
515 "type": "tabular"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
516 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
517 ],
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
518 "position": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
519 "left": 2184,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
520 "top": 341
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
521 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
522 "post_job_actions": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
523 "RenameDatasetActionoutput1": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
524 "action_arguments": {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
525 "newname": "Snip Results"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
526 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
527 "action_type": "RenameDatasetAction",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
528 "output_name": "output1"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
529 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
530 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
531 "tool_errors": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
532 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
533 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"False\\\", \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1, \\\"sampe_input2\\\": null}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
534 "tool_version": "0.1.0",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
535 "type": "tool",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
536 "uuid": "b7bac673-aed8-4abd-a873-f842b9497ac8",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
537 "workflow_outputs": [
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
538 {
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
539 "label": null,
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
540 "output_name": "output1",
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
541 "uuid": "fb7fbbba-05bd-4477-a0ee-8e51bcbeddd2"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
542 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
543 ]
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
544 }
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
545 },
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
546 "uuid": "6c6ee2ed-be38-4787-9a8e-5ab9a872a00e"
11cb57237849 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521
chrisd
parents:
diff changeset
547 }