Mercurial > repos > tduigou > basic_assembly_workflow

annotate BASIC_Assembly_Workflow.ga @ 0:7d42adefc60a draft default tip

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 15 Dec 2021 15:59:19 +0000
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "",
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4 "format-version": "0.1",
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5 "name": "BASIC_Assembly_Workflow",
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6 "steps": {
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7 "0": {
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8 "annotation": "",
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9 "content_id": null,
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10 "errors": null,
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11 "id": 0,
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12 "input_connections": {},
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13 "inputs": [
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14 {
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15 "description": "",
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16 "name": "SBML pathways"
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17 }
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18 ],
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19 "label": "SBML pathways",
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20 "name": "Input dataset",
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21 "outputs": [],
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22 "position": {
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23 "bottom": 335.8000030517578,
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24 "height": 61.80000305175781,
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25 "left": -118.5,
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26 "right": 81.5,
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27 "top": 274,
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28 "width": 200,
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31 },
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32 "tool_id": null,
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33 "tool_state": "{\"optional\": false}",
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34 "tool_version": null,
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35 "type": "data_input",
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36 "uuid": "274db529-8d38-4f2b-84ce-8bc14e5fc35e",
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37 "workflow_outputs": [
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38 {
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39 "label": null,
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40 "output_name": "output",
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41 "uuid": "0058aece-8f90-4470-ba24-ba9cf7a08fdc"
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42 }
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43 ]
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44 },
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45 "1": {
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46 "annotation": "",
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47 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.1.0",
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48 "errors": null,
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49 "id": 1,
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50 "input_connections": {
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51 "pathway": {
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52 "id": 0,
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53 "output_name": "output"
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54 }
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55 },
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56 "inputs": [],
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57 "label": null,
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58 "name": "Selenzyme",
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59 "outputs": [
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60 {
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61 "name": "uniprot_ids",
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62 "type": "xml"
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63 },
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64 {
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65 "name": "uniprot_ids_csv",
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66 "type": "csv"
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67 }
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68 ],
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69 "position": {
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70 "bottom": 464.6000061035156,
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71 "height": 123.60000610351562,
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72 "left": 117.5,
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73 "right": 317.5,
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74 "top": 341,
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75 "width": 200,
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76 "x": 117.5,
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77 "y": 341
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78 },
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79 "post_job_actions": {},
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80 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.1.0",
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81 "tool_shed_repository": {
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82 "changeset_revision": "481f7c35323d",
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83 "name": "selenzy",
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84 "owner": "tduigou",
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85 "tool_shed": "toolshed.g2.bx.psu.edu"
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86 },
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87 "tool_state": "{\"adv\": {\"nb_ids\": \"-1\", \"nb_targets\": \"500\", \"direction\": \"0.0\", \"NoMSA\": \"true\", \"taxonIDs\": \"83333\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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88 "tool_version": "0.1.0",
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89 "type": "tool",
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90 "uuid": "b8f4e97e-a3e1-4743-80bf-29b3bf2c41eb",
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91 "workflow_outputs": [
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92 {
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93 "label": "Uniprot IDs",
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94 "output_name": "uniprot_ids",
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95 "uuid": "93661860-776f-4cb8-baa7-eda965d2c194"
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96 },
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97 {
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98 "label": "Uniprot IDs",
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99 "output_name": "uniprot_ids_csv",
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100 "uuid": "a62113ab-6728-48d5-acb4-14bc2bc6795d"
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101 }
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102 ]
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103 },
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104 "2": {
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105 "annotation": "",
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106 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
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107 "errors": null,
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108 "id": 2,
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109 "input_connections": {
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110 "rpsbml_file": {
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111 "id": 1,
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112 "output_name": "uniprot_ids"
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113 }
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114 },
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115 "inputs": [
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116 {
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117 "description": "runtime parameter for tool BasicDesign",
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118 "name": "adv"
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119 },
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120 {
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121 "description": "runtime parameter for tool BasicDesign",
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122 "name": "rpsbml_file"
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123 }
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124 ],
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125 "label": null,
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126 "name": "BasicDesign",
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127 "outputs": [
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128 {
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129 "name": "sbol_dir",
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130 "type": "input"
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131 },
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132 {
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133 "name": "Constructs",
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134 "type": "csv"
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135 },
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136 {
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137 "name": "User parts plate",
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138 "type": "csv"
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139 },
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140 {
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141 "name": "Biolegio plate",
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142 "type": "csv"
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143 }
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144 ],
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145 "position": {
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146 "bottom": 583.8000030517578,
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147 "height": 214.8000030517578,
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148 "left": 386,
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149 "right": 586,
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150 "top": 369,
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151 "width": 200,
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152 "x": 386,
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153 "y": 369
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154 },
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155 "post_job_actions": {},
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156 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
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157 "tool_shed_repository": {
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158 "changeset_revision": "de9f53630349",
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159 "name": "rpbasicdesign",
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160 "owner": "tduigou",
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161 "tool_shed": "toolshed.g2.bx.psu.edu"
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162 },
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163 "tool_state": "{\"adv\": {\"parts_files\": {\"__class__\": \"RuntimeValue\"}, \"lms_id\": \"LMS\", \"lmp_id\": \"LMP\", \"cds_permutation\": \"true\"}, \"backbone_id\": \"BASIC_SEVA_37_CmR-p15A.1\", \"rpsbml_file\": {\"__class__\": \"RuntimeValue\"}, \"sample_size\": \"88\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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164 "tool_version": "0.3.4",
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165 "type": "tool",
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166 "uuid": "678a53d3-1241-4f82-8d40-3da99f2be890",
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167 "workflow_outputs": [
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168 {
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169 "label": null,
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170 "output_name": "Biolegio plate",
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171 "uuid": "a34be5bd-9da4-461c-bec5-1c4dc5a8c18f"
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172 },
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173 {
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174 "label": null,
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175 "output_name": "sbol_dir",
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176 "uuid": "469241a2-0ecb-42f5-bcea-53aca636bb46"
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177 },
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178 {
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179 "label": null,
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180 "output_name": "Constructs",
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181 "uuid": "8755e80f-1ebe-4210-b0df-8acf8218a62c"
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182 },
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183 {
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184 "label": null,
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185 "output_name": "User parts plate",
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186 "uuid": "ff9e10e0-bfd3-4d0f-98f1-87fd94771293"
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187 }
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188 ]
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189 },
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190 "3": {
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191 "annotation": "",
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192 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.0.0",
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193 "errors": null,
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194 "id": 3,
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195 "input_connections": {
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196 "construct_file": {
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197 "id": 2,
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198 "output_name": "Constructs"
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199 },
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200 "plate_files": [
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201 {
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202 "id": 2,
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203 "output_name": "User parts plate"
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204 },
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205 {
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206 "id": 2,
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207 "output_name": "Biolegio plate"
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208 }
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209 ]
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210 },
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211 "inputs": [
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212 {
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213 "description": "runtime parameter for tool DNA-Bot",
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214 "name": "adv"
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215 }
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216 ],
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217 "label": null,
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218 "name": "DNA-Bot",
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219 "outputs": [
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220 {
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221 "name": "dnabot_scripts",
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222 "type": "tar"
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223 }
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224 ],
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225 "position": {
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226 "bottom": 644.8000030517578,
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227 "height": 194.8000030517578,
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228 "left": 641.5,
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229 "right": 841.5,
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231 "width": 200,
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232 "x": 641.5,
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233 "y": 450
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234 },
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235 "post_job_actions": {},
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236 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.0.0",
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237 "tool_shed_repository": {
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238 "changeset_revision": "6d55c77a17ab",
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239 "name": "dnabot",
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240 "owner": "tduigou",
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241 "tool_shed": "toolshed.g2.bx.psu.edu"
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242 },
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243 "tool_state": "{\"adv\": {\"default_settings_file\": {\"__class__\": \"RuntimeValue\"}, \"etoh_well\": \"A11\", \"soc_column\": \"1\"}, \"construct_file\": {\"__class__\": \"ConnectedValue\"}, \"plate_files\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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244 "tool_version": "3.0.0",
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245 "type": "tool",
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246 "uuid": "d5a18d74-8189-48d7-83ca-a63f6f8e1d39",
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247 "workflow_outputs": [
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248 {
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249 "label": "DNA-Bot scripts",
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250 "output_name": "dnabot_scripts",
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251 "uuid": "e0eabfa3-2dbd-44bc-9471-f8589a1a1861"
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252 }
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253 ]
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254 }
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255 },
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256 "tags": [],
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257 "uuid": "64390e96-9d57-441a-81cf-7544414ea50c",
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258 "version": 4
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259 }