Mercurial > repos > fubar > tool_factory_2
annotate toolfactory/sample_toolfactory_tools.ga @ 35:5d38cb3d9be8 draft
added patched galaxyxml code temporarily until PR accepted
author | fubar |
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date | Sat, 08 Aug 2020 19:55:55 -0400 |
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35
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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": "workflow to generate a bunch of sample toolfactory tools", |
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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": "rgToolFactory2.py" |
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17 } |
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18 ], |
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19 "label": "rgToolFactory2.py", |
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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": 235.25, |
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24 "height": 81, |
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25 "left": 711.84375, |
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26 "right": 911.84375, |
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27 "top": 154.25, |
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28 "width": 200, |
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29 "x": 711.84375, |
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30 "y": 154.25 |
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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": "b717b6ee-51d0-415d-876d-f19b42f67666", |
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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": "09acd6fd-4e2b-44a8-8757-35eca8d0de89" |
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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": null, |
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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 "inputs": [ |
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52 { |
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53 "description": "", |
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54 "name": "README.md" |
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55 } |
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56 ], |
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57 "label": "README.md", |
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58 "name": "Input dataset", |
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59 "outputs": [], |
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60 "position": { |
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61 "bottom": 760.25, |
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62 "height": 61, |
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63 "left": 711.84375, |
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64 "right": 911.84375, |
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65 "top": 699.25, |
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66 "width": 200, |
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67 "x": 711.84375, |
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68 "y": 699.25 |
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69 }, |
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70 "tool_id": null, |
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71 "tool_state": "{\"optional\": false}", |
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72 "tool_version": null, |
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73 "type": "data_input", |
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74 "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27", |
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75 "workflow_outputs": [ |
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76 { |
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77 "label": null, |
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78 "output_name": "output", |
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79 "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095" |
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80 } |
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81 ] |
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82 }, |
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83 "2": { |
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84 "annotation": "", |
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85 "content_id": null, |
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86 "errors": null, |
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87 "id": 2, |
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88 "input_connections": {}, |
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89 "inputs": [ |
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90 { |
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91 "description": "", |
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92 "name": "testtext" |
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93 } |
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94 ], |
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95 "label": "testtext", |
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96 "name": "Input dataset", |
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97 "outputs": [], |
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98 "position": { |
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99 "bottom": 235.25, |
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100 "height": 61, |
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101 "left": 989.84375, |
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102 "right": 1189.84375, |
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103 "top": 174.25, |
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104 "width": 200, |
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105 "x": 989.84375, |
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106 "y": 174.25 |
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107 }, |
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108 "tool_id": null, |
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109 "tool_state": "{\"optional\": false}", |
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110 "tool_version": null, |
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111 "type": "data_input", |
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112 "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9", |
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113 "workflow_outputs": [ |
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114 { |
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115 "label": null, |
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116 "output_name": "output", |
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117 "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa" |
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118 } |
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119 ] |
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120 }, |
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121 "3": { |
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122 "annotation": "", |
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123 "content_id": "rgTF2", |
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124 "errors": null, |
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125 "id": 3, |
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126 "input_connections": { |
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127 "ppass|history_inputs_0|input_files": { |
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128 "id": 1, |
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129 "output_name": "output" |
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130 } |
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131 }, |
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132 "inputs": [], |
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133 "label": null, |
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134 "name": "toolfactory", |
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135 "outputs": [ |
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136 { |
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137 "name": "ToolFactory_Outputs", |
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138 "type": "input" |
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139 }, |
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140 { |
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141 "name": "new_tool", |
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142 "type": "tgz" |
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143 } |
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144 ], |
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145 "position": { |
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146 "bottom": 636.25, |
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147 "height": 222, |
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148 "left": 989.84375, |
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149 "right": 1189.84375, |
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150 "top": 414.25, |
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151 "width": 200, |
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152 "x": 989.84375, |
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153 "y": 414.25 |
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154 }, |
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155 "post_job_actions": {}, |
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156 "tool_id": "rgTF2", |
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157 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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158 "tool_version": "2.00", |
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159 "type": "tool", |
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164 "output_name": "ToolFactory_Outputs", |
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169 "output_name": "new_tool", |
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174 "4": { |
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175 "annotation": "", |
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176 "content_id": "rgTF2", |
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177 "errors": null, |
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179 "input_connections": { |
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180 "ppass|history_inputs_0|input_files": { |
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181 "id": 1, |
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182 "output_name": "output" |
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183 } |
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184 }, |
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185 "inputs": [], |
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186 "label": null, |
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187 "name": "toolfactory", |
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188 "outputs": [ |
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189 { |
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190 "name": "ToolFactory_Outputs", |
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191 "type": "input" |
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192 }, |
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193 { |
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194 "name": "new_tool", |
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195 "type": "tgz" |
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196 } |
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197 ], |
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200 "height": 242, |
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201 "left": 989.84375, |
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202 "right": 1189.84375, |
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203 "top": 674.25, |
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204 "width": 200, |
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205 "x": 989.84375, |
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206 "y": 674.25 |
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207 }, |
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208 "post_job_actions": {}, |
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209 "tool_id": "rgTF2", |
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210 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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211 "tool_version": "2.00", |
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212 "type": "tool", |
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213 "uuid": "ea0f8bbe-6b0d-4aff-bf06-6192faf8fe22", |
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214 "workflow_outputs": [ |
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216 "label": null, |
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217 "output_name": "ToolFactory_Outputs", |
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218 "uuid": "70755c1b-6f92-43a3-aacb-8cc508a89b74" |
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221 "label": null, |
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222 "output_name": "new_tool", |
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223 "uuid": "ea9482d9-7836-442d-b753-ce4a201fd8c9" |
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224 } |
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227 "5": { |
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228 "annotation": "", |
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229 "content_id": "rgTF2", |
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230 "errors": null, |
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232 "input_connections": { |
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233 "ppass|history_inputs_0|input_files": { |
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234 "id": 1, |
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235 "output_name": "output" |
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237 }, |
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238 "inputs": [], |
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239 "label": null, |
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240 "name": "toolfactory", |
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241 "outputs": [ |
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242 { |
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243 "name": "ToolFactory_Outputs", |
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244 "type": "input" |
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245 }, |
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246 { |
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247 "name": "new_tool", |
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248 "type": "tgz" |
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249 } |
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250 ], |
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251 "position": { |
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252 "bottom": 1216.25, |
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253 "height": 262, |
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254 "left": 989.84375, |
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255 "right": 1189.84375, |
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256 "top": 954.25, |
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257 "width": 200, |
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258 "x": 989.84375, |
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259 "y": 954.25 |
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260 }, |
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261 "post_job_actions": {}, |
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262 "tool_id": "rgTF2", |
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263 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.outfile\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"reverse argparse\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"infile\", \"input_help\": \"parameter_help\", \"input_CL\": \"infile\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"outfile\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevargparse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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264 "tool_version": "2.00", |
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265 "type": "tool", |
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266 "uuid": "065b274a-ae73-43b0-b015-8b60d90db78f", |
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267 "workflow_outputs": [ |
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268 { |
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269 "label": null, |
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270 "output_name": "ToolFactory_Outputs", |
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271 "uuid": "bec62d2d-b462-49bb-9646-28fea9136778" |
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274 "label": null, |
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275 "output_name": "new_tool", |
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276 "uuid": "2e1ed464-bcff-4354-8bf3-ed01167b280f" |
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277 } |
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279 }, |
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280 "6": { |
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281 "annotation": "", |
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282 "content_id": "rgTF2", |
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283 "errors": null, |
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284 "id": 6, |
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285 "input_connections": { |
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317 "tool_version": "2.00", |
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368 "tool_id": "rgTF2", |
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369 "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"system\", \"__current_case__\": 1, \"exe_package\": \"sed\", \"exe_package_version\": \"\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"sed runner\", \"help_text\": \"sed '/old/new/g input.txt\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input text\", \"input_help\": \"parameter_help\", \"input_CL\": \"3\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"param_type\": \"text\", \"param_value\": \"s/Old/New/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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370 "tool_version": "2.00", |
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371 "type": "tool", |
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381 "output_name": "new_tool", |
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388 "content_id": "rgTF2", |
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391 "input_connections": { |
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392 "ppass|history_inputs_0|input_files": { |
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394 "output_name": "new_tool" |
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397 "inputs": [], |
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399 "name": "toolfactory", |
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400 "outputs": [ |
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401 { |
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402 "name": "ToolFactory_Outputs", |
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406 "name": "new_tool", |
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407 "type": "tgz" |
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419 }, |
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420 "post_job_actions": {}, |
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421 "tool_id": "rgTF2", |
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422 "tool_state": "{\"__input_ext\": \"tgz\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"your galaxy root to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\", \"param_CL\": \"galaxy_root\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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423 "tool_version": "2.00", |
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424 "type": "tool", |
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425 "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd", |
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426 "workflow_outputs": [ |
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427 { |
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428 "label": null, |
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429 "output_name": "ToolFactory_Outputs", |
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430 "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027" |
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431 }, |
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432 { |
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433 "label": null, |
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434 "output_name": "new_tool", |
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435 "uuid": "744499de-5d7e-4415-b427-315057c81ebc" |
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436 } |
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437 ] |
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438 } |
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439 }, |
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440 "tags": [], |
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441 "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b", |
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442 "version": 1 |
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443 } |