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93
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1 <tool id="CustomDataGenerator" name="Custom Data Generator" version="2.0.0">
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2
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3 <macros>
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4 <import>marea_macros.xml</import>
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5 </macros>
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6
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385
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7 <requirements>
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93
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8 <requirement type="package" version="1.24.4">numpy</requirement>
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9 <requirement type="package" version="2.0.3">pandas</requirement>
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385
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10 <requirement type="package" version="0.29.0">cobra</requirement>
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93
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11 <requirement type="package" version="5.2.2">lxml</requirement>
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385
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12 </requirements>
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93
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13
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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385
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16 python $__tool_directory__/custom_data_generator.py
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354
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17 --tool_dir $__tool_directory__
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385
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18 --medium_selector $cond_model.medium_selector
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345
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19 #if $cond_model.model_selector == 'Custom_model'
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20 --input $cond_model.input
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21 --name $cond_model.name
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22 #else
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23 --model $cond_model.model_selector
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24 --name $cond_model.model_selector
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25 #end if
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385
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26 #if $cond_model.medium_selector == 'Custom'
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27 --medium $cond_model.medium
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345
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28 #end if
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93
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29 --out_log $log
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376
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30 --out_tabular $out_tabular
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93
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31 ]]>
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32 </command>
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33 <inputs>
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345
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34 <conditional name="cond_model">
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384
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35 <param name="model_selector" argument="--model_selector" type="select" label="Model:">
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36 <option value="HMRcore">HMRcore</option>
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37 <option value="Recon">Recon 2.2</option>
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38 <option value="ENGRO2" selected="true">ENGRO 2</option>
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39 <option value="Custom_model">Custom</option>
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40 </param>
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379
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41 <!-- ENGRO2 -->
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42 <when value="ENGRO2">
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43 <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" />
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44 <conditional name="medium_selector">
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382
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45 <expand macro="options_ras_to_bounds_medium"/>
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379
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46 <when value="Custom">
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47 <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
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48 </when>
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49 </conditional>
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50 </when>
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51
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52 <!-- Recon -->
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53 <when value="Recon">
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54 <param name="name" argument="--name" type="text" value="Recon" hidden="true" />
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55 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
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56 <option value="Default" selected="true">Default (Recon built-in medium)</option>
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57 <option value="Custom">Custom medium file</option>
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58 </param>
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59 <conditional name="medium_selector">
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60 <when value="Custom">
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61 <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
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62 </when>
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63 </conditional>
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64 </when>
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65
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66 <!-- HMRcore -->
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67 <when value="HMRcore">
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68 <param name="name" argument="--name" type="text" value="HMRcore" hidden="true" />
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69 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
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70 <option value="Default" selected="true">Default (HMRcore built-in medium)</option>
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71 <option value="Custom">Custom medium file</option>
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72 </param>
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73 <conditional name="medium_selector">
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74 <when value="Custom">
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75 <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
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76 </when>
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77 </conditional>
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78 </when>
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79
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80 <!-- Custom model -->
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345
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81 <when value="Custom_model">
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82 <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" />
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379
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83 <param name="name" argument="--name" type="text" label="Model's name:" value="CustomModel" />
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84 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
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85 <option value="Default" selected="true">Don't use a separate medium file (use model defaults)</option>
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86 <option value="Custom">Custom medium file (required)</option>
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87 </param>
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88 <conditional name="medium_selector">
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89 <when value="Custom">
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90 <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
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91 </when>
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92 </conditional>
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345
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93 </when>
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94 </conditional>
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95
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93
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96 </inputs>
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97
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98 <outputs>
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378
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99 <data name="log" format="txt" label="CustomDataGenerator - Log" />
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376
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100
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378
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101 <data name="out_tabular" format="tabular"
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376
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102 label="${cond_model.model_selector}_data_tabular"
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385
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103 optional="true"/>
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104 </outputs>
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105
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106 <help>
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107 <![CDATA[
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108 What it does
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109 -------------
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110
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111 This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format.
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112 Reactions and rules can be used as inputs for the RAS and RPS generator tools.
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113
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114 Accepted files:
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115 - A model: JSON, XML, MAT or YAML (.yml) file reporting reactions and rules contained in the model. Supported compressed formats: .zip, .gz and .bz2. Filename must follow the pattern: {model_name}.{extension}.[zip|gz|bz2]
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116
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117 Output:
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118 -------------
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119
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120 The tool generates:
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121 - rules: reporting the rules for each reaction in the custom model given. Format: csv (tab separated).
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122 - reactions: reporting the reactions in the custom model given. Format: csv (tab separated).
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123 - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv (tab separated).
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124 - medium composition: reporting the list of exchange/transport reactions. Format: csv (tab separated).
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125 - a log file (.txt).
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126 ]]>
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127 </help>
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128 <expand macro="citations" />
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129 </tool><tool id="CustomDataGenerator" name="Custom Data Generator" version="2.0.0">
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130
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131 <macros>
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132 <import>marea_macros.xml</import>
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133 </macros>
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134
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135 <requirements>
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136 <requirement type="package" version="1.24.4">numpy</requirement>
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137 <requirement type="package" version="2.0.3">pandas</requirement>
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138 <requirement type="package" version="0.29.0">cobra</requirement>
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139 <requirement type="package" version="5.2.2">lxml</requirement>
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140 </requirements>
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141
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142 <command detect_errors="exit_code">
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143 <![CDATA[
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144 python $__tool_directory__/custom_data_generator.py
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145 --tool_dir $__tool_directory__
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146 --medium_selector $cond_model.medium_selector
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147 #if $cond_model.model_selector == 'Custom_model'
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148 --input $cond_model.input
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149 --name $cond_model.name
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150 #else
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151 --model $cond_model.model_selector
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152 --name $cond_model.model_selector
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153 #end if
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154 #if $cond_model.medium_selector == 'Custom'
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155 --medium $cond_model.medium
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156 #end if
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157 --out_log $log
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158 --out_tabular $out_tabular
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159 ]]>
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160 </command>
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161 <inputs>
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162 <conditional name="cond_model">
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163 <param name="model_selector" argument="--model_selector" type="select" label="Model:">
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164 <option value="HMRcore">HMRcore</option>
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165 <option value="Recon">Recon 2.2</option>
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166 <option value="ENGRO2" selected="true">ENGRO 2</option>
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167 <option value="Custom_model">Custom</option>
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168 </param>
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169 <!-- ENGRO2 -->
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170 <when value="ENGRO2">
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171 <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" />
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172 <conditional name="medium_selector">
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173 <expand macro="options_ras_to_bounds_medium"/>
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174 <when value="Custom">
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175 <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
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176 </when>
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177 </conditional>
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178 </when>
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179
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180 <!-- Recon -->
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181 <when value="Recon">
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182 <param name="name" argument="--name" type="text" value="Recon" hidden="true" />
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183 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
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184 <option value="Default" selected="true">Default (Recon built-in medium)</option>
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185 <option value="Custom">Custom medium file</option>
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186 </param>
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187 <conditional name="medium_selector">
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188 <when value="Custom">
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189 <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
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190 </when>
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191 </conditional>
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192 </when>
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193
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194 <!-- HMRcore -->
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195 <when value="HMRcore">
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196 <param name="name" argument="--name" type="text" value="HMRcore" hidden="true" />
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197 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
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198 <option value="Default" selected="true">Default (HMRcore built-in medium)</option>
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199 <option value="Custom">Custom medium file</option>
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200 </param>
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201 <conditional name="medium_selector">
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202 <when value="Custom">
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203 <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
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204 </when>
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205 </conditional>
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206 </when>
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207
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208 <!-- Custom model -->
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209 <when value="Custom_model">
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210 <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" />
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211 <param name="name" argument="--name" type="text" label="Model's name:" value="CustomModel" />
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212 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
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213 <option value="Default" selected="true">Don't use a separate medium file (use model defaults)</option>
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214 <option value="Custom">Custom medium file (required)</option>
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215 </param>
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216 <conditional name="medium_selector">
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217 <when value="Custom">
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218 <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
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219 </when>
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220 </conditional>
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221 </when>
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222 </conditional>
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223
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224 </inputs>
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225
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226 <outputs>
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227 <data name="log" format="txt" label="CustomDataGenerator - Log" />
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228
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229 <data name="out_tabular" format="tabular"
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230 label="${cond_model.model_selector}_data_tabular"
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231 optional="true"/>
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232 </outputs>
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362
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233
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93
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234 <help>
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235 <![CDATA[
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236 What it does
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237 -------------
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238
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239 This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format.
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240 Reactions and rules can be used as inputs for the RAS and RPS generator tools.
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241
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242 Accepted files:
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381
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243 - A model: JSON, XML, MAT or YAML (.yml) file reporting reactions and rules contained in the model. Supported compressed formats: .zip, .gz and .bz2. Filename must follow the pattern: {model_name}.{extension}.[zip|gz|bz2]
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93
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244
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245 Output:
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246 -------------
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247
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248 The tool generates:
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249 - rules: reporting the rules for each reaction in the custom model given. Format: csv (tab separated).
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250 - reactions: reporting the reactions in the custom model given. Format: csv (tab separated).
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251 - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv (tab separated).
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252 - medium composition: reporting the list of exchange/transport reactions. Format: csv (tab separated).
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253 - a log file (.txt).
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254 ]]>
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255 </help>
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256 <expand macro="citations" />
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257 </tool> |
