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1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="2.0.0">
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2 <macros>
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3 <import>marea_macros.xml</import>
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4 </macros>
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5
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6 <requirements>
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7 <requirement type="package" version="1.24.4">numpy</requirement>
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8 <requirement type="package" version="2.0.3">pandas</requirement>
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9 <requirement type="package" version="5.2.2">lxml</requirement>
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10 <requirement type="package" version="1.10.1">scipy</requirement>
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11 <requirement type="package" version="1.5.1">svglib</requirement>
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12 <requirement type="package" version="2.2.3">pyvips</requirement>
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13 <requirement type="package" version="2.7.1">cairosvg</requirement>
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14 <requirement type="package" version="0.29.0">cobra</requirement>
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15 </requirements>
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16
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17 <command detect_errors="exit_code">
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18 <![CDATA[
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19 python $__tool_directory__/marea.py
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20
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21 --tool_dir $__tool_directory__
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22 --option $cond.type_selector
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23 --out_log $log
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24
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25 #if $cond.type_selector == 'datasets':
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26
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27 --using_RAS $cond.using_ras.check
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28 --using_RPS $cond.using_rps.check
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29
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30 #if $cond.using_ras.check == 'true':
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31 --input_datas
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32 #for $data in $cond.using_ras.input_datasets:
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33 ${data.input}
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34 #end for
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35
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36 --names
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37 #for $data in $cond.using_ras.input_datasets:
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38 ${data.input_name}
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39 #end for
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40 #end if
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41
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42 #if $cond.using_rps.check == 'true':
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43 --input_datas_rps
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44 #for $data in $cond.using_rps.input_datasets_rps:
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45 ${data.input_rps}
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46 #end for
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47
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48 --names_rps
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49 #for $data in $cond.using_rps.input_datasets_rps:
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50 ${data.input_name_rps}
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51 #end for
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52 #end if
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53
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54 #elif $cond.type_selector == 'dataset_class':
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55
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56 --using_RAS $cond.using_ras_all.check
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57 --using_RPS $cond.using_rps_all.check
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58
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59 #if $cond.using_ras_all.check == 'true':
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60 --input_data ${cond.using_ras_all.input_data}
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61 --input_class ${cond.using_ras_all.input_class}
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62 #end if
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63
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64 #if $cond.using_rps_all.check == 'true':
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65 --input_data_rps ${cond.using_rps_all.input_data_rps}
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66 --input_class_rps ${cond.using_rps_all.input_class_rps}
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67 #end if
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68 #end if
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69
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70 --comparison ${comparis.comparison}
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71 #if $comparis.comparison == 'onevsmany'
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72 --control '${cond.comparis.controlgroup}'
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73 #end if
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74
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75 --choice_map '${cond_choice_map.choice_map}'
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76 #if $cond_choice_map.choice_map == 'Custom':
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77 --custom_map ${cond_choice_map.custom_map}
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78 #end if
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79
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80 #if $advanced.choice == 'true':
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81 --pValue ${advanced.pValue}
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82 --fChange ${advanced.fChange}
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83 --generate_svg ${advanced.generateSvg}
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84 --generate_pdf ${advanced.generatePdf}
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85 --net ${advanced.netRPS}
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86 #else
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87 --pValue 0.05
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88 --fChange 1.2
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89 --generate_svg false
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90 --generate_pdf true
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91 --net false
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92 #end if
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93 ]]>
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94 </command>
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95
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96 <inputs>
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97 <conditional name="cond">
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98 <param name="type_selector" argument="--option" type="select" label="Input format:">
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99 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
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100 <option value="dataset_class">RAS of all samples + sample group specification</option>
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101 </param>
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102
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103 <when value="datasets">
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104 <conditional name = "using_ras">
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105 <param name = "check" argument = "--using_ras" type = "boolean" checked = "true" label = "Using RAS datasets." />
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106
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107 <when value = "true">
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108 <repeat name="input_datasets" title="RAS dataset" min="2">
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109 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
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110 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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111 </repeat>
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112 </when>
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113 </conditional>
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114
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115 <conditional name = "using_rps">
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116 <param name = "check" argument = "--using_rps" type = "boolean" checked = "false" label = "Using RPS datasets." />
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117
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118 <when value = "true">
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119 <repeat name="input_datasets_rps" title="RPS dataset" min="2">
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120 <param name="input_rps" argument="--input_datas_rps" type="data" format="tabular, csv, tsv" label="add dataset" />
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121 <param name="input_name_rps" argument="--names_rps" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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122 </repeat>
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123 </when>
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124 </conditional>
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125 </when>
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126
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127 <when value="dataset_class">
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128 <conditional name = "using_ras_all">
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129 <param name = "check" argument = "--using_ras_all" type = "boolean" checked = "true" label = "Using RAS datasets." />
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130
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131 <when value = "true">
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132 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
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133 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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134 </when>
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135 </conditional>
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136
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137 <conditional name = "using_rps_all">
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138 <param name = "check" argument = "--using_rps_all" type = "boolean" checked = "false" label = "Using RPS datasets." />
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139
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140 <when value = "true">
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141 <param name="input_data_rps" argument="--input_data_rps" type="data" format="tabular, csv, tsv" label="RPS of all samples" />
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142 <param name="input_class_rps" argument="--input_class_rps" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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143 </when>
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144 </conditional>
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145 </when>
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146 </conditional>
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147
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148 <conditional name="comparis">
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149 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
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150 <option value="manyvsmany" selected="true">One vs One</option>
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151 <option value="onevsrest">One vs All</option>
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152 <option value="onevsmany">One vs Control</option>
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153 </param>
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154 <when value="onevsmany">
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155 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
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156 </when>
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157 </conditional>
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158
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159 <conditional name="cond_choice_map">
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160 <param name="choice_map" argument="--choice_map" type="select" label="Choose metabolic map:">
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161 <option value="HMRcore" selected="true">HMRcore</option>
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162 <option value="ENGRO2">ENGRO2</option>
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163 <option value="Custom">Custom</option>
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164 </param>
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165
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166 <when value="Custom">
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167 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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168 </when>
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169 </conditional>
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170
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171 <conditional name="advanced">
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172 <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
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173 <option value="true" selected="true">No</option>
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174 <option value="false">Yes</option>
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175 </param>
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176
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177 <when value="true">
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178 <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" />
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179 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
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180 <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
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181 <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />
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182
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183 <param name="netRPS" argument="--net" type="boolean" checked="false" label="Should RPS enrichment use net values?" help="If checked and RPS datasets are present the arrow tips of a reversible arrow will be colored with the net contribution of both directions' RPS values" />
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184 </when>
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185 </conditional>
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186 </inputs>
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187
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188 <outputs>
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189 <data format="txt" name="log" label="MaREA - Log" />
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190 <collection name="results" type="list" label="MaREA - Results">
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191 <discover_datasets pattern="__name_and_ext__" directory="result"/>
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192 </collection>
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193 </outputs>
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194
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195 <help>
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196 <![CDATA[
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197
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198 What it does
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199 -------------
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200
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201 This tool analyzes and visualizes differences in the Reaction Activity Scores (RASs) of groups of samples, as computed by the Expression2RAS tool, of groups of samples.
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202
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203 Accepted files are:
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204 - option 1) two or more RAS datasets, each referring to samples in a given group. The user can specify a label for each group (as e.g. "classA" and "classB");
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205 - option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
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206
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207 RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
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208
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209 Column header: sample ID.
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210 Row header: reaction ID.
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211
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212 Optional files:
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213 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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214
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215 The tool generates:
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216 - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
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217 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
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218 - 3) a log file (.txt).
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219
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220 Output options:
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221 To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’).
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222
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223 Alternative options are:
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224 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
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225 - comparison of each group vs. a control group (option ‘One vs Control). If this option is selected the user must indicate the control group label.
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226
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227 Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA".
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228
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229 Example input
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230 -------------
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231
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232 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
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233
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234 RAS Dataset 1:
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235
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236 +------------+----------------+----------------+----------------+
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237 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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238 +============+================+================+================+
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239 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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240 +------------+----------------+----------------+----------------+
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241 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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242 +------------+----------------+----------------+----------------+
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243 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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244 +------------+----------------+----------------+----------------+
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245 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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246 +------------+----------------+----------------+----------------+
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247 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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248 +------------+----------------+----------------+----------------+
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249
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250 RAS Dataset 2:
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251
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252 +------------+----------------+----------------+----------------+
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253 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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254 +============+================+================+================+
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255 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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256 +------------+----------------+----------------+----------------+
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257 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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258 +------------+----------------+----------------+----------------+
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259 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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260 +------------+----------------+----------------+----------------+
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261 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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262 +------------+----------------+----------------+----------------+
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263 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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264 +------------+----------------+----------------+----------------+
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265
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266 "RAS of all samples + sample group specification" option:
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267
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268 RAS Dataset:
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269
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270 +------------+----------------+----------------+----------------+
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271 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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272 +============+================+================+================+
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273 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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274 +------------+----------------+----------------+----------------+
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275 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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276 +------------+----------------+----------------+----------------+
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277 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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278 +------------+----------------+----------------+----------------+
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279 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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280 +------------+----------------+----------------+----------------+
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281 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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282 +------------+----------------+----------------+----------------+
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283
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284 Group-file
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285
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286 +---------------+-----------+
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287 | Patient ID | Class |
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288 +===============+===========+
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289 | TCGAAA3529 | MSI |
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290 +---------------+-----------+
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291 | TCGAA62671 | MSS |
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292 +---------------+-----------+
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293 | TCGAA62672 | MSI |
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294 +---------------+-----------+
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295
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296 Advanced options
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297 ----------------
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298
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299 P-Value threshold: the threshold used for significance Kolmogorov-Smirnov (KS) test, to verify whether the distributions of RASs over the samples in two sets are significantly different
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300
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301 Fold-Change threshold: threshold of the fold-change between the average RAS of two groups. Among the reactions that pass the KS test, only fold-change values larger than the indicated threshold will be visualized on the output metabolic map;
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302
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303
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304 .. class:: infomark
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305
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306 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
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307
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308 .. class:: infomark
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309
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310 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
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311
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312 .. class:: infomark
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313
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314 **TIP**: This tool using the RAS scores computed by `Ras tool`_.
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315
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316 @REFERENCE@
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317
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318 .. _Ras tool: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA+RAS+Generator%2F1.0.6&version=1.0.6&__identifer=auulv6gbp76
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319 .. _Convert delimiters to TAB: http://bimib.disco.unimib.it:5555/?tool_id=Convert+characters1&version=1.0.0&__identifer=76g7trea4j6
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320 .. _MaREA cluster analysis: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA_cluester%2F1.1.2&version=1.1.2&__identifer=lxbyzn2me9
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321
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322 ]]>
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323 </help>
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324 <expand macro="citations" />
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325 </tool> |
