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1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.7">
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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 <requirements>
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6 <requirement type="package" version="0.23.0">pandas</requirement>
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7 <requirement type="package" version="1.1.0">scipy</requirement>
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8 <requirement type="package" version="0.10.1">cobra</requirement>
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9 <requirement type="package" version="4.2.1">lxml</requirement>
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10 <requirement type="package" version="0.8.1">svglib</requirement>
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11 <requirement type="package" version="3.4.0">reportlab</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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15 python $__tool_directory__/marea.py
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16
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17 --tool_dir $__tool_directory__
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18 --option $cond.type_selector
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19 --out_log $log
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20
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21 #if $cond.type_selector == 'datasets':
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22 --input_datas
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23 #for $data in $cond.input_Datasets:
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24 ${data.input}
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25 #end for
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26 --names
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27 #for $data in $cond.input_Datasets:
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28 ${data.input_name}
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29 #end for
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30 --comparison ${cond.comparis.comparison}
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31 #if $cond.comparis.comparison == 'onevsmany'
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32 --control '${cond.comparis.controlgroup}'
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33 #end if
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34
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35 #if $cond.advanced.choice == 'true':
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36 #if $cond.advanced.cond_map.cond_map_choice == 'true':
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37 --custom_rules true
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38 --custom_map ${cond.advanced.cond_map.custom_map}
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39 #end if
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40 --pValue ${cond.advanced.pValue}
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41 --fChange ${cond.advanced.fChange}
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42 --generate_svg ${cond.advanced.generateSvg}
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43 --generate_pdf ${cond.advanced.generatePdf}
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44 #else
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45 --pValue 0.05
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46 --fChange 1.5
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47 --generate_svg false
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48 --generate_pdf true
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49 #end if
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50 #elif $cond.type_selector == 'dataset_class':
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51 --input_data ${input_data}
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52 --input_class ${input_class}
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53 --comparison ${cond.comparis.comparison}
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54 #if $cond.comparis.comparison == 'onevsmany'
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55 --control '${cond.comparis.controlgroup}'
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56 #end if
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57 #if $cond.advanced.choice == 'true':
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58 #if $cond.advanced.cond_map.cond_map_choice == 'true':
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59 --custom_rules true
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60 --custom_map ${cond.advanced.cond_map.custom_map}
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61 #end if
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62 --pValue ${cond.advanced.pValue}
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63 --fChange ${cond.advanced.fChange}
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64 --generate_svg ${cond.advanced.generateSvg}
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65 --generate_pdf ${cond.advanced.generatePdf}
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66 #else
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67 --pValue 0.05
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68 --fChange 1.5
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69 --generate_svg false
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70 --generate_pdf true
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71 #end if
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72 #end if
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73 ]]>
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74 </command>
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75 <inputs>
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76 <conditional name="cond">
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77 <param name="type_selector" argument="--option" type="select" label="Input format:">
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78 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
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79 <option value="dataset_class">RAS of all samples + sample group specification</option>
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80 </param>
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81 <when value="datasets">
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82 <repeat name="input_Datasets" title="RAS dataset" min="2">
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83 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
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84 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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85 </repeat>
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86 <conditional name="comparis">
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87 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
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88 <option value="manyvsmany" selected="true">One vs One</option>
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89 <option value="onevsrest">One vs All</option>
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90 <option value="onevsmany">One vs Control</option>
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91 </param>
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92 <when value="onevsmany">
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93 <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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94 </when>
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95 </conditional>
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96 <conditional name="advanced">
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97 <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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98 <option value="true" selected="true">No</option>
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99 <option value="false">Yes</option>
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100 </param>
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101 <when value="false"></when>
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102 <when value="true">
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103 <conditional name="cond_map">
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104 <param name="cond_map_choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
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105 <option value="false" selected="true">No</option>
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106 <option value="true">Yes</option>
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107 </param>
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108 <when value="true">
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109 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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110 </when>
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111 </conditional>
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112 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
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113 <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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114 <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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115 <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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116 </when>
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117 </conditional>
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118 </when>
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119 <when value="dataset_class">
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120 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
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121 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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122 <conditional name="comparis">
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123 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
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124 <option value="manyvsmany" selected="true">One vs One</option>
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125 <option value="onevsrest">One vs All</option>
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126 <option value="onevsmany">One vs Control</option>
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127 </param>
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128 <when value="onevsmany">
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129 <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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130 </when>
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131 </conditional>
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132 <conditional name="advanced">
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133 <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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134 <option value="true" selected="true">No</option>
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135 <option value="false">Yes</option>
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136 </param>
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137 <when value="false"></when>
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138 <when value="true">
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139 <conditional name="cond_map">
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140 <param name="cond_map_choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
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141 <option value="false" selected="true">No</option>
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142 <option value="true">Yes</option>
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143 </param>
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144 <when value="true">
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145 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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146 </when>
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147 </conditional>
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148 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
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149 <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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150 <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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151 <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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152 </when>
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153 </conditional>
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154 </when>
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155 </conditional>
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156 </inputs>
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157 <outputs>
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158 <data format="txt" name="log" label="MaREA - Log" />
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159 <collection name="results" type="list" label="MaREA - Results">
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160 <discover_datasets pattern="__name_and_ext__" directory="result"/>
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161 </collection>
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162 </outputs>
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163 <help>
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164 <![CDATA[
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165
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166 What it does
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167 -------------
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168
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169 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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170
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171 Accepted files are:
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172 - 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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173 - option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
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174
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175 RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
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176
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177 Column header: sample ID.
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178 Raw header: reaction ID.
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179
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180 Optional files:
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181 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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182
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183 The tool generates:
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184 - 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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185 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
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186 - 3) a log file (.txt).
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187
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188 Output options:
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189 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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190
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191 Alternative options are:
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192 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
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193 - 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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194
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195 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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196
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197 Example input
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198 -------------
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199
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200 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
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201
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202 RAS Dataset 1:
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203
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204 +------------+----------------+----------------+----------------+
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205 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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206 +============+================+================+================+
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207 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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208 +------------+----------------+----------------+----------------+
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209 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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210 +------------+----------------+----------------+----------------+
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211 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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212 +------------+----------------+----------------+----------------+
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213 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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214 +------------+----------------+----------------+----------------+
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215 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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216 +------------+----------------+----------------+----------------+
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217
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218 RAS Dataset 2:
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219
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220 +------------+----------------+----------------+----------------+
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221 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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222 +============+================+================+================+
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223 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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224 +------------+----------------+----------------+----------------+
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225 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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226 +------------+----------------+----------------+----------------+
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227 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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228 +------------+----------------+----------------+----------------+
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229 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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230 +------------+----------------+----------------+----------------+
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231 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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232 +------------+----------------+----------------+----------------+
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233
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234 "RAS of all samples + sample group specification" option:
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235
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236 RAS Dataset:
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237
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238 +------------+----------------+----------------+----------------+
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239 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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240 +============+================+================+================+
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241 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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242 +------------+----------------+----------------+----------------+
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243 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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244 +------------+----------------+----------------+----------------+
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245 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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246 +------------+----------------+----------------+----------------+
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247 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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248 +------------+----------------+----------------+----------------+
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249 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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250 +------------+----------------+----------------+----------------+
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251
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252 Group-file
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253
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254 +---------------+-----------+
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255 | Patient ID | Class |
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256 +===============+===========+
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257 | TCGAAA3529 | MSI |
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258 +---------------+-----------+
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259 | TCGAA62671 | MSS |
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260 +---------------+-----------+
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261 | TCGAA62672 | MSI |
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262 +---------------+-----------+
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263
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264 Advanced options
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265 ----------------
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266
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267 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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268
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269 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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270
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271
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272 .. class:: infomark
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273
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274 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
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275
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276 .. class:: infomark
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277
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278 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
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279
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280 .. class:: infomark
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281
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282 **TIP**: This tool using the RAS scores computed by `Ras tool`_.
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283
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284 @REFERENCE@
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285
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286 .. _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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287 .. _Convert delimiters to TAB: http://bimib.disco.unimib.it:5555/?tool_id=Convert+characters1&version=1.0.0&__identifer=76g7trea4j6
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288 .. _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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289
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290 ]]>
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291 </help>
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292 <expand macro="citations" />
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293 </tool>
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294
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