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1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.1">
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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.advanced.cond_map.cond_map_choice} == 'true':
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32 --custom_rules true
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33 --custom_map ${cond.advanced.cond_map.custom_map}
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34 #end if
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31
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35 #if $cond.advanced.choice == 'true':
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36 --pValue ${cond.advanced.pValue}
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37 --fChange ${cond.advanced.fChange}
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38 --generate_svg ${cond.advanced.generateSvg}
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39 --generate_pdf ${cond.advanced.generatePdf}
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40 #else
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41 --pValue 0.05
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42 --fChange 1.5
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43 --generate_svg false
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44 --generate_pdf true
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45 --generate_ras false
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46 #end if
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47 #elif $cond.type_selector == 'dataset_class':
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48 --input_data ${input_data}
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49 --input_class ${input_class}
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50 --comparison ${cond.comparis.comparison}
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51 #if $cond.comparis.comparison == 'onevsmany'
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52 --control ${cond.comparis.controlgroup}
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53 #end if
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54 #if $cond.advanced.cond_map.cond_map_choice == 'true':
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55 --custom_rules true
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56 --custom_map ${cond.advanced.cond_map.custom_map}
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57 #end if
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58 #if $cond.advanced.choice == 'true':
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59 --pValue ${cond.advanced.pValue}
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60 --fChange ${cond.advanced.fChange}
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61 --generate_svg ${cond.advanced.generateSvg}
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62 --generate_pdf ${cond.advanced.generatePdf}
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63 #else
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64 --pValue 0.05
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65 --fChange 1.5
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66 --generate_svg false
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67 --generate_pdf true
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68 #end if
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28
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69 #end if
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70 ]]>
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71 </command>
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72 <inputs>
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73 <conditional name="cond">
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74 <param name="type_selector" argument="--option" type="select" label="Input format:">
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75 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
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76 <option value="dataset_class">RAS of all samples + sample group specification</option>
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77 </param>
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78 <when value="datasets">
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79 <repeat name="input_Datasets" title="RAS dataset" min="2">
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80 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
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81 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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82 </repeat>
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83 <conditional name="comparis">
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84 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
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85 <option value="manyvsmany" selected="true">One vs One</option>
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86 <option value="onevsrest">One vs All</option>
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87 <option value="onevsmany">One vs Control</option>
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88 </param>
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89 <when value="onevsmany">
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90 <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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91 </when>
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92 </conditional>
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93 <conditional name="advanced">
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94 <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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95 <option value="true" selected="true">No</option>
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96 <option value="false">Yes</option>
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97 </param>
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98 <when value="false"></when>
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99 <when value="true">
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100 <conditional name="cond_map">
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101 <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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102 <option value="false" selected="true">No</option>
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103 <option value="true">Yes</option>
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104 </param>
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105 <when value="true">
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106 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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107 </when>
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108 </conditional>
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109 <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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110 <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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111 <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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112 <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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113 </when>
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114 </conditional>
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115 </when>
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116 <when value="dataset_class">
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117 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
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118 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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119 <conditional name="comparis">
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120 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
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121 <option value="manyvsmany" selected="true">One vs One</option>
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122 <option value="onevsrest">One vs All</option>
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123 <option value="onevsmany">One vs Control</option>
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124 </param>
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125 <when value="onevsmany">
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126 <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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127 </when>
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128 </conditional>
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129 <conditional name="advanced">
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130 <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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131 <option value="true" selected="true">No</option>
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132 <option value="false">Yes</option>
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133 </param>
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134 <when value="false"></when>
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135 <when value="true">
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136 <conditional name="cond_map">
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137 <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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138 <option value="false" selected="true">No</option>
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139 <option value="true">Yes</option>
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140 </param>
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141 <when value="true">
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142 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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143 </when>
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144 </conditional>
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145 <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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146 <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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147 <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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148 <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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149 </when>
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150 </conditional>
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151 </when>
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152 </conditional>
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153 </inputs>
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154 <outputs>
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155 <data format="txt" name="log" label="MaREA - Log" />
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156 <collection name="results" type="list" label="MaREA - Results">
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157 <discover_datasets pattern="__name_and_ext__" directory="result"/>
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158 </collection>
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159 </outputs>
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160 <help>
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161 <![CDATA[
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162
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163 What it does
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164 -------------
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165
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166 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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167
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168 Accepted files are:
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169 - 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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170 - option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
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171
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172 RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
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173
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174 Column header: sample ID.
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175 Raw header: reaction ID.
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176
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177 Optional files:
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178 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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179
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180 The tool generates:
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181 - 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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182 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
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183 - 3) a log file (.txt).
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184
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185 Output options:
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186 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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187
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188 Alternative options are:
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189 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
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190 - 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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191
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192 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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193
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194 Example input
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195 -------------
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196
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197 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
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198
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199 RAS Dataset 1:
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200
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201 +------------+----------------+----------------+----------------+
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202 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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203 +============+================+================+================+
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204 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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205 +------------+----------------+----------------+----------------+
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206 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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207 +------------+----------------+----------------+----------------+
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208 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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209 +------------+----------------+----------------+----------------+
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210 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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211 +------------+----------------+----------------+----------------+
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212 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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213 +------------+----------------+----------------+----------------+
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214
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215 RAS Dataset 2:
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216
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217 +------------+----------------+----------------+----------------+
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218 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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219 +============+================+================+================+
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220 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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221 +------------+----------------+----------------+----------------+
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222 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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223 +------------+----------------+----------------+----------------+
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224 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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225 +------------+----------------+----------------+----------------+
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226 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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227 +------------+----------------+----------------+----------------+
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228 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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229 +------------+----------------+----------------+----------------+
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230
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231 "RAS of all samples + sample group specification" option:
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232
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233 RAS Dataset:
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234
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235 +------------+----------------+----------------+----------------+
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236 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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237 +============+================+================+================+
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238 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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239 +------------+----------------+----------------+----------------+
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240 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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241 +------------+----------------+----------------+----------------+
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242 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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243 +------------+----------------+----------------+----------------+
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244 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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245 +------------+----------------+----------------+----------------+
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246 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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247 +------------+----------------+----------------+----------------+
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248
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249 Group-file
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250
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251 +---------------+-----------+
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252 | Patient ID | Class |
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253 +===============+===========+
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254 | TCGAAA3529 | MSI |
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255 +---------------+-----------+
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256 | TCGAA62671 | MSS |
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257 +---------------+-----------+
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258 | TCGAA62672 | MSI |
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259 +---------------+-----------+
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260
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261 Advanced options
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262 ----------------
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263
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264 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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265
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266 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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267
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268
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269 .. class:: infomark
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270
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271 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
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272
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273 .. class:: infomark
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274
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275 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
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276
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277 @REFERENCE@
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278
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279 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
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280 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
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281 .. _MaREA cluster analysis: http://link del tool di cluster.org
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282
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283 ]]>
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284 </help>
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285 <expand macro="citations" />undefined</tool>
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286
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