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1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.1">
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2 <description></description>
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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 <requirements>
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7 <requirement type="package" version="0.23.0">pandas</requirement>
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8 <requirement type="package" version="1.1.0">scipy</requirement>
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9 <requirement type="package" version="0.10.1">cobra</requirement>
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10 <requirement type="package" version="4.2.1">lxml</requirement>
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11 <requirement type="package" version="0.8.1">svglib</requirement>
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12 <requirement type="package" version="3.4.0">reportlab</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 python $__tool_directory__/marea.py
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17 --rules_selector $cond_rule.rules_selector
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18 #if $cond_rule.rules_selector == 'Custom':
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19 --custom ${cond_rule.Custom_rules}
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20 --yes_no ${cond_rule.cond_map.yes_no}
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21 #if $cond_rule.cond_map.yes_no == 'yes':
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22 --custom_map $cond_rule.cond_map.Custom_map
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23 #end if
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24 #end if
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25 #if $advanced.choice == 'true':
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26 --none ${advanced.None}
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27 --pValue ${advanced.pValue}
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28 --fChange ${advanced.fChange}
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29 --generate_svg ${advanced.generateSvg}
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30 --generate_pdf ${advanced.generatePdf}
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31 --generate_ras ${advanced.generateRas}
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32 #else
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33 --none true
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34 --pValue 0.05
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35 --fChange 1.5
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36 --generate_svg false
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37 --generate_pdf true
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38 --generate_ras false
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39 #end if
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40 --tool_dir $__tool_directory__
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41 --option $cond.type_selector
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42 --out_log $log
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43
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44 #if $cond.type_selector == 'datasets':
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45 --input_datas
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46 #for $data in $cond.input_Datasets:
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47 ${data.input}
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48 #end for
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49 --names
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50 #for $data in $cond.input_Datasets:
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51 ${data.input_name}
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52 #end for
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53 #elif $cond.type_selector == 'dataset_class':
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54 --input_data ${input_data}
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55 --input_class ${input_class}
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56 #end if
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57 ]]>
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58 </command>
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59
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60 <inputs>
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61 <conditional name="cond_rule">
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62 <expand macro="options"/>
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63 <when value="HMRcore">
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64 </when>
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65 <when value="Recon">
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66 </when>
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67 <when value="Custom">
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68 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
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69 <conditional name="cond_map">
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70 <param name="yes_no" type="select" label="Custom map? (optional)">
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71 <option value="no" selected="true">no</option>
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72 <option value="yes">yes</option>
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73 </param>
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74 <when value="yes">
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75 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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76 </when>
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77 <when value="no">
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78 </when>
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79 </conditional>
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80 </when>
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81 </conditional>
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82 <conditional name="cond">
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83 <param name="type_selector" argument="--option" type="select" label="Input format:">
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84 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
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85 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
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86 </param>
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87 <when value="datasets">
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88 <repeat name="input_Datasets" title="RNAseq" min="2">
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89 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
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90 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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91 </repeat>
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92 </when>
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93 <when value="dataset_class">
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94 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
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95 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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96 </when>
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97 </conditional>
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98
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99 <conditional name="advanced">
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100 <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
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101 <option value="true" selected="true">No</option>
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102 <option value="false">Yes</option>
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103 </param>
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104 <when value="false">
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105 </when>
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106 <when value="true">
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107 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
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108 <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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109 <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" />
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110 <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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111 <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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112 <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />
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113 </when>
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114 </conditional>
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115 </inputs>
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116
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117 <outputs>
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118 <data format="txt" name="log" label="${tool.name} - Log" />
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119 <collection name="results" type="list" label="${tool.name} - Results">
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120 <discover_datasets pattern="__name_and_ext__" directory="result"/>
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121 </collection>
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122 <collection name="ras" type="list" label="${tool.name} - RAS" format_source="tabular">
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123 <filter>advanced['choice'] and advanced['generateRas']</filter>
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124 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
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125 </collection>
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126 </outputs>
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127 <tests>
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128 <test>
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129 <param name="pValue" value="0.56"/>
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130 <output name="log" file="log.txt"/>
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131 </test>
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132 </tests>
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133 <help>
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134 <![CDATA[
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135
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136 What it does
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137 -------------
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138
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139 This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
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140
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141 Accepted files are:
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142 - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*");
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143 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
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144
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145 Optional files:
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146 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
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147
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148 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
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149 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
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150 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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151
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152 The tool generates:
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153 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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154 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
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155 3) a log file (.txt).
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156
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157 RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID.
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158
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159 Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2).
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160
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161 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
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162
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163 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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164
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165
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166 Example input
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167 -------------
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168
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169 **"Custom Rules"** option:
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170
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171 Custom Rules Dastaset:
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172
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173 @CUSTOM_RULES_EXEMPLE@
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174
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175 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
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176
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177 RNA-seq Dataset 1:
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178
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179 @DATASET_EXEMPLE1@
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180
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181 RNA-seq Dataset 2:
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182
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183 @DATASET_EXEMPLE2@
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184
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185 **"RNAseq of all samples + sample group specification"** option:
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186
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187 RNA-seq Dataset:
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188
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189 @DATASET_EXEMPLE1@
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190
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191 Class-file:
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192
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193 +------------+------------+
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194 | Patient_ID | class |
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195 +============+============+
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196 | TCGAAA3529 | MSI |
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197 +------------+------------+
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198 | TCGAA62671 | MSS |
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199 +------------+------------+
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200 | TCGAA62672 | MSI |
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201 +------------+------------+
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202
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203 |
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204
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205 .. class:: infomark
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206
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207 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
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208
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209 .. class:: infomark
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210
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211 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
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212
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213 @REFERENCE@
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214
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215 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
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216 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
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217 .. _MaREA cluster analysis: http://link del tool di cluster.org
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218
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219 ]]>
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220 </help>
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221 <expand macro="citations" />
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222 </tool>
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223
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