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1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.3">
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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
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26 --tool_dir $__tool_directory__
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27 --option $cond.type_selector
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28 --out_log $log
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29
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30 #if $cond.type_selector == 'datasets':
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31 --input_datas
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32 #for $data in $cond.input_Datasets:
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33 ${data.input}
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34 #end for
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35 --names
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36 #for $data in $cond.input_Datasets:
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37 ${data.input_name}
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38 #end for
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31
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39 #if $cond.advanced.choice == 'true':
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40 --none ${cond.advanced.None}
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41 --pValue ${cond.advanced.pValue}
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42 --fChange ${cond.advanced.fChange}
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43 --generate_svg ${cond.advanced.generateSvg}
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44 --generate_pdf ${cond.advanced.generatePdf}
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45 --generate_ras ${cond.advanced.generateRas}
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46 #else
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47 --none true
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48 --pValue 0.05
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49 --fChange 1.5
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50 --generate_svg false
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51 --generate_pdf true
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52 --generate_ras false
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53 #end if
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54 #elif $cond.type_selector == 'dataset_class':
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55 --input_data ${input_data}
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56 --input_class ${input_class}
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57 #if $cond.advanced.choice == 'true':
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58 --none ${cond.advanced.None}
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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 --generate_ras ${cond.advanced.generateRas}
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64 #else
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65 --none true
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66 --pValue 0.05
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67 --fChange 1.5
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68 --generate_svg false
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69 --generate_pdf true
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70 --generate_ras false
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71 #end if
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72 #end if
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28
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73 #if $cond.type_selector == 'datasets_rasonly':
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74 --input_datas ${input_Datasets}
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75 --single_ras_file $ras_single
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76 --none ${cond.advanced.None}
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28
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77 #end if
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78 ]]>
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79 </command>
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80
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81 <inputs>
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82 <conditional name="cond_rule">
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83 <expand macro="options"/>
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84 <when value="HMRcore">
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85 </when>
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86 <when value="Recon">
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87 </when>
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88 <when value="Custom">
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89 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
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90 <conditional name="cond_map">
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91 <param name="yes_no" type="select" label="Custom map? (optional)">
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92 <option value="no" selected="true">no</option>
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93 <option value="yes">yes</option>
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94 </param>
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95 <when value="yes">
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96 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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97 </when>
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98 <when value="no">
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99 </when>
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100 </conditional>
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101 </when>
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102 </conditional>
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103 <conditional name="cond">
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104 <param name="type_selector" argument="--option" type="select" label="Input format:">
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105 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
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106 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
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107 <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
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108 </param>
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109 <when value="datasets">
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110 <repeat name="input_Datasets" title="RNAseq" min="2">
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111 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
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112 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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113 </repeat>
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31
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114 <conditional name="advanced">
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115 <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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116 <option value="true" selected="true">No</option>
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117 <option value="false">Yes</option>
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118 </param>
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119 <when value="false">
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120 </when>
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121 <when value="true">
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122 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
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123 <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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124 <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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125 <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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126 <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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127 <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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128 </when>
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129 </conditional>
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130 </when>
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131 <when value="datasets_rasonly">
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132 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
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133 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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134 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
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135 </when>
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136 <when value="dataset_class">
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137 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
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138 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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31
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139 <conditional name="advanced">
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140 <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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141 <option value="true" selected="true">No</option>
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142 <option value="false">Yes</option>
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143 </param>
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144 <when value="false">
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145 </when>
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146 <when value="true">
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147 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
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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 <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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153 </when>
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154 </conditional>
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155 </when>
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156 </conditional>
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157
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31
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158
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159
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160
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161 </inputs>
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162
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163 <outputs>
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31
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164 <data format="txt" name="log" label="MaREA - Log" />
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165 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
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166 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
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167 </data>
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168 <collection name="results" type="list" label="MaREA - Results">
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169 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
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170 <discover_datasets pattern="__name_and_ext__" directory="result"/>
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171 </collection>
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172 <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
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173 <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
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174 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
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175 </collection>
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176
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177 </outputs>
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178 <tests>
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179 <test>
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180 <param name="pValue" value="0.56"/>
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181 <output name="log" file="log.txt"/>
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182 </test>
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183 </tests>
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184 <help>
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185 <![CDATA[
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186
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187 What it does
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188 -------------
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189
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190 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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191
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192 Accepted files are:
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193 - 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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194 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
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195
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196 Optional files:
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197 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
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198
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199 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
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200 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
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201 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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202
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203 The tool generates:
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204 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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205 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
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206 3) a log file (.txt).
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207
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208 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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209
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210 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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211
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212 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
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213
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214 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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215
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216
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217 Example input
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218 -------------
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219
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220 **"Custom Rules"** option:
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221
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222 Custom Rules Dastaset:
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223
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224 @CUSTOM_RULES_EXEMPLE@
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225
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226 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
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227
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228 RNA-seq Dataset 1:
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229
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230 @DATASET_EXEMPLE1@
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231
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232 RNA-seq Dataset 2:
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233
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234 @DATASET_EXEMPLE2@
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235
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236 **"RNAseq of all samples + sample group specification"** option:
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237
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238 RNA-seq Dataset:
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239
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240 @DATASET_EXEMPLE1@
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241
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242 Class-file:
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243
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244 +------------+------------+
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245 | Patient_ID | class |
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246 +============+============+
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247 | TCGAAA3529 | MSI |
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248 +------------+------------+
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249 | TCGAA62671 | MSS |
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250 +------------+------------+
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251 | TCGAA62672 | MSI |
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252 +------------+------------+
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253
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254 |
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255
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256 .. class:: infomark
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257
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258 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
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259
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260 .. class:: infomark
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261
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262 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
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263
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264 @REFERENCE@
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265
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266 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
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267 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
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268 .. _MaREA cluster analysis: http://link del tool di cluster.org
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269
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270 ]]>
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271 </help>
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272 <expand macro="citations" />
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273 </tool>
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274
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