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1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.7">
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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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16
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15 python $__tool_directory__/marea.py
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16
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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
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31 #if $cond.advanced.choice == 'true':
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32 --pValue ${cond.advanced.pValue}
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33 --fChange ${cond.advanced.fChange}
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34 --generate_svg ${cond.advanced.generateSvg}
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35 --generate_pdf ${cond.advanced.generatePdf}
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36 #else
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37 --pValue 0.05
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38 --fChange 1.5
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39 --generate_svg false
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40 --generate_pdf true
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41 --generate_ras false
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42 #end if
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43 #elif $cond.type_selector == 'dataset_class':
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44 --input_data ${input_data}
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45 --input_class ${input_class}
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47
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46 --comparison ${cond.comparis.comparison}
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47 #if $cond.comparis.comparison == 'onevsmany'
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48 --control ${cond.comparis.controlgroup}
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49 #end if
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50 #if $cond.advanced.choice == 'true':
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51 --pValue ${cond.advanced.pValue}
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52 --fChange ${cond.advanced.fChange}
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53 --generate_svg ${cond.advanced.generateSvg}
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54 --generate_pdf ${cond.advanced.generatePdf}
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55 #else
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56 --pValue 0.05
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57 --fChange 1.5
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58 --generate_svg false
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59 --generate_pdf true
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60 #end if
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28
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61 #end if
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62 ]]>
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63 </command>
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64 <inputs>
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65 <conditional name="cond">
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66 <param name="type_selector" argument="--option" type="select" label="Input format:">
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67 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
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68 <option value="dataset_class">RAS of all samples + sample group specification</option>
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69 </param>
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70 <when value="datasets">
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71 <repeat name="input_Datasets" title="RAS dataset" min="2">
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72 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
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73 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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74 </repeat>
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75 <conditional name="comparis">
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76 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
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77 <option value="manyvsmany" selected="true">One vs One</option>
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78 <option value="onevsrest">One vs All</option>
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79 <option value="onevsmany">One vs Control</option>
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80 </param>
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81 <when value="onevsmany">
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82 <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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83 </when>
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84 </conditional>
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85 <conditional name="advanced">
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86 <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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87 <option value="true" selected="true">No</option>
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88 <option value="false">Yes</option>
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89 </param>
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90 <when value="false"></when>
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91 <when value="true">
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92 <conditional name="cond_map">
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93 <param name="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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94 <option value="false" selected="true">No</option>
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95 <option value="true">Yes</option>
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96 </param>
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97 <when value="true">
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98 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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99 </when>
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100 </conditional>
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101 <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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102 <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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103 <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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104 <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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105 </when>
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106 </conditional>
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107 </when>
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108 <when value="dataset_class">
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109 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
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110 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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111 <conditional name="comparis">
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112 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
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113 <option value="manyvsmany" selected="true">One vs One</option>
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114 <option value="onevsrest">One vs All</option>
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115 <option value="onevsmany">One vs Control</option>
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116 </param>
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117 <when value="onevsmany">
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118 <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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119 </when>
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120 </conditional>
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121 <conditional name="advanced">
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122 <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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123 <option value="true" selected="true">No</option>
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124 <option value="false">Yes</option>
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125 </param>
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126 <when value="false"></when>
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127 <when value="true">
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128 <conditional name="cond_map">
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129 <param name="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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130 <option value="false" selected="true">No</option>
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131 <option value="true">Yes</option>
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132 </param>
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133 <when value="true">
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134 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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135 </when>
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136 </conditional>
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137 <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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138 <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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139 <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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140 <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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141 </when>
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142 </conditional>
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143 </when>
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144 </conditional>
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145 </inputs>
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146 <outputs>
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147 <data format="txt" name="log" label="MaREA - Log" />
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148 <collection name="results" type="list" label="MaREA - Results">
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149 <discover_datasets pattern="__name_and_ext__" directory="result"/>
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150 </collection>
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151 </outputs>
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152 <help>
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153 <![CDATA[
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154
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155 What it does
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156 -------------
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157
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158 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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159
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160 Accepted files are:
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161 - 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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162 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
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163
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164 Optional files:
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165 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
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166
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167 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
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168 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
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169 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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170
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171 The tool generates:
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172 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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173 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
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174 3) a log file (.txt).
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175
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176 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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177
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178 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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179
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180 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
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181
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182 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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183
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184
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185 Example input
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186 -------------
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187
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188 **"Custom Rules"** option:
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189
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190 Custom Rules Dastaset:
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191
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192 @CUSTOM_RULES_EXEMPLE@
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193
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194 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
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195
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196 RNA-seq Dataset 1:
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197
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198 @DATASET_EXEMPLE1@
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199
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200 RNA-seq Dataset 2:
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201
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202 @DATASET_EXEMPLE2@
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203
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204 **"RNAseq of all samples + sample group specification"** option:
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205
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206 RNA-seq Dataset:
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207
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208 @DATASET_EXEMPLE1@
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209
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210 Class-file:
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211
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212 +------------+------------+
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213 | Patient_ID | class |
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214 +============+============+
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215 | TCGAAA3529 | MSI |
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216 +------------+------------+
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217 | TCGAA62671 | MSS |
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218 +------------+------------+
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219 | TCGAA62672 | MSI |
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220 +------------+------------+
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221
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222 |
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223
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224 .. class:: infomark
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225
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226 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
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227
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228 .. class:: infomark
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229
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230 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
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231
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232 @REFERENCE@
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233
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234 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
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235 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
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236 .. _MaREA cluster analysis: http://link del tool di cluster.org
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237
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238 ]]>
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239 </help>
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240 <expand macro="citations" />undefined</tool>
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241
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