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1 <tool id="FluxToMap" name="Metabolic Flux Enrichment Analysis" version="2.0.0">
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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
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6 <requirements>
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7 <requirement type="package" version="1.24.4">numpy</requirement>
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8 <requirement type="package" version="2.0.3">pandas</requirement>
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9 <requirement type="package" version="0.13.0">seaborn</requirement>
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10 <requirement type="package" version="1.10.1">scipy</requirement>
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11 <requirement type="package" version="1.5.1">svglib</requirement>
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12 <requirement type="package" version="2.2.3">pyvips</requirement>
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13 <requirement type="package" version="2.7.1">cairosvg</requirement>
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14 <requirement type="package" version="0.29.0">cobra</requirement>
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15 <requirement type="package" version="5.2.2">lxml</requirement>
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16 </requirements>
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17
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18 <command detect_errors="exit_code">
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19 <![CDATA[
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20 python $__tool_directory__/flux_to_map.py
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21
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22 --tool_dir $__tool_directory__
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23 --option $cond.type_selector
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24 --out_log $log
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25 --color_map $color_map
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26
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27 #if $cond.type_selector == 'datasets':
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28
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29 --input_datas_fluxes
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30 #for $data in $cond.input_datasets_fluxes:
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31 ${data.input_fluxes}
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32 #end for
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33
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34 --names_fluxes
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35 #for $data in $cond.input_datasets_fluxes:
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36 ${data.input_name_fluxes}
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37 #end for
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38
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39 #elif $cond.type_selector == 'dataset_class':
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40
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41 --input_data_fluxes $input_data_fluxes
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42 --input_class_fluxes $input_class_fluxes
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43
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44 #end if
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45
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46 --comparison ${comparis.comparison}
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47 #if $comparis.comparison == 'onevsmany'
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48 --control '${cond.comparis.controlgroup}'
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49 #end if
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50
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51 --choice_map '${cond_choice_map.choice_map}'
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52 #if $cond_choice_map.choice_map == 'Custom':
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53 --custom_map ${cond_choice_map.custom_map}
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54 #end if
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55
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56 #if $advanced.choice == 'true':
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57 --pValue ${advanced.pValue}
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58 --fChange ${advanced.fChange}
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59 --generate_svg ${advanced.generateSvg}
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60 --generate_pdf ${advanced.generatePdf}
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61 #else
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62 --pValue 0.05
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63 --fChange 1.2
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64 --generate_svg false
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65 --generate_pdf true
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66 #end if
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67 ]]>
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68 </command>
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69
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70 <inputs>
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71
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72 <conditional name="cond">
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73 <param name="type_selector" argument="--option" type="select" label="Input format:">
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74 <option value="datasets" selected="true">Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N</option>
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75 <option value="dataset_class">All fluxes + sample group specification</option>
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76 </param>
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77
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78 <when value="datasets">
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79 <repeat name="input_datasets_fluxes" title="Fluxes dataset" min="2">
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80 <param name="input_fluxes" argument="--input_datas_fluxes" type="data" format="tabular, csv, tsv" label="add dataset" />
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81 <param name="input_name_fluxes" argument="--names_fluxes" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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82 </repeat>
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83 </when>
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84
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85 <when value="dataset_class">
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86 <param name="input_data_fluxes" argument="--input_data_fluxes" type="data" format="tabular, csv, tsv" label="All fluxes" />
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87 <param name="input_class_fluxes" argument="--input_class_fluxes" type="data" format="tabular, csv, tsv" label="Sample group specification" />
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88 </when>
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89 </conditional>
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90
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91 <conditional name="comparis">
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92 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
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93 <option value="manyvsmany" selected="true">One vs One</option>
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94 <option value="onevsrest">One vs All</option>
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95 <option value="onevsmany">One vs Control</option>
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96 </param>
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97 <when value="onevsmany">
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98 <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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99 </when>
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100 </conditional>
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101
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102 <conditional name="cond_choice_map">
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103 <param name="choice_map" argument="--choice_map" type="select" label="Choose metabolic map:">
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104 <option value="ENGRO2" selected="true">ENGRO2</option>
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105 <option value="HMRcore" >HMRcore</option>
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106 <option value="Custom">Custom</option>
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107 </param>
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108
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109 <when value="Custom">
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110 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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111 </when>
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112 </conditional>
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113
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114 <param name="color_map" argument="--color_map" type="select" label="Color map:">
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115 <option value="viridis" selected="true">Viridis</option>
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116 <option value="jet">Jet</option>
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117 </param>
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118
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119 <conditional name="advanced">
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120 <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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121 <option value="true" selected="true">No</option>
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122 <option value="false">Yes</option>
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123 </param>
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124
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125 <when value="true">
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126 <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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127 <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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128 <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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129 <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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130 </when>
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131 </conditional>
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132 </inputs>
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133
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134 <outputs>
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135 <data format="txt" name="log" label="FluxToMap - Log" />
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136 <collection name="results" type="list" label="FluxToMap - Results">
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137 <discover_datasets pattern="__name_and_ext__" directory="result"/>
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138 </collection>
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139 </outputs>
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140
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141 <help>
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142 <![CDATA[
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143
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144 What it does
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145 -------------
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146
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147 This tool analyzes and visualizes differences in reactions fluxes of groups of samples, returned by the Flux Simulation tool, of groups of samples.
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148
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217
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149 Accepted files are (Files must have different names):
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150 - option 1) two or more fluxes datasets, each referring to samples in a given group. The user can specify a label for each group;
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151 - option 2) one fluxes dataset and one group-file specifying the group each sample belongs to (e.g. the accepted group file is thought to be the one returned by the Clustering tool).
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152
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153 Optional files:
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154 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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155
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156 The tool generates:
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166
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157 - A tab-separated file: reporting fold-change and p-values of fluxes between a pair of conditions/classes;
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158 - A metabolic map file (downloadable as .svg and .png): visualizing up- and down-regulated reactions between a pair of conditions/classes;
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169
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159 - Two metabolic maps to visualize the mean and median fluxes normalized amongst all classes. The associated color map is also generated (absolute ranges);
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166
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160 - A log file (.txt).
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165
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161
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162 Output options:
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165
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163 - 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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164
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165 Alternative options are:
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166 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
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167 - 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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168
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169 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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170
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171 Example input
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172 -------------
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173
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174 "Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N" option:
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175
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176 Fluxes Dataset 1:
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177
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178 +------------+----------------+----------------+----------------+
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179 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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180 +============+================+================+================+
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181 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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182 +------------+----------------+----------------+----------------+
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183 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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184 +------------+----------------+----------------+----------------+
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185 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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186 +------------+----------------+----------------+----------------+
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187 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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188 +------------+----------------+----------------+----------------+
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189 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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190 +------------+----------------+----------------+----------------+
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191
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192 Fluxes Dataset 2:
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193
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194 +------------+----------------+----------------+----------------+
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195 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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196 +============+================+================+================+
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197 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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198 +------------+----------------+----------------+----------------+
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199 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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200 +------------+----------------+----------------+----------------+
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201 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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202 +------------+----------------+----------------+----------------+
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203 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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204 +------------+----------------+----------------+----------------+
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205 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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206 +------------+----------------+----------------+----------------+
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207
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208 "Fluxes of all samples + sample group specification" option:
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209
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210 Fluxes Dataset:
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211
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212 +------------+----------------+----------------+----------------+
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213 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
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214 +============+================+================+================+
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215 | r1642 | 0.523167 | 0.371355 | 0.925661 |
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216 +------------+----------------+----------------+----------------+
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217 | r1643 | 0.568765 | 0.765567 | 0.456789 |
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218 +------------+----------------+----------------+----------------+
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219 | r1640 | 0.876545 | 0.768933 | 0.987654 |
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220 +------------+----------------+----------------+----------------+
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221 | r1641 | 0.456788 | 0.876543 | 0.876542 |
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222 +------------+----------------+----------------+----------------+
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223 | r1646 | 0.876543 | 0.786543 | 0.897654 |
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224 +------------+----------------+----------------+----------------+
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225
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226 Group-file
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227
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228 +---------------+-----------+
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229 | Patient ID | Class |
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230 +===============+===========+
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231 | TCGAAA3529 | MSI |
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232 +---------------+-----------+
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233 | TCGAA62671 | MSS |
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234 +---------------+-----------+
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235 | TCGAA62672 | MSI |
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236 +---------------+-----------+
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237
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238
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239 **TIP**: If your dataset is not split into classes, use MaREA cluster analysis.
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240
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241
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242 ]]>
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243 </help>
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244 <expand macro="citations" />
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245 </tool> |
