4
+ − 1 <tool id="FluxToMap" name="Metabolic Flux Enrichment Analysis" version="2.0.0">
+ − 2 <macros>
+ − 3 <import>marea_macros.xml</import>
+ − 4 </macros>
+ − 5
+ − 6 <requirements>
+ − 7 <requirement type="package" version="1.24.4">numpy</requirement>
+ − 8 <requirement type="package" version="2.0.3">pandas</requirement>
+ − 9 <requirement type="package" version="0.13.0">seaborn</requirement>
+ − 10 <requirement type="package" version="1.10.1">scipy</requirement>
+ − 11 <requirement type="package" version="1.5.1">svglib</requirement>
+ − 12 <requirement type="package" version="2.2.3">pyvips</requirement>
+ − 13 <requirement type="package" version="2.7.1">cairosvg</requirement>
+ − 14 <requirement type="package" version="0.29.0">cobra</requirement>
+ − 15 <requirement type="package" version="5.2.2">lxml</requirement>
+ − 16 </requirements>
+ − 17
+ − 18 <command detect_errors="exit_code">
+ − 19 <![CDATA[
+ − 20 python $__tool_directory__/flux_to_map.py
+ − 21
+ − 22 --tool_dir $__tool_directory__
+ − 23 --option $cond.type_selector
+ − 24 --out_log $log
+ − 25 --color_map $color_map
+ − 26
+ − 27 #if $cond.type_selector == 'datasets':
+ − 28
+ − 29 --input_datas_fluxes
+ − 30 #for $data in $cond.input_datasets_fluxes:
+ − 31 ${data.input_fluxes}
+ − 32 #end for
+ − 33
+ − 34 --names_fluxes
+ − 35 #for $data in $cond.input_datasets_fluxes:
+ − 36 ${data.input_name_fluxes}
+ − 37 #end for
+ − 38
+ − 39 #elif $cond.type_selector == 'dataset_class':
+ − 40
+ − 41 --input_data_fluxes $input_data_fluxes
+ − 42 --input_class_fluxes $input_class_fluxes
+ − 43
+ − 44 #end if
+ − 45
+ − 46 --comparison ${comparis.comparison}
+ − 47 #if $comparis.comparison == 'onevsmany'
+ − 48 --control '${cond.comparis.controlgroup}'
+ − 49 #end if
+ − 50
+ − 51 --choice_map '${cond_choice_map.choice_map}'
+ − 52 #if $cond_choice_map.choice_map == 'Custom':
+ − 53 --custom_map ${cond_choice_map.custom_map}
+ − 54 #end if
+ − 55
+ − 56 #if $advanced.choice == 'true':
+ − 57 --pValue ${advanced.pValue}
+ − 58 --fChange ${advanced.fChange}
+ − 59 --generate_svg ${advanced.generateSvg}
+ − 60 --generate_pdf ${advanced.generatePdf}
+ − 61 #else
+ − 62 --pValue 0.05
+ − 63 --fChange 1.2
+ − 64 --generate_svg false
+ − 65 --generate_pdf true
+ − 66 #end if
+ − 67 ]]>
+ − 68 </command>
+ − 69
+ − 70 <inputs>
+ − 71
+ − 72 <conditional name="cond">
+ − 73 <param name="type_selector" argument="--option" type="select" label="Input format:">
+ − 74 <option value="datasets" selected="true">Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N</option>
+ − 75 <option value="dataset_class">All fluxes + sample group specification</option>
+ − 76 </param>
+ − 77
+ − 78 <when value="datasets">
+ − 79 <repeat name="input_datasets_fluxes" title="Fluxes dataset" min="2">
+ − 80 <param name="input_fluxes" argument="--input_datas_fluxes" type="data" format="tabular, csv, tsv" label="add dataset" />
+ − 81 <param name="input_name_fluxes" argument="--names_fluxes" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
+ − 82 </repeat>
+ − 83 </when>
+ − 84
+ − 85 <when value="dataset_class">
+ − 86 <param name="input_data_fluxes" argument="--input_data_fluxes" type="data" format="tabular, csv, tsv" label="All fluxes" />
+ − 87 <param name="input_class_fluxes" argument="--input_class_fluxes" type="data" format="tabular, csv, tsv" label="Sample group specification" />
+ − 88 </when>
+ − 89 </conditional>
+ − 90
+ − 91 <conditional name="comparis">
+ − 92 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
+ − 93 <option value="manyvsmany" selected="true">One vs One</option>
+ − 94 <option value="onevsrest">One vs All</option>
+ − 95 <option value="onevsmany">One vs Control</option>
+ − 96 </param>
+ − 97 <when value="onevsmany">
+ − 98 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
+ − 99 </when>
+ − 100 </conditional>
+ − 101
+ − 102 <conditional name="cond_choice_map">
+ − 103 <param name="choice_map" argument="--choice_map" type="select" label="Choose metabolic map:">
+ − 104 <option value="ENGRO2" selected="true">ENGRO2</option>
+ − 105 <option value="HMRcore" >HMRcore</option>
+ − 106 <option value="Custom">Custom</option>
+ − 107 </param>
+ − 108
+ − 109 <when value="Custom">
+ − 110 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
+ − 111 </when>
+ − 112 </conditional>
+ − 113
+ − 114 <param name="color_map" argument="--color_map" type="select" label="Color map:">
+ − 115 <option value="viridis" selected="true">Viridis</option>
+ − 116 <option value="jet">Jet</option>
+ − 117 </param>
+ − 118
+ − 119 <conditional name="advanced">
+ − 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.">
+ − 121 <option value="true" selected="true">No</option>
+ − 122 <option value="false">Yes</option>
+ − 123 </param>
+ − 124
+ − 125 <when value="true">
+ − 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" />
+ − 127 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
+ − 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?" />
+ − 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?" />
+ − 130 </when>
+ − 131 </conditional>
+ − 132 </inputs>
+ − 133
+ − 134 <outputs>
+ − 135 <data format="txt" name="log" label="FluxToMap - Log" />
+ − 136 <collection name="results" type="list" label="FluxToMap - Results">
+ − 137 <discover_datasets pattern="__name_and_ext__" directory="result"/>
+ − 138 </collection>
+ − 139 </outputs>
+ − 140
+ − 141 <help>
+ − 142 <![CDATA[
+ − 143
+ − 144 What it does
+ − 145 -------------
+ − 146
+ − 147 This tool analyzes and visualizes differences in reactions fluxes of groups of samples, returned by the Flux Simulation tool, of groups of samples.
+ − 148
+ − 149 Accepted files are:
+ − 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;
+ − 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).
+ − 152
+ − 153 Optional files:
+ − 154 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
+ − 155
+ − 156 The tool generates:
+ − 157 - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
+ − 158 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
+ − 159 - 3) a log file (.txt).
+ − 160
+ − 161 Output options:
+ − 162 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’).
+ − 163
+ − 164 Alternative options are:
+ − 165 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
+ − 166 - 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.
+ − 167
+ − 168 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".
+ − 169
+ − 170 Example input
+ − 171 -------------
+ − 172
+ − 173 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
+ − 174
+ − 175 RAS Dataset 1:
+ − 176
+ − 177 +------------+----------------+----------------+----------------+
+ − 178 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
+ − 179 +============+================+================+================+
+ − 180 | r1642 | 0.523167 | 0.371355 | 0.925661 |
+ − 181 +------------+----------------+----------------+----------------+
+ − 182 | r1643 | 0.568765 | 0.765567 | 0.456789 |
+ − 183 +------------+----------------+----------------+----------------+
+ − 184 | r1640 | 0.876545 | 0.768933 | 0.987654 |
+ − 185 +------------+----------------+----------------+----------------+
+ − 186 | r1641 | 0.456788 | 0.876543 | 0.876542 |
+ − 187 +------------+----------------+----------------+----------------+
+ − 188 | r1646 | 0.876543 | 0.786543 | 0.897654 |
+ − 189 +------------+----------------+----------------+----------------+
+ − 190
+ − 191 RAS Dataset 2:
+ − 192
+ − 193 +------------+----------------+----------------+----------------+
+ − 194 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
+ − 195 +============+================+================+================+
+ − 196 | r1642 | 0.523167 | 0.371355 | 0.925661 |
+ − 197 +------------+----------------+----------------+----------------+
+ − 198 | r1643 | 0.568765 | 0.765567 | 0.456789 |
+ − 199 +------------+----------------+----------------+----------------+
+ − 200 | r1640 | 0.876545 | 0.768933 | 0.987654 |
+ − 201 +------------+----------------+----------------+----------------+
+ − 202 | r1641 | 0.456788 | 0.876543 | 0.876542 |
+ − 203 +------------+----------------+----------------+----------------+
+ − 204 | r1646 | 0.876543 | 0.786543 | 0.897654 |
+ − 205 +------------+----------------+----------------+----------------+
+ − 206
+ − 207 "RAS of all samples + sample group specification" option:
+ − 208
+ − 209 RAS Dataset:
+ − 210
+ − 211 +------------+----------------+----------------+----------------+
+ − 212 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
+ − 213 +============+================+================+================+
+ − 214 | r1642 | 0.523167 | 0.371355 | 0.925661 |
+ − 215 +------------+----------------+----------------+----------------+
+ − 216 | r1643 | 0.568765 | 0.765567 | 0.456789 |
+ − 217 +------------+----------------+----------------+----------------+
+ − 218 | r1640 | 0.876545 | 0.768933 | 0.987654 |
+ − 219 +------------+----------------+----------------+----------------+
+ − 220 | r1641 | 0.456788 | 0.876543 | 0.876542 |
+ − 221 +------------+----------------+----------------+----------------+
+ − 222 | r1646 | 0.876543 | 0.786543 | 0.897654 |
+ − 223 +------------+----------------+----------------+----------------+
+ − 224
+ − 225 Group-file
+ − 226
+ − 227 +---------------+-----------+
+ − 228 | Patient ID | Class |
+ − 229 +===============+===========+
+ − 230 | TCGAAA3529 | MSI |
+ − 231 +---------------+-----------+
+ − 232 | TCGAA62671 | MSS |
+ − 233 +---------------+-----------+
+ − 234 | TCGAA62672 | MSI |
+ − 235 +---------------+-----------+
+ − 236
+ − 237
+ − 238 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
+ − 239
+ − 240 .. class:: infomark
+ − 241
+ − 242 **TIP**: This tool using the RAS scores computed by `Ras tool`_.
+ − 243
+ − 244 ]]>
+ − 245 </help>
+ − 246 <expand macro="citations" />
+ − 247 </tool>