Mercurial > repos > metexplore > met4j

annotate tools/convert/Sbml2CompoundGraph/Sbml2CompoundGraph.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="develop">
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3 <description>Advanced creation of a compound graph representation of a SBML file content</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath"
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11 #if str($inputSide) != 'None':
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12 -sc "$inputSide"
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13 #end if
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14 #if str($mergingStrat):
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15 -mc "$mergingStrat"
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16 #end if
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17 $mergeEdges
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18 $removeIsolated
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19 $degree
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20 #if str($weightFile) != 'None':
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21 -cw "$weightFile"
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22 #end if
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23 $undirected
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24 $computeWeight
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25 #if str($format):
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26 -f "$format"
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27 #end if
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28 -o "$output"
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29 ]]></command>
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30 <inputs>
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31 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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32 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
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33 <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
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34 <option selected="true" value="no">no</option>
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35 <option value="by_name">by_name</option>
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36 <option value="by_id">by_id</option>
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37 </param>
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38 <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
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39 <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
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40 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/>
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41 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
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42 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
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43 <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
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44 <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
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45 <option value="gml">gml</option>
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46 <option selected="true" value="tab">tab</option>
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47 <option value="nodeList">nodeList</option>
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48 <option value="json">json</option>
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49 <option value="matrix">matrix</option>
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50 </param>
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51 </inputs>
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52 <outputs>
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53 <data format="txt" name="output"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57
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60 <param name="inputPath" value="XF_network.sbml"/>
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64 <param name="inputSide" value="XF_network_C_Side.tab"/>
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68 <param name="format" value="gml"/>
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72 <output name="output">
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76 <assert_contents>
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80 <has_line_matching expression=".*node.*" n="1101"/>
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84 <has_line_matching expression=".*edge.*" n="5581"/>
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88 </assert_contents>
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92 </output>
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96 </test>
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97 <test>
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99
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101 <param name="inputPath" value="XF_network.sbml"/>
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102
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103
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104
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105 <param name="inputSide" value="XF_network_C_Side.tab"/>
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109 <param name="undirected" value="true"/>
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113 <param name="computeWeight" value="true"/>
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117 <param name="removeIsolated" value="true"/>
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118
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119
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120
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121 <param name="degree" value="true"/>
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123
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124
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125 <param name="mergingStrat" value="by_id"/>
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126
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128
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129 <param name="format" value="gml"/>
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133 <output name="output">
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136
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137 <assert_contents>
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141 <has_line_matching expression=".*node.*" n="793"/>
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145 <has_line_matching expression=".*edge.*" n="9372"/>
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149 </assert_contents>
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153 </output>
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157 </test>
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158 </tests>
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159 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes.
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160 While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations.
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161 In contrary to the Sbml2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help>
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162 <citations/>
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163 </tool>