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annotate tools/networkAnalysis/CompoundNet/CompoundNet.xml @ 3:6bd9aad9626d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
author metexplore
date Fri, 29 Jul 2022 13:23:40 +0000
parents e69a78624877
children ae4c301919c4
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dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="met4j_CompoundNet" name="CompoundNet" version="1.1.0">
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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:1.1.0</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath"
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11 #if str($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 $asMatrix
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26 -o "$outputPath"
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27 ]]></command>
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28 <inputs>
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29 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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30 <param argument="-sc" format="" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
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31 <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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32 <option selected="true" value="no">no</option>
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33 <option value="by_name">by_name</option>
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34 <option value="by_id">by_id</option>
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35 </param>
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36 <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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37 <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
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38 <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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39 <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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40 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
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41 <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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42 <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/>
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43 </inputs>
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44 <outputs>
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45 <data format="" name="outputPath"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="inputPath" value="XF_network.sbml"/>
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50 <param name="inputSide" value="XF_network_C_Side.tab"/>
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51 <output name="outputPath">
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52 <assert_contents>
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53 <has_line_matching expression=".*node.*" n="1101"/>
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54 <has_line_matching expression=".*edge.*" n="5581"/>
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55 </assert_contents>
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56 </output>
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57 </test>
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58 <test>
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59 <param name="inputPath" value="XF_network.sbml"/>
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60 <param name="inputSide" value="XF_network_C_Side.tab"/>
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61 <param name="undirected" value="true"/>
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62 <param name="computeWeight" value="true"/>
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63 <param name="removeIsolated" value="true"/>
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64 <param name="degree" value="true"/>
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65 <param name="mergingStrat" value="by_id"/>
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66 <output name="outputPath">
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67 <assert_contents>
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68 <has_line_matching expression=".*node.*" n="793"/>
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69 <has_line_matching expression=".*edge.*" n="9372"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 </tests>
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74 <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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75 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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76 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 degree² weighting to get relevant structure without structural data.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help>
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77 <citations/>
0
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78 </tool>