Mercurial > repos > metexplore > met4j

annotate tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="2.0.1">
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3 <description>Create a compound to compound distance matrix.</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:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
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11 #if str($sideCompoundFile) != 'None':
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12 -sc "$sideCompoundFile"
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13 #end if
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14 #if str($seedFile) != 'None':
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15 -s "$seedFile"
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16 #end if
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17 $degree
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18 #if str($weightFile) != 'None':
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19 -w "$weightFile"
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20 #end if
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21 $undirected
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22 -o "$outputPath"
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23 ]]></command>
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24 <inputs>
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25 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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26 <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
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27 <param argument="-s" format="txt" label="an optional file containing list of compounds of interest. The returned distance matrix contains only the corresponding rows and columns" name="seedFile" optional="true" type="data" value=""/>
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28 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting (-w must not be set)" name="degree" truevalue="-dw" type="boolean" value="false"/>
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29 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
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30 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
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31 </inputs>
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32 <outputs>
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33 <data format="csv" name="outputPath"/>
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34 </outputs>
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35 <tests>
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36 <test>
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38 <param name="inputPath" value="toy_model.xml"/>
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40 <output ftype="csv" name="outputPath">
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42 <assert_contents>
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0
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44 <has_n_lines n="9"/>
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46 <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/>
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48 <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/>
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0
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50 </assert_contents>
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52 </output>
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54 </test>
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55 <test>
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57 <param name="inputPath" value="toy_model.xml"/>
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59 <param name="sideCompoundFile" value="sides.txt"/>
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61 <param name="degree" value="true"/>
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63 <param name="undirected" value="true"/>
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65 <output ftype="csv" name="outputPath">
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67 <assert_contents>
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69 <has_n_lines n="8"/>
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71 <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/>
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73 <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/>
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75 <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/>
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77 <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/>
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79 <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/>
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81 </assert_contents>
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83 </output>
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85 </test>
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86 </tests>
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87 <help><![CDATA[Create a compound to compound distance matrix.
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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88 The distance between two compounds is computed as the length of the shortest path connecting the two in the compound graph, where two compounds are linked if they are respectively substrate and product of the same reaction.
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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89 An optional edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.The default weighting use target's degree squared. Alternatively, custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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90 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help>
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9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
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91 <citations/>
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dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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92 </tool>