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annotate tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml @ 0:dcd16521b969 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author metexplore
date Fri, 10 Jun 2022 10:31:34 +0000
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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_DistanceMatrix" name="DistanceMatrix" version="0.11.0">
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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:0.11.0</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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11 #if str($sideCompoundFile) != 'None':
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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12 -s "$sideCompoundFile"
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13 #end if
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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14 $degree
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15 #if str($weightFile) != 'None':
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16 -w "$weightFile"
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17 #end if
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18 $undirected
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19 -o "$outputPath"
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20 ]]></command>
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21 <inputs>
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22 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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23 <param argument="-s" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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24 <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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25 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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26 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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27 </inputs>
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28 <outputs>
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29 <data format="csv" name="outputPath"/>
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30 </outputs>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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31 <tests>
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32 <test>
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33 <param name="inputPath" value="toy_model.xml"/>
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34 <output ftype="csv" name="outputPath">
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35 <assert_contents>
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36 <has_n_lines n="9"/>
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37 <has_line_matching expression="B,1.0,0.0,Infinity,2.0,1.0,Infinity,2.0,Infinity" n="1"/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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38 </assert_contents>
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39 </output>
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40 </test>
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41 <test>
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42 <param name="inputPath" value="toy_model.xml"/>
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43 <param name="sideCompoundFile" value="sides.txt"/>
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44 <param name="degree" value="true"/>
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45 <param name="undirected" value="true"/>
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46 <output ftype="csv" name="outputPath">
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47 <assert_contents>
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48 <has_n_lines n="8"/>
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49 <has_line_matching expression="B,9.0,0.0,13.0,16.0,32.0,17.0,36.0" n="1"/>
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help><![CDATA[Create a compound to compound distance matrix.
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55 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.
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56 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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57 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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58 </tool>