Mercurial > repos > metexplore > met4j_reactiondistancematrix

annotate ReactionDistanceMatrix.xml @ 3:392f9fe363e8 draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:31:23 +0000
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886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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2 <tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="@TOOL_VERSION@">
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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3 <description>Create a reaction to reaction distance matrix.</description>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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4 <macros>
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5 <import>macros.xml</import>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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6 </macros>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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7 <expand macro="bio_tools"/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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8 <expand macro="requirements"/>
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d05c0c639108 planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 6bb33ff0ff022029543e5e5ace7d16418715aa1c
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9 <command detect_errors="exit_code"><![CDATA[met4j networkAnalysis.ReactionDistanceMatrix -i "$inputPath"
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886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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10 #if str($sideCompoundFile) != 'None':
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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11 -sc "$sideCompoundFile"
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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12 #end if
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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13 $degree
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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14 #if str($rExclude) != 'None':
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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15 -re "$rExclude"
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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16 #end if
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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17 #if str($rxnFile) != 'None':
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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18 -s "$rxnFile"
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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19 #end if
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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20 #if str($weightFile) != 'None':
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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21 -w "$weightFile"
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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22 #end if
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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23 $undirected
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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24 -o "$outputPath"
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25 ]]></command>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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26 <inputs>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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27 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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28 <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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29 <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"/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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30 <param argument="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" type="data" value=""/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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31 <param argument="-s" format="txt" label="an optional file containing list of reactions of interest." name="rxnFile" optional="true" type="data" value=""/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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32 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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33 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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34 </inputs>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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35 <outputs>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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36 <data format="csv" name="outputPath"/>
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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37 </outputs>
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38 <tests/>
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39 <help><![CDATA[Create a reaction to reaction distance matrix.
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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40 The distance between two reactions is computed as the length of the shortest path connecting the two in the reaction graph, where two reactions are linked if they produce a metabolite consumed by the other or the other way around.
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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41 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.
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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42 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.
886e0872fa6c planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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43 @ATTRIBUTION@]]></help>
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44 <citations/>
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45 </tool>