Mercurial > repos > metexplore > met4j_loadpoint

annotate LoadPoint.xml @ 3:48d5953d2ba8 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 15:30:34 +0000
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_LoadPoint" name="LoadPoint" version="@TOOL_VERSION@">
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3 <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[met4j networkAnalysis.LoadPoint -i "$inputPath"
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10 #if str($sideCompoundFile) != 'None':
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11 -s "$sideCompoundFile"
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12 #end if
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13 #if str($k):
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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14 -k "$k"
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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15 #end if
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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16 -o "$outputPath"
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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17 ]]></command>
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18 <inputs>
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19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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20 <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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21 <param argument="-k" label="Number of alternative paths to consider between a pair of connected metabolites" name="k" optional="true" type="text" value="1">
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22 <sanitizer invalid_char="_">
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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23 <valid initial="string.printable"/>
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24 </sanitizer>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data format="tsv" name="outputPath"/>
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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29 </outputs>
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30 <tests/>
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31 <help><![CDATA[Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug targets.
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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32 From Rahman et al. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinf. (2006):
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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33 For a given metabolic network, the load L on metabolite m can be defined as :
5aafcd772390 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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34 ln [(pm/km)/(∑Mi=1Pi)/(∑Mi=1Ki)]
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35 p is the number of shortest paths passing through a metabolite m;
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36 k is the number of nearest neighbour links for m in the network;
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37 P is the total number of shortest paths;
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38 K is the sum of links in the metabolic network of M metabolites (where M is the number of metabolites in the network).
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39 Use of the logarithm makes the relevant values more distinguishable.
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40 @ATTRIBUTION@]]></help>
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41 <citations>
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42 <citation type="doi">10.1093/bioinformatics/btl181</citation>
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43 </citations>
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44 </tool>