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annotate tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="develop">
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3 <description>Provides tabulated compound graph edge list, with one column with target's degree.</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:develop</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DegreeWeighting#if str($pow):
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11 -pow "$pow"
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12 #end if
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13 -s "$inputPath"
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14 #if str($inputSide) != 'None':
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15 -sc "$inputSide"
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16 #end if
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17 #if str($mergingStrat):
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18 -mc "$mergingStrat"
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19 #end if
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20 $mergeEdges
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21 $undirected
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22 $computeWeight
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23 $removeNaN
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24 -o "$outputPath"
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25 ]]></command>
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26 <inputs>
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27 <param argument="-pow" label="set weights as the degree raised to the power of number in parameter." name="pow" optional="true" type="text" value="1">
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28 <sanitizer invalid_char="_">
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29 <valid initial="string.printable"/>
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30 </sanitizer>
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31 </param>
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32 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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33 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
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34 <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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35 <option selected="true" value="no">no</option>
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36 <option value="by_name">by_name</option>
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37 <option value="by_id">by_id</option>
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38 </param>
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39 <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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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="-nan" checked="false" falsevalue="" label="do not output edges with undefined weight" name="removeNaN" truevalue="-nan" type="boolean" value="false"/>
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43 </inputs>
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44 <outputs>
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45 <data format="tsv" name="outputPath"/>
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46 </outputs>
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47 <tests/>
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48 <help><![CDATA[Provides tabulated compound graph edge list, with one column with target's degree.Degree has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help>
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49 <citations>
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50 <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
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51 </citations>
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52 </tool>