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comparison tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml @ 1:9b162ee6ff8e draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
author metexplore
date Mon, 27 Jun 2022 13:41:08 +0000
parents dcd16521b969
children e69a78624877
comparison
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0:dcd16521b969 1:9b162ee6ff8e
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="0.11.0"> 2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="0.12.0">
3 <description>Create a compound to compound distance matrix.</description> 3 <description>Create a compound to compound distance matrix.</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -s "$sideCompoundFile" 12 -sc "$sideCompoundFile"
13 #end if
14 #if str($seedFile) != 'None':
15 -s "$seedFile"
13 #end if 16 #end if
14 $degree 17 $degree
15 #if str($weightFile) != 'None': 18 #if str($weightFile) != 'None':
16 -w "$weightFile" 19 -w "$weightFile"
17 #end if 20 #end if
18 $undirected 21 $undirected
19 -o "$outputPath" 22 -o "$outputPath"
20 ]]></command> 23 ]]></command>
21 <inputs> 24 <inputs>
22 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 25 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
23 <param argument="-s" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> 26 <param argument="-sc" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
27 <param argument="-s" format="text" 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=""/>
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"/> 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"/>
25 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> 29 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
26 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> 30 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
27 </inputs> 31 </inputs>
28 <outputs> 32 <outputs>
53 </tests> 57 </tests>
54 <help><![CDATA[Create a compound to compound distance matrix. 58 <help><![CDATA[Create a compound to compound distance matrix.
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. 59 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.
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. 60 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.
57 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help> 61 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help>
62 <citations/>
58 </tool> 63 </tool>