Mercurial > repos > metexplore > met4j

annotate build/tools/BipartiteDistanceMatrix/BipartiteDistanceMatrix.xml @ 7:1436e9cde9c9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author metexplore
date Tue, 04 Jul 2023 10:21:26 +0000
parents 7a6f2380fc1d
children 1274e2a62479
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
7
1436e9cde9c9 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents: 6
diff changeset
2 <tool id="met4j_BipartiteDistanceMatrix" name="BipartiteDistanceMatrix" version="1.4.0">
6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
3 <description>Create a compound to reactions distance matrix.</description>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
4 <xrefs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
5 <xref type="bio.tools">met4j</xref>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
6 </xrefs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
7 <requirements>
7
1436e9cde9c9 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents: 6
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container>
6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
9 </requirements>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.BipartiteDistanceMatrix -i "$inputPath"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
11 #if str($sideCompoundFile) != 'None':
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
12 -sc "$sideCompoundFile"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
13 #end if
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
14 #if str($rExclude) != 'None':
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
15 -re "$rExclude"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
16 #end if
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
17 #if str($metFile) != 'None':
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
18 -m "$metFile"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
19 #end if
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
20 #if str($rxnFile) != 'None':
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
21 -r "$rxnFile"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
22 #end if
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
23 #if str($weightFile) != 'None':
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
24 -w "$weightFile"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
25 #end if
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
26 $undirected
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
27 $full
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
28 -o "$outputPath"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
29 ]]></command>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
30 <inputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
31 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
32 <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
33 <param argument="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" type="data" value=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
34 <param argument="-m" format="txt" label="an optional file containing list of compounds of interest." name="metFile" optional="true" type="data" value=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
35 <param argument="-r" format="txt" label="an optional file containing list of reactions of interest." name="rxnFile" optional="true" type="data" value=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
36 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
37 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
38 <param argument="-f" checked="false" falsevalue="" label="compute full pairwise matrix from both reactions and compounds lists" name="full" truevalue="-f" type="boolean" value="false"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
39 </inputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
40 <outputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
41 <data format="csv" name="outputPath"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
42 </outputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
43 <tests/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
44 <help><![CDATA[Create a compound to reactions distance matrix.
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
45 The distance between two nodes (metabolite or reaction) is computed as the length of the shortest path connecting the two in the bipartite graph, Bipartite graph are composed of two distinct sets of nodes and two nodes can be linked only if they are from distinct sets.
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
46 Therefore a metabolite node can be linked to a reaction node if the metabolite is a substrate or product of the reaction.
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
47 An optional custom 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.Custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
48 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
49 <citations/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
50 </tool>