Mercurial > repos > metexplore > met4j

annotate tools/networkAnalysis/NetworkSummary/NetworkSummary.xml @ 3:6bd9aad9626d 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 a078bf88575dac3d09462252eae92c24f34d0414
author metexplore
date Fri, 29 Jul 2022 13:23:40 +0000
parents e69a78624877
children ae4c301919c4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents: 2
diff changeset
2 <tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.1.0">
0
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
3 <description>Create a report summarizing several graph measures characterising the structure of the network.</description>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
4 <xrefs>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
5 <xref type="bio.tools">met4j</xref>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
6 </xrefs>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
7 <requirements>
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents: 2
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
0
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
9 </requirements>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath"
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
11 #if str($sideCompoundFile) != 'None':
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
12 -s "$sideCompoundFile"
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
13 #end if
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
14 $skipdist
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
15 $directed
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
16 -o "$outputPath"
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
17 ]]></command>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
18 <inputs>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
20 <param argument="-s" format="" label="an optional file containing list of side compounds to ignore (recommended)" name="sideCompoundFile" optional="true" type="data" value=""/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
21 <param argument="-sd" checked="false" falsevalue="" label="skip full distance matrix computation (quick summary)" name="skipdist" truevalue="-sd" type="boolean" value="false"/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
22 <param argument="-d" checked="false" falsevalue="" label="use reaction direction for distances" name="directed" truevalue="-d" type="boolean" value="false"/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
23 </inputs>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
24 <outputs>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
25 <data format="" name="outputPath"/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
26 </outputs>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
27 <tests>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
28 <test>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
29 <param name="inputPath" value="toy_model.xml"/>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
30 <output name="outputPath">
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
31 </output>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
32 </test>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
33 </tests>
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
34 <help><![CDATA[Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help>
1
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents: 0
diff changeset
35 <citations/>
0
dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
metexplore
parents:
diff changeset
36 </tool>