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comparison tools/networkAnalysis/CompoundNet/CompoundNet.xml @ 5:35c9abcd8934 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
author metexplore
date Thu, 12 Jan 2023 13:45:13 +0000
parents ae4c301919c4
children 7a6f2380fc1d
comparison
equal deleted inserted replaced
4:ae4c301919c4 5:35c9abcd8934
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_CompoundNet" name="CompoundNet" version="1.2.0"> 2 <tool id="met4j_CompoundNet" name="CompoundNet" version="1.2.1">
3 <description>Advanced creation of a compound graph representation of a SBML file content</description> 3 <description>Advanced creation of a compound graph representation of a SBML file content</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:1.2.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath"
11 #if str($inputSide) != 'None': 11 #if str($inputSide) != 'None':
12 -sc "$inputSide" 12 -sc "$inputSide"
13 #end if 13 #end if
25 $asMatrix 25 $asMatrix
26 -o "$outputPath" 26 -o "$outputPath"
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 29 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
30 <param argument="-sc" format="" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/> 30 <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
31 <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"> 31 <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">
32 <option selected="true" value="no">no</option> 32 <option selected="true" value="no">no</option>
33 <option value="by_name">by_name</option> 33 <option value="by_name">by_name</option>
34 <option value="by_id">by_id</option> 34 <option value="by_id">by_id</option>
35 </param> 35 </param>
40 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> 40 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
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"/> 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"/>
42 <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/> 42 <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/>
43 </inputs> 43 </inputs>
44 <outputs> 44 <outputs>
45 <data format="" name="outputPath"/> 45 <data format="gml" name="outputPath"/>
46 </outputs> 46 </outputs>
47 <tests> 47 <tests>
48 <test> 48 <test>
49 <param name="inputPath" value="XF_network.sbml"/> 49 <param name="inputPath" value="XF_network.sbml"/>
50 <param name="inputSide" value="XF_network_C_Side.tab"/> 50 <param name="inputSide" value="XF_network_C_Side.tab"/>