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comparison build/tools/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
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children 1436e9cde9c9
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.3.0">
3 <description>Create a tabulated file with metabolite attributes from a SBML file</description>
4 <xrefs>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml"
11 -o "$outputFile"
12 ]]></command>
13 <inputs>
14 <param argument="-s" format="sbml" label="Sbml file" name="sbml" optional="false" type="data" value=""/>
15 </inputs>
16 <outputs>
17 <data format="tsv" name="outputFile"/>
18 </outputs>
19 <tests>
20 <test>
21 <param name="sbml" value="toy_model.xml"/>
22 <output ftype="tsv" name="outputFile">
23 <assert_contents>
24 <has_n_lines n="9"/>
25 <has_n_columns n="6"/>
26 <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/>
27 <has_line_matching expression=".*C.*NC.*" n="1"/>
28 </assert_contents>
29 </output>
30 </test>
31 </tests>
32 <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help>
33 <citations/>
34 </tool>