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comparison build/tools/Kegg2Sbml/Kegg2Sbml.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_Kegg2Sbml" name="Kegg2Sbml" version="1.3.0">
3 <description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</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 convert.Kegg2Sbml#if str($org):
11 -org "$org"
12 #end if
13 -sbml "$sbml"
14 ]]></command>
15 <inputs>
16 <param argument="-org" label="[] Kegg org id. Must be 3 letters (" name="org" optional="true" type="text" value="">
17 <sanitizer invalid_char="_">
18 <valid initial="string.printable"/>
19 </sanitizer>
20 </param>
21 </inputs>
22 <outputs>
23 <data format="sbml" name="sbml"/>
24 </outputs>
25 <tests/>
26 <help><![CDATA[Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.
27 Errors returned by this program could be due to Kegg API dysfunctions or limitations. Try later if this problem occurs.]]></help>
28 <citations/>
29 </tool>