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comparison tools/convert/Kegg2Sbml/Kegg2Sbml.xml @ 0:dcd16521b969 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author metexplore
date Fri, 10 Jun 2022 10:31:34 +0000
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children 9b162ee6ff8e
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-1:000000000000 0:dcd16521b969
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="0.11.0">
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:0.11.0</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 <!-- <test maxseconds="600">
27 <param name="org" value="buc"/>
28 <output ftype="sbml" name="sbml">
29 <assert_contents>
30 <is_valid_xml/>
31
32 </assert_contents>
33 </output>
34 </test> -->
35 </tests>
36 <help><![CDATA[Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.
37 Errors returned by this program could be due to Kegg API dysfunctions or limitations. Try later if this problem occurs.]]></help>
38 </tool>