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comparison tools/convert/FbcToNotes/FbcToNotes.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
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10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_FbcToNotes" name="FbcToNotes" version="2.0.0"> 2 <tool id="met4j_FbcToNotes" name="FbcToNotes" version="2.0.1">
3 <description>Convert FBC package annotations to sbml html notes</description> 3 <description>Convert FBC package annotations to sbml html notes</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:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath"
11 -o "$outputPath" 11 -o "$outputPath"
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
16 <outputs> 16 <outputs>
17 <data format="sbml" name="outputPath"/> 17 <data format="sbml" name="outputPath"/>
18 </outputs> 18 </outputs>
19 <tests> 19 <tests>
20 <test> 20 <test>
21
21 <param name="inputPath" value="ECOL.xml"/> 22 <param name="inputPath" value="ECOL.xml"/>
23
22 <output ftype="sbml" name="outputPath"> 24 <output ftype="sbml" name="outputPath">
25
23 <assert_contents> 26 <assert_contents>
27
24 <is_valid_xml/> 28 <is_valid_xml/>
29
25 <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/> 30 <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/>
31
26 </assert_contents> 32 </assert_contents>
33
27 </output> 34 </output>
35
28 </test> 36 </test>
29 </tests> 37 </tests>
30 <help><![CDATA[Convert FBC package annotations to sbml html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help> 38 <help><![CDATA[Convert FBC package annotations to sbml html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help>
31 <citations> 39 <citations>
32 <citation type="doi">10.1515/jib-2017-0082</citation> 40 <citation type="doi">10.1515/jib-2017-0082</citation>