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comparison tools/convert/FbcToNotes/FbcToNotes.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 7a6f2380fc1d
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_FbcToNotes" name="FbcToNotes" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_FbcToNotes" name="FbcToNotes" version="develop">
3 <description>Convert FBC package annotations to sbml 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:MET4J_VERSION_TEST</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</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>
14 <param argument="-i" format="sbml" label="input file" name="inputPath" optional="false" type="data" value=""/> 14 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
15 </inputs> 15 </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>
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21 <param name="inputPath" value="ECOL.xml"/> 32 <param name="inputPath" value="ECOL.xml"/>
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22 <output ftype="sbml" name="outputPath"> 44 <output ftype="sbml" name="outputPath">
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23 <assert_contents> 56 <assert_contents>
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24 <is_valid_xml/> 68 <is_valid_xml/>
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25 <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/> 80 <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/>
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26 </assert_contents> 92 </assert_contents>
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27 </output> 104 </output>
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28 </test> 116 </test>
29 </tests> 117 </tests>
30 <help><![CDATA[Convert FBC package annotations to sbml notes]]></help> 118 <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/> 119 <citations>
120 <citation type="doi">10.1515/jib-2017-0082</citation>
121 </citations>
32 </tool> 122 </tool>