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comparison tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
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9:0976a6257300 10:6a112eaf8f38
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="develop"> 2 <tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="2.0.0">
3 <description>Create a tabulated file with metabolite attributes from a SBML file</description> 3 <description>Create a tabulated file with metabolite attributes from a SBML file</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:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetMetaboliteAttributes -i "$sbml" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetMetaboliteAttributes -i "$sbml"
11 -o "$outputFile" 11 -o "$outputFile"
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
16 <outputs> 16 <outputs>
17 <data format="tsv" name="outputFile"/> 17 <data format="tsv" name="outputFile"/>
18 </outputs> 18 </outputs>
19 <tests> 19 <tests>
20 <test> 20 <test>
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27 <param name="sbml" value="toy_model.xml"/> 21 <param name="sbml" value="toy_model.xml"/>
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34 <output ftype="tsv" name="outputFile"> 22 <output ftype="tsv" name="outputFile">
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41 <assert_contents> 23 <assert_contents>
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48 <has_n_lines n="9"/> 24 <has_n_lines n="9"/>
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55 <has_n_columns n="6"/> 25 <has_n_columns n="6"/>
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62 <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/> 26 <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/>
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69 <has_line_matching expression=".*C.*NC.*" n="1"/> 27 <has_line_matching expression=".*C.*NC.*" n="1"/>
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76 </assert_contents> 28 </assert_contents>
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83 </output> 29 </output>
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90 </test> 30 </test>
91 </tests> 31 </tests>
92 <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help> 32 <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help>
93 <citations/> 33 <citations/>
94 </tool> 34 </tool>