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comparison tools/attributes/GetMetaboliteAttributes/GetMetaboliteAttributes.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
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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_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="2.0.0"> 2 <tool id="met4j_GetMetaboliteAttributes" name="GetMetaboliteAttributes" version="2.0.1">
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: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 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>
21
21 <param name="sbml" value="toy_model.xml"/> 22 <param name="sbml" value="toy_model.xml"/>
23
22 <output ftype="tsv" name="outputFile"> 24 <output ftype="tsv" name="outputFile">
25
23 <assert_contents> 26 <assert_contents>
27
24 <has_n_lines n="9"/> 28 <has_n_lines n="9"/>
29
25 <has_n_columns n="6"/> 30 <has_n_columns n="6"/>
31
26 <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/> 32 <has_line_matching expression=".*1S/C2H6O/c1-2-3/h3H,2H2,1H3.*" n="1"/>
33
27 <has_line_matching expression=".*C.*NC.*" n="1"/> 34 <has_line_matching expression=".*C.*NC.*" n="1"/>
35
28 </assert_contents> 36 </assert_contents>
37
29 </output> 38 </output>
39
30 </test> 40 </test>
31 </tests> 41 </tests>
32 <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help> 42 <help><![CDATA[Create a tabulated file with metabolite attributes from a SBML file]]></help>
33 <citations/> 43 <citations/>
34 </tool> 44 </tool>