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comparison tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
parents 35c9abcd8934
children
comparison
equal deleted inserted replaced
5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="1.2.1"> 2 <tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="MET4J_VERSION_TEST">
3 <description>Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology</description> 3 <description>Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology</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:1.2.1</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath"
11 #if str($inputSide) != 'None': 11 #if str($inputSide) != 'None':
12 -sc "$inputSide" 12 -sc "$inputSide"
13 #end if 13 #end if
43 <data format="tsv" name="outputPath"/> 43 <data format="tsv" name="outputPath"/>
44 </outputs> 44 </outputs>
45 <tests> 45 <tests>
46 <test> 46 <test>
47 <param name="inputPath" value="XF_network.sbml"/> 47 <param name="inputPath" value="XF_network.sbml"/>
48 <param name="targetsFilePath" value="SeedsAndTargets-result.tab"/>
49 <param name="source" value="true"/> 48 <param name="source" value="true"/>
50 <output ftype="tsv" name="outputPath"> 49 <output ftype="tsv" name="outputPath">
51 <assert_contents> 50 <assert_contents>
52 <has_n_columns n="1"/> 51 <has_n_columns n="1"/>
53 <has_n_lines n="109"/> 52 <has_n_lines n="109"/>
55 </assert_contents> 54 </assert_contents>
56 </output> 55 </output>
57 </test> 56 </test>
58 <test> 57 <test>
59 <param name="inputPath" value="XF_network.sbml"/> 58 <param name="inputPath" value="XF_network.sbml"/>
60 <param name="targetsFilePath" value="SeedsAndTargets-result.tab"/>
61 <param name="sink" value="true"/> 59 <param name="sink" value="true"/>
62 <param name="useInternal" value="true"/> 60 <param name="useInternal" value="true"/>
63 <param name="comp" value="e"/> 61 <param name="comp" value="e"/>
64 <output ftype="tsv" name="outputPath"> 62 <output ftype="tsv" name="outputPath">
65 <assert_contents> 63 <assert_contents>
69 </assert_contents> 67 </assert_contents>
70 </output> 68 </output>
71 </test> 69 </test>
72 <test> 70 <test>
73 <param name="inputPath" value="XF_network.sbml"/> 71 <param name="inputPath" value="XF_network.sbml"/>
74 <param name="targetsFilePath" value="SeedsAndTargets-result.tab"/>
75 <param name="sink" value="true"/> 72 <param name="sink" value="true"/>
76 <param name="useBorensteinAlg" value="true"/> 73 <param name="useBorensteinAlg" value="true"/>
77 <param name="comp" value="e"/> 74 <param name="comp" value="e"/>
78 <output ftype="tsv" name="outputPath"> 75 <output ftype="tsv" name="outputPath">
79 <assert_contents> 76 <assert_contents>