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comparison build/tools/GetEntities/GetEntities.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_GetEntities" name="GetEntities" version="2.0.0"> 2 <tool id="met4j_GetEntities" name="GetEntities" version="2.0.1">
3 <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</description> 3 <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</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.GetEntities -i "$sbml" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetEntities -i "$sbml"
11 $printMetabolites 11 $printMetabolites
12 $printReactions 12 $printReactions
13 $printCompartments 13 $printCompartments
28 <outputs> 28 <outputs>
29 <data format="tsv" name="outputFile"/> 29 <data format="tsv" name="outputFile"/>
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>
32 <test> 32 <test>
33
33 <param name="sbml" value="Human-GEM_pathways.xml"/> 34 <param name="sbml" value="Human-GEM_pathways.xml"/>
35
34 <output ftype="tsv" name="outputFile"> 36 <output ftype="tsv" name="outputFile">
37
35 <assert_contents> 38 <assert_contents>
39
36 <has_text_matching expression="GENE" n="86"/> 40 <has_text_matching expression="GENE" n="86"/>
41
37 <has_text_matching expression="METABOLITE" n="111"/> 42 <has_text_matching expression="METABOLITE" n="111"/>
43
38 <has_text_matching expression="REACTION" n="75"/> 44 <has_text_matching expression="REACTION" n="75"/>
45
39 <has_text_matching expression="PATHWAY" n="3"/> 46 <has_text_matching expression="PATHWAY" n="3"/>
47
40 <has_text_matching expression="COMPARTMENT" n="5"/> 48 <has_text_matching expression="COMPARTMENT" n="5"/>
49
41 </assert_contents> 50 </assert_contents>
51
42 </output> 52 </output>
53
43 </test> 54 </test>
44 <test> 55 <test>
56
45 <param name="sbml" value="Human-GEM_pathways.xml"/> 57 <param name="sbml" value="Human-GEM_pathways.xml"/>
58
46 <param name="printReactions" value="true"/> 59 <param name="printReactions" value="true"/>
60
47 <param name="printMetabolites" value="true"/> 61 <param name="printMetabolites" value="true"/>
62
48 <param name="printGenes" value="true"/> 63 <param name="printGenes" value="true"/>
64
49 <param name="printCompartments" value="true"/> 65 <param name="printCompartments" value="true"/>
66
50 <param name="noTypeCol" value="true"/> 67 <param name="noTypeCol" value="true"/>
68
51 <output ftype="tsv" name="outputFile"> 69 <output ftype="tsv" name="outputFile">
70
52 <assert_contents> 71 <assert_contents>
72
53 <has_n_lines n="277"/> 73 <has_n_lines n="277"/>
74
54 </assert_contents> 75 </assert_contents>
76
55 </output> 77 </output>
78
56 </test> 79 </test>
57 </tests> 80 </tests>
58 <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.]]></help> 81 <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.]]></help>
59 <citations/> 82 <citations/>
60 </tool> 83 </tool>