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comparison build/tools/Sbml2Graph/Sbml2Graph.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
children
comparison
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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_Sbml2Graph" name="Sbml2Graph" version="2.0.0"> 2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.1">
3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description> 3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</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 convert.Sbml2Graph -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
11 $bipartite 11 $bipartite
12 $compound 12 $compound
13 $reaction 13 $reaction
32 <outputs> 32 <outputs>
33 <data format="txt" name="output"/> 33 <data format="txt" name="output"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37
37 <param name="inputPath" value="toy_model.xml"/> 38 <param name="inputPath" value="toy_model.xml"/>
39
38 <param name="format" value="gml"/> 40 <param name="format" value="gml"/>
41
39 <output name="output"> 42 <output name="output">
43
40 <assert_contents> 44 <assert_contents>
45
41 <has_line_matching expression=".*node.*" n="8"/> 46 <has_line_matching expression=".*node.*" n="8"/>
47
42 <has_line_matching expression=".*edge.*" n="9"/> 48 <has_line_matching expression=".*edge.*" n="9"/>
49
43 </assert_contents> 50 </assert_contents>
51
44 </output> 52 </output>
53
45 </test> 54 </test>
46 <test> 55 <test>
56
47 <param name="inputPath" value="toy_model.xml"/> 57 <param name="inputPath" value="toy_model.xml"/>
58
48 <param name="bipartite" value="true"/> 59 <param name="bipartite" value="true"/>
60
49 <param name="compound" value="false"/> 61 <param name="compound" value="false"/>
62
50 <param name="format" value="gml"/> 63 <param name="format" value="gml"/>
64
51 <output name="output"> 65 <output name="output">
66
52 <assert_contents> 67 <assert_contents>
68
53 <has_line_matching expression=".*node.*" n="15"/> 69 <has_line_matching expression=".*node.*" n="15"/>
70
54 <has_line_matching expression=".*edge.*" n="17"/> 71 <has_line_matching expression=".*edge.*" n="17"/>
72
55 </assert_contents> 73 </assert_contents>
74
56 </output> 75 </output>
76
57 </test> 77 </test>
58 <test> 78 <test>
79
59 <param name="inputPath" value="toy_model.xml"/> 80 <param name="inputPath" value="toy_model.xml"/>
81
60 <param name="reaction" value="true"/> 82 <param name="reaction" value="true"/>
83
61 <param name="compound" value="false"/> 84 <param name="compound" value="false"/>
85
62 <param name="format" value="gml"/> 86 <param name="format" value="gml"/>
87
63 <output name="output"> 88 <output name="output">
89
64 <assert_contents> 90 <assert_contents>
91
65 <has_line_matching expression=".*node.*" n="7"/> 92 <has_line_matching expression=".*node.*" n="7"/>
93
66 <has_line_matching expression=".*edge.*" n="8"/> 94 <has_line_matching expression=".*edge.*" n="8"/>
95
67 </assert_contents> 96 </assert_contents>
97
68 </output> 98 </output>
99
69 </test> 100 </test>
70 </tests> 101 </tests>
71 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. 102 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
72 The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help> 103 The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help>
73 <citations> 104 <citations>