comparison tools/convert/Sbml2Graph/Sbml2Graph.xml @ 0:dcd16521b969 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author metexplore
date Fri, 10 Jun 2022 10:31:34 +0000
parents
children 9b162ee6ff8e
comparison
equal deleted inserted replaced
-1:000000000000 0:dcd16521b969
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="0.11.0">
3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description>
4 <xrefs>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
11 $bipartite
12 $compound
13 $reaction
14 $tab
15 $gml
16 -o "$outputPath"
17 ]]></command>
18 <inputs>
19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
20 <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/>
21 <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/>
22 <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/>
23 <param argument="-tab" checked="false" falsevalue="" label="export in tabulated file" name="tab" truevalue="-tab" type="boolean" value="false"/>
24 <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/>
25 </inputs>
26 <outputs>
27 <data format="text" name="outputPath"/>
28 </outputs>
29 <tests>
30 <test>
31 <param name="inputPath" value="toy_model.xml"/>
32 <output name="outputPath">
33 <assert_contents>
34 <has_n_lines n="101"/>
35 </assert_contents>
36 </output>
37 </test>
38 <test>
39 <param name="inputPath" value="toy_model.xml"/>
40 <param name="bipartite" value="true"/>
41 <param name="compound" value="false"/>
42 <output name="outputPath">
43 <assert_contents>
44 <has_n_lines n="184"/>
45 </assert_contents>
46 </output>
47 </test>
48 <test>
49 <param name="inputPath" value="toy_model.xml"/>
50 <param name="reaction" value="true"/>
51 <param name="compound" value="false"/>
52 <output name="outputPath">
53 <assert_contents>
54 <has_n_lines n="90"/>
55 </assert_contents>
56 </output>
57 </test>
58 </tests>
59 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
60 The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help>
61 </tool>