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comparison build/tools/Sbml2Graph/Sbml2Graph.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 1274e2a62479
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.5.0"> 2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="develop">
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:1.5.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</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
14 $tab 14 #if str($format):
15 $gml 15 -f "$format"
16 -o "$outputPath" 16 #end if
17 -o "$output"
17 ]]></command> 18 ]]></command>
18 <inputs> 19 <inputs>
19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 20 <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="-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="-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="-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="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
24 <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/> 25 <option value="gml">gml</option>
26 <option selected="true" value="tab">tab</option>
27 <option value="nodeList">nodeList</option>
28 <option value="json">json</option>
29 <option value="matrix">matrix</option>
30 </param>
25 </inputs> 31 </inputs>
26 <outputs> 32 <outputs>
27 <data format="txt" name="outputPath"/> 33 <data format="txt" name="output"/>
28 </outputs> 34 </outputs>
29 <tests> 35 <tests>
30 <test> 36 <test>
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31 <param name="inputPath" value="toy_model.xml"/> 40 <param name="inputPath" value="toy_model.xml"/>
32 <output name="outputPath"> 41
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44 <param name="format" value="gml"/>
45
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48 <output name="output">
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33 <assert_contents> 52 <assert_contents>
34 <has_n_lines n="101"/> 53
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56 <has_line_matching expression=".*node.*" n="8"/>
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60 <has_line_matching expression=".*edge.*" n="9"/>
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35 </assert_contents> 64 </assert_contents>
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36 </output> 68 </output>
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37 </test> 72 </test>
38 <test> 73 <test>
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39 <param name="inputPath" value="toy_model.xml"/> 77 <param name="inputPath" value="toy_model.xml"/>
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40 <param name="bipartite" value="true"/> 81 <param name="bipartite" value="true"/>
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41 <param name="compound" value="false"/> 85 <param name="compound" value="false"/>
42 <output name="outputPath"> 86
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89 <param name="format" value="gml"/>
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93 <output name="output">
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43 <assert_contents> 97 <assert_contents>
44 <has_n_lines n="184"/> 98
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101 <has_line_matching expression=".*node.*" n="15"/>
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105 <has_line_matching expression=".*edge.*" n="17"/>
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45 </assert_contents> 109 </assert_contents>
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46 </output> 113 </output>
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47 </test> 117 </test>
48 <test> 118 <test>
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49 <param name="inputPath" value="toy_model.xml"/> 122 <param name="inputPath" value="toy_model.xml"/>
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50 <param name="reaction" value="true"/> 126 <param name="reaction" value="true"/>
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51 <param name="compound" value="false"/> 130 <param name="compound" value="false"/>
52 <output name="outputPath"> 131
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134 <param name="format" value="gml"/>
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138 <output name="output">
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53 <assert_contents> 142 <assert_contents>
54 <has_n_lines n="90"/> 143
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147 <has_line_matching expression=".*node.*" n="7"/>
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151 <has_line_matching expression=".*edge.*" n="8"/>
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55 </assert_contents> 156 </assert_contents>
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56 </output> 161 </output>
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57 </test> 165 </test>
58 </tests> 166 </tests>
59 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format. 167 <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> 168 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>
61 <citations/> 169 <citations>
170 <citation type="doi">10.1109/tcbb.2008.79</citation>
171 </citations>
62 </tool> 172 </tool>