Mercurial > repos > metexplore > met4j

annotate 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
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="2.0.1">
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3 <description>Create a graph representation of a SBML file content, and export it in graph file format.</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
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11 $bipartite
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12 $compound
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13 $reaction
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14 #if str($format):
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15 -f "$format"
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16 #end if
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17 -o "$output"
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18 ]]></command>
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19 <inputs>
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20 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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21 <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/>
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22 <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/>
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23 <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/>
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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">
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25 <option value="gml">gml</option>
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26 <option selected="true" value="tab">tab</option>
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27 <option value="nodeList">nodeList</option>
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28 <option value="json">json</option>
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29 <option value="matrix">matrix</option>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format="txt" name="output"/>
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34 </outputs>
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35 <tests>
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36 <test>
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38 <param name="inputPath" value="toy_model.xml"/>
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40 <param name="format" value="gml"/>
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42 <output name="output">
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44 <assert_contents>
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46 <has_line_matching expression=".*node.*" n="8"/>
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48 <has_line_matching expression=".*edge.*" n="9"/>
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50 </assert_contents>
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52 </output>
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54 </test>
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55 <test>
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57 <param name="inputPath" value="toy_model.xml"/>
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59 <param name="bipartite" value="true"/>
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61 <param name="compound" value="false"/>
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63 <param name="format" value="gml"/>
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65 <output name="output">
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67 <assert_contents>
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69 <has_line_matching expression=".*node.*" n="15"/>
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71 <has_line_matching expression=".*edge.*" n="17"/>
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73 </assert_contents>
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75 </output>
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77 </test>
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78 <test>
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80 <param name="inputPath" value="toy_model.xml"/>
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82 <param name="reaction" value="true"/>
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84 <param name="compound" value="false"/>
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86 <param name="format" value="gml"/>
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88 <output name="output">
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90 <assert_contents>
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92 <has_line_matching expression=".*node.*" n="7"/>
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94 <has_line_matching expression=".*edge.*" n="8"/>
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96 </assert_contents>
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98 </output>
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100 </test>
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101 </tests>
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102 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
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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>
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104 <citations>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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105 <citation type="doi">10.1109/tcbb.2008.79</citation>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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106 </citations>
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107 </tool>