Mercurial > repos > metexplore > met4j_sbml2graph

annotate Sbml2Graph.xml @ 3:c17685061077 draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:31:41 +0000
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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="@TOOL_VERSION@">
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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 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[met4j convert.Sbml2Graph -i "$inputPath"
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10 $bipartite
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11 $compound
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12 $reaction
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13 #if str($format):
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14 -f "$format"
5e7aa3ae9c16 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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15 #end if
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16 -o "$output"
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17 ]]></command>
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18 <inputs>
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19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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20 <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/>
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21 <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/>
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22 <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/>
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23 <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">
5e7aa3ae9c16 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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24 <option value="gml">gml</option>
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25 <option selected="true" value="tab">tab</option>
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26 <option value="nodeList">nodeList</option>
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27 <option value="json">json</option>
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28 <option value="matrix">matrix</option>
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c17685061077 planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
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29 <option value="jsonviz">jsonviz</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 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
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37 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.
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38 @ATTRIBUTION@]]></help>
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39 <citations>
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40 <citation type="doi">10.1109/tcbb.2008.79</citation>
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41 </citations>
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42 </tool>