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annotate build/tools/Sbml2Graph/Sbml2Graph.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
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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="2.0.0">
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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:2.0.0</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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37 <param name="inputPath" value="toy_model.xml"/>
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38 <param name="format" value="gml"/>
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39 <output name="output">
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40 <assert_contents>
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41 <has_line_matching expression=".*node.*" n="8"/>
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42 <has_line_matching expression=".*edge.*" n="9"/>
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43 </assert_contents>
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44 </output>
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45 </test>
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46 <test>
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47 <param name="inputPath" value="toy_model.xml"/>
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48 <param name="bipartite" value="true"/>
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49 <param name="compound" value="false"/>
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50 <param name="format" value="gml"/>
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51 <output name="output">
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52 <assert_contents>
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53 <has_line_matching expression=".*node.*" n="15"/>
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54 <has_line_matching expression=".*edge.*" n="17"/>
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55 </assert_contents>
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56 </output>
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57 </test>
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58 <test>
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59 <param name="inputPath" value="toy_model.xml"/>
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60 <param name="reaction" value="true"/>
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61 <param name="compound" value="false"/>
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62 <param name="format" value="gml"/>
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63 <output name="output">
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64 <assert_contents>
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65 <has_line_matching expression=".*node.*" n="7"/>
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66 <has_line_matching expression=".*edge.*" n="8"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
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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>
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73 <citations>
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74 <citation type="doi">10.1109/tcbb.2008.79</citation>
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75 </citations>
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76 </tool>