Mercurial > repos > metexplore > met4j_sbml2graph

annotate Sbml2Graph.xml @ 2:1a4b8947e680 draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 71335d4a636672d264cc4f443c07856907571928
author metexplore
date Fri, 21 Nov 2025 10:22:29 +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 "$format"
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15 #end if
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16 -o "$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">
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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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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data format="txt" name="output"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="inputPath" value="toy_model.xml"/>
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37 <param name="format" value="gml"/>
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38 <output name="output">
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39 <assert_contents>
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40 <has_line_matching expression=".*node.*" n="8"/>
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41 <has_line_matching expression=".*edge.*" n="9"/>
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42 </assert_contents>
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43 </output>
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44 </test>
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45 <test>
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46 <param name="inputPath" value="toy_model.xml"/>
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47 <param name="bipartite" value="true"/>
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48 <param name="compound" value="false"/>
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49 <param name="format" value="gml"/>
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50 <output name="output">
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51 <assert_contents>
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52 <has_line_matching expression=".*node.*" n="15"/>
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53 <has_line_matching expression=".*edge.*" n="17"/>
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54 </assert_contents>
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55 </output>
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56 </test>
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57 <test>
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58 <param name="inputPath" value="toy_model.xml"/>
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59 <param name="reaction" value="true"/>
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60 <param name="compound" value="false"/>
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61 <param name="format" value="gml"/>
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62 <output name="output">
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63 <assert_contents>
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64 <has_line_matching expression=".*node.*" n="7"/>
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65 <has_line_matching expression=".*edge.*" n="8"/>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
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71 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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72 @ATTRIBUTION@]]></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>