Mercurial > repos > metexplore > met4j

annotate tools/convert/Sbml2Graph/Sbml2Graph.xml @ 5:35c9abcd8934 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
author metexplore
date Thu, 12 Jan 2023 13:45:13 +0000
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children 7a6f2380fc1d
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dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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1 <?xml version="1.0" encoding="UTF-8"?>
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35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
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2 <tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.2.1">
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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:1.2.1</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 $tab
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15 $gml
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16 -o "$outputPath"
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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="-tab" checked="false" falsevalue="" label="export in tabulated file" name="tab" truevalue="-tab" type="boolean" value="false"/>
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24 <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/>
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25 </inputs>
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26 <outputs>
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27 <data format="txt" name="outputPath"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="inputPath" value="toy_model.xml"/>
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32 <output name="outputPath">
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33 <assert_contents>
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34 <has_n_lines n="101"/>
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35 </assert_contents>
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36 </output>
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37 </test>
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38 <test>
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39 <param name="inputPath" value="toy_model.xml"/>
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40 <param name="bipartite" value="true"/>
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41 <param name="compound" value="false"/>
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42 <output name="outputPath">
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43 <assert_contents>
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44 <has_n_lines n="184"/>
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45 </assert_contents>
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46 </output>
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47 </test>
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48 <test>
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49 <param name="inputPath" value="toy_model.xml"/>
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50 <param name="reaction" value="true"/>
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51 <param name="compound" value="false"/>
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52 <output name="outputPath">
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53 <assert_contents>
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54 <has_n_lines n="90"/>
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55 </assert_contents>
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56 </output>
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57 </test>
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58 </tests>
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59 <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
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60 The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help>
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61 <citations/>
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62 </tool>