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annotate build/tools/DecomposeSBML/DecomposeSBML.xml @ 8:1274e2a62479 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
author metexplore
date Wed, 26 Jul 2023 15:33:45 +0000
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1 <?xml version="1.0" encoding="UTF-8"?>
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1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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2 <tool id="met4j_DecomposeSBML" name="DecomposeSBML" version="1.5.0">
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3 <description>Parse SBML to render list of composing entities: metabolites, reactions, genes and others.</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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1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.DecomposeSBML -i "$sbml"
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11 $printMetabolites
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12 $printReactions
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13 $printCompartments
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14 $printPathways
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15 $printGenes
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16 $noTypeCol
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17 -o "$outputFile"
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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="sbml" optional="false" type="data" value=""/>
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21 <param argument="-m" checked="false" falsevalue="" label="Extract Metabolites" name="printMetabolites" truevalue="-m" type="boolean" value="false"/>
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22 <param argument="-r" checked="false" falsevalue="" label="Extract Reactions" name="printReactions" truevalue="-r" type="boolean" value="false"/>
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23 <param argument="-c" checked="false" falsevalue="" label="Extract Compartments" name="printCompartments" truevalue="-c" type="boolean" value="false"/>
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24 <param argument="-p" checked="false" falsevalue="" label="Extract Pathways" name="printPathways" truevalue="-p" type="boolean" value="false"/>
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25 <param argument="-g" checked="false" falsevalue="" label="Extract Genes" name="printGenes" truevalue="-g" type="boolean" value="false"/>
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26 <param argument="-nt" checked="false" falsevalue="" label="Do not output type column" name="noTypeCol" truevalue="-nt" type="boolean" value="false"/>
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27 </inputs>
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28 <outputs>
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29 <data format="tsv" name="outputFile"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="sbml" value="Human-GEM_pathways.xml"/>
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34 <output ftype="tsv" name="outputFile">
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35 <assert_contents>
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36 <has_text_matching expression="GENE" n="86"/>
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37 <has_text_matching expression="METABOLITE" n="111"/>
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38 <has_text_matching expression="REACTION" n="75"/>
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39 <has_text_matching expression="PATHWAY" n="3"/>
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40 <has_text_matching expression="COMPARTMENT" n="5"/>
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41 </assert_contents>
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42 </output>
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43 </test>
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44 <test>
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45 <param name="sbml" value="Human-GEM_pathways.xml"/>
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46 <param name="printReactions" value="true"/>
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47 <param name="printMetabolites" value="true"/>
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48 <param name="printGenes" value="true"/>
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49 <param name="printCompartments" value="true"/>
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50 <param name="noTypeCol" value="true"/>
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51 <output ftype="tsv" name="outputFile">
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52 <assert_contents>
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53 <has_n_lines n="277"/>
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54 </assert_contents>
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55 </output>
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56 </test>
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57 </tests>
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58 <help><![CDATA[Parse SBML to render list of composing entities: metabolites, reactions, genes, pathways and compartments. The output file is a tsv with two columns, one with entities identifiers, and one with the entity type. If no entity type is selected, by default all of them are taken into account. Only identifiers are written, attributes can be extracted from dedicated apps or from the SBML2Tab.]]></help>
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59 <citations/>
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60 </tool>