Mercurial > repos > metexplore > met4j_getentities

annotate GetEntities.xml @ 1:d31c63d9ed01 draft

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 6bb33ff0ff022029543e5e5ace7d16418715aa1c
author metexplore
date Mon, 25 Aug 2025 16:06:29 +0000
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d9790f6b04ba planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_GetEntities" name="GetEntities" version="@TOOL_VERSION@">
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3 <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</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 attributes.GetEntities -i "$sbml"
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10 $printMetabolites
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11 $printReactions
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12 $printCompartments
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13 $printPathways
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14 $printGenes
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15 $noTypeCol
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16 -o "$outputFile"
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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="sbml" optional="false" type="data" value=""/>
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20 <param argument="-m" checked="false" falsevalue="" label="Extract Metabolites" name="printMetabolites" truevalue="-m" type="boolean" value="false"/>
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21 <param argument="-r" checked="false" falsevalue="" label="Extract Reactions" name="printReactions" truevalue="-r" type="boolean" value="false"/>
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22 <param argument="-c" checked="false" falsevalue="" label="Extract Compartments" name="printCompartments" truevalue="-c" type="boolean" value="false"/>
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23 <param argument="-p" checked="false" falsevalue="" label="Extract Pathways" name="printPathways" truevalue="-p" type="boolean" value="false"/>
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24 <param argument="-g" checked="false" falsevalue="" label="Extract Genes" name="printGenes" truevalue="-g" type="boolean" value="false"/>
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25 <param argument="-nt" checked="false" falsevalue="" label="Do not write type column" name="noTypeCol" truevalue="-nt" type="boolean" value="false"/>
d9790f6b04ba planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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26 </inputs>
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27 <outputs>
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28 <data format="tsv" name="outputFile"/>
d9790f6b04ba planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="sbml" value="Human-GEM_pathways.xml"/>
d9790f6b04ba planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
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33 <output ftype="tsv" name="outputFile">
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34 <assert_contents>
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35 <has_text_matching expression="GENE" n="86"/>
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36 <has_text_matching expression="METABOLITE" n="111"/>
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37 <has_text_matching expression="REACTION" n="75"/>
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38 <has_text_matching expression="PATHWAY" n="3"/>
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39 <has_text_matching expression="COMPARTMENT" n="5"/>
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40 </assert_contents>
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41 </output>
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42 </test>
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43 <test>
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44 <param name="sbml" value="Human-GEM_pathways.xml"/>
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45 <param name="printReactions" value="true"/>
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46 <param name="printMetabolites" value="true"/>
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47 <param name="printGenes" value="true"/>
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48 <param name="printCompartments" value="true"/>
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49 <param name="noTypeCol" value="true"/>
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50 <output ftype="tsv" name="outputFile">
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51 <assert_contents>
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52 <has_n_lines n="277"/>
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.
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58 @ATTRIBUTION@]]></help>
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59 <citations/>
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60 </tool>