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annotate tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.1">
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3 <description>Get gene lists from a list of reactions and a SBML file.</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:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
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11 -r "$reactionFile"
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12 #if str($sep):
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13 -sep "$sep"
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14 #end if
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15 $hasHeader
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16 #if str($i) != 'nan':
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17 -col "$i"
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18 #end if
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19 -o "$outputFile"
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20 ]]></command>
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21 <inputs>
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22 <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
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23 <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
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24 <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="&#9;">
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25 <sanitizer invalid_char="_">
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26 <valid initial="string.printable"/>
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27 </sanitizer>
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28 </param>
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29 <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
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30 <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
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31 </inputs>
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32 <outputs>
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33 <data format="tsv" name="outputFile"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37
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38 <param name="sbml" value="XF_network.sbml"/>
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39
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40 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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42 <output ftype="tsv" name="outputFile">
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44 <assert_contents>
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45
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46 <has_n_lines n="2"/>
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48 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
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50 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
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52 </assert_contents>
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54 </output>
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56 </test>
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57 </tests>
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58 <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
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59 <citations/>
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60 </tool>