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comparison tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml @ 3:6bd9aad9626d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
author metexplore
date Fri, 29 Jul 2022 13:23:40 +0000
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children ae4c301919c4
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2:e69a78624877 3:6bd9aad9626d
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.1.0">
3 <description>Get gene lists from a list of reactions and a GSMN.</description>
4 <xrefs>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
11 -r "$reactionFile"
12 #if str($sep):
13 -sep "$sep"
14 #end if
15 $hasHeader
16 #if str($i) != 'nan':
17 -col "$i"
18 #end if
19 -o "$outputFile"
20 ]]></command>
21 <inputs>
22 <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
23 <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
24 <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="&#9;">
25 <sanitizer invalid_char="_">
26 <valid initial="string.printable"/>
27 </sanitizer>
28 </param>
29 <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
30 <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
31 </inputs>
32 <outputs>
33 <data format="tsv" name="outputFile"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="sbml" value="XF_network.sbml"/>
38 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
39 <output ftype="tsv" name="outputFile">
40 <assert_contents>
41 <has_n_lines n="2"/>
42 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
43 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
44 </assert_contents>
45 </output>
46 </test>
47 </tests>
48 <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN 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>
49 <citations/>
50 </tool>