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comparison tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml @ 0:dcd16521b969 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author metexplore
date Fri, 10 Jun 2022 10:31:34 +0000
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children 9b162ee6ff8e
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1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.11.0">
3 <description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</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:0.11.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
11 -cgpr "$colgpr"
12 #end if
13 #if str($colid) != 'nan':
14 -ci "$colid"
15 #end if
16 $p
17 #if str($nSkip):
18 -n "$nSkip"
19 #end if
20 -sbml "$sbml"
21 #if str($tab) != 'None':
22 -tab "$tab"
23 #end if
24 #if str($c):
25 -c "$c"
26 #end if
27 -out "$out"
28 ]]></command>
29 <inputs>
30 <param argument="-cgpr" label="[2] number of the column where are the gprs" name="colgpr" optional="true" type="integer" value="2"/>
31 <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/>
32 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions" name="p" truevalue="-p" type="boolean" value="false"/>
33 <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">
34 <sanitizer invalid_char="_">
35 <valid initial="string.printable"/>
36 </sanitizer>
37 </param>
38 <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
39 <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/>
40 <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#">
41 <sanitizer invalid_char="_">
42 <valid initial="string.printable"/>
43 </sanitizer>
44 </param>
45 </inputs>
46 <outputs>
47 <data format="sbml" name="out"/>
48 </outputs>
49 <tests>
50 <test>
51 <param name="sbml" value="toy_model.xml"/>
52 <param name="tab" value="gpr.tsv"/>
53 <output ftype="sbml" name="out">
54 <assert_contents>
55 <is_valid_xml/>
56 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
57 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
58 <has_line_matching expression=".*fbc:id=.G3.*" n="1"/>
59 <has_line_matching expression=".*fbc:id=.G4.*" n="1"/>
60 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/>
61 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/>
62 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/>
63 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/>
64 <has_line_matching expression=".*fbc:and.*" n="2"/>
65 </assert_contents>
66 </output>
67 </test>
68 </tests>
69 <help><![CDATA[Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way
70 The ids must correspond between the tabulated file and the SBML file.
71 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
72 GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307
73 (The GPR will be written in the SBML file in two locations:
74 - in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p>
75 - as fbc gene product association : <fbc:geneProductAssociation>
76 <fbc:or>
77 <fbc:geneProductRef fbc:geneProduct="XC_3282"/>
78 <fbc:geneProductRef fbc:geneProduct="XC_0401"/>
79 </fbc:or>
80 </fbc:geneProductAssociation>
81 ]]></help>
82 </tool>