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comparison tools/attributes/SetGprs/SetGprs.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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children 6a112eaf8f38
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_SetGprs" name="SetGprs" version="develop">
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:develop</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetGprs#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 "$nSkip"
19 #end if
20 -i "$sbml"
21 #if str($tab) != 'None':
22 -tab "$tab"
23 #end if
24 #if str($c):
25 -c "$c"
26 #end if
27 -o "$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="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
39 <param argument="-tab" format="tsv" label="Input 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
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57 <param name="sbml" value="toy_model.xml"/>
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64 <param name="tab" value="gpr.tsv"/>
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71 <output ftype="sbml" name="out">
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78 <assert_contents>
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85 <is_valid_xml/>
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92 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
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99 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
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106 <has_line_matching expression=".*fbc:id=.G3.*" n="1"/>
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113 <has_line_matching expression=".*fbc:id=.G4.*" n="1"/>
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120 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/>
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127 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/>
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134 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/>
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141 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/>
142
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148 <has_line_matching expression=".*fbc:and.*" n="2"/>
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155 </assert_contents>
156
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162 </output>
163
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169 </test>
170 </tests>
171 <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
172 The ids must correspond between the tabulated file and the SBML file.
173 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
174 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
175 (The GPR will be written in the SBML file in two locations:
176 - in the reaction html notes (GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 ))
177 - as fbc gene product association (see FBC package specifications: https://doi.org/10.1515/jib-2017-0082)]]></help>
178 <citations>
179 <citation type="doi">10.1038/nprot.2011.308</citation>
180 <citation type="doi">10.1515/jib-2017-0082</citation>
181 </citations>
182 </tool>