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comparison build/tools/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
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children 1436e9cde9c9
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.3.0">
3 <description>Add refs to network objects from a tabulated file containing the metabolite ids and the formulas</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:1.3.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan':
11 -cr "$colRef"
12 #end if
13 -ref "$ref"
14 #if str($colid):
15 -ci "$colid"
16 #end if
17 $p
18 $s
19 #if str($o):
20 -o "$o"
21 #end if
22 #if str($nSkip):
23 -n "$nSkip"
24 #end if
25 -sbml "$sbml"
26 #if str($tab) != 'None':
27 -tab "$tab"
28 #end if
29 #if str($c):
30 -c "$c"
31 #end if
32 -out "$out"
33 ]]></command>
34 <inputs>
35 <param argument="-cr" label="[2] number of the column where are the references" name="colRef" optional="true" type="integer" value="2"/>
36 <param argument="-ref" label="Name of the ref. Must exist in identifiers.org" name="ref" optional="false" type="text" value="">
37 <sanitizer invalid_char="_">
38 <valid initial="string.printable"/>
39 </sanitizer>
40 </param>
41 <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
42 <sanitizer invalid_char="_">
43 <valid initial="string.printable"/>
44 </sanitizer>
45 </param>
46 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
47 <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>
48 <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
49 <sanitizer invalid_char="_">
50 <valid initial="string.printable"/>
51 </sanitizer>
52 </param>
53 <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">
54 <sanitizer invalid_char="_">
55 <valid initial="string.printable"/>
56 </sanitizer>
57 </param>
58 <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
59 <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/>
60 <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="#">
61 <sanitizer invalid_char="_">
62 <valid initial="string.printable"/>
63 </sanitizer>
64 </param>
65 </inputs>
66 <outputs>
67 <data format="sbml" name="out"/>
68 </outputs>
69 <tests>
70 <test>
71 <param name="sbml" value="toy_model.xml"/>
72 <param name="tab" value="refs.tsv"/>
73 <param name="ref" value="InChi"/>
74 <param name="o" value="METABOLITE"/>
75 <output ftype="sbml" name="out">
76 <assert_contents>
77 <is_valid_xml/>
78 <has_line_matching expression=".*C2H6O.*" n="3"/>
79 <has_line_matching expression=".*C6H8O6.*" n="1"/>
80 </assert_contents>
81 </output>
82 </test>
83 </tests>
84 <help><![CDATA[Add refs to network objects from a tabulated file containing the metabolite ids and the formulas
85 Reference name given as parameter (-ref) must correspond to an existing id the registry of identifiers.org (https://registry.identifiers.org/registry)
86 The corresponding key:value pair will be written as metabolite or reaction annotation]]></help>
87 <citations/>
88 </tool>