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comparison SetReferences.xml @ 0:36a717a12a46 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
author metexplore
date Thu, 13 Mar 2025 15:52:22 +0000
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children 4e0e0b696427
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-1:000000000000 0:36a717a12a46
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_SetReferences" name="SetReferences" version="@TOOL_VERSION@">
3 <description>Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="bio_tools"/>
8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[met4j fr.inrae.toulouse.metexplore.met4j_toolbox.attributes.SetReferences#if str($colRef) != 'nan':
10 -cr "$colRef"
11 #end if
12 -ref "$ref"
13 #if str($colid):
14 -ci "$colid"
15 #end if
16 $p
17 $s
18 #if str($o):
19 -t "$o"
20 #end if
21 #if str($nSkip):
22 -n "$nSkip"
23 #end if
24 -i "$sbml"
25 #if str($tab) != 'None':
26 -tab "$tab"
27 #end if
28 #if str($c):
29 -c "$c"
30 #end if
31 -o "$out"
32 ]]></command>
33 <inputs>
34 <param argument="-cr" label="[2] number of the column where are the references" name="colRef" optional="true" type="integer" value="2"/>
35 <param argument="-ref" label="Name of the reference. Must exist in identifiers.org (https://registry.identifiers.org/registry)" name="ref" optional="false" type="text" value="">
36 <sanitizer invalid_char="_">
37 <valid initial="string.printable"/>
38 </sanitizer>
39 </param>
40 <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
41 <sanitizer invalid_char="_">
42 <valid initial="string.printable"/>
43 </sanitizer>
44 </param>
45 <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"/>
46 <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"/>
47 <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
48 <sanitizer invalid_char="_">
49 <valid initial="string.printable"/>
50 </sanitizer>
51 </param>
52 <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">
53 <sanitizer invalid_char="_">
54 <valid initial="string.printable"/>
55 </sanitizer>
56 </param>
57 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
58 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
59 <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="#">
60 <sanitizer invalid_char="_">
61 <valid initial="string.printable"/>
62 </sanitizer>
63 </param>
64 </inputs>
65 <outputs>
66 <data format="sbml" name="out"/>
67 </outputs>
68 <tests>
69 <test>
70 <param name="sbml" value="toy_model.xml"/>
71 <param name="tab" value="refs.tsv"/>
72 <param name="ref" value="InChi"/>
73 <param name="o" value="METABOLITE"/>
74 <output ftype="sbml" name="out">
75 <assert_contents>
76 <is_valid_xml/>
77 <has_line_matching expression=".*C2H6O.*" n="3"/>
78 <has_line_matching expression=".*C6H8O6.*" n="1"/>
79 </assert_contents>
80 </output>
81 </test>
82 </tests>
83 <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references
84 Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry)
85 The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)
86 @ATTRIBUTION@]]></help>
87 <citations>
88 <citation type="doi">10.1038/nbt1156</citation>
89 </citations>
90 </tool>