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comparison build/tools/SetChemicalFormulas/SetChemicalFormulas.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_SetChemicalFormulas" name="SetChemicalFormulas" version="develop">
3 <description>Set Formula to network metabolites 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:develop</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetChemicalFormulas#if str($colformula) != 'nan':
11 -cf "$colformula"
12 #end if
13 #if str($colid) != 'nan':
14 -ci "$colid"
15 #end if
16 $p
17 $s
18 #if str($nSkip):
19 -n "$nSkip"
20 #end if
21 -i "$sbml"
22 #if str($tab) != 'None':
23 -tab "$tab"
24 #end if
25 #if str($c):
26 -c "$c"
27 #end if
28 -o "$out"
29 ]]></command>
30 <inputs>
31 <param argument="-cf" label="[2] number of the column where are the formulas" name="colformula" optional="true" type="integer" value="2"/>
32 <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/>
33 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/>
34 <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"/>
35 <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">
36 <sanitizer invalid_char="_">
37 <valid initial="string.printable"/>
38 </sanitizer>
39 </param>
40 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
41 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
42 <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="#">
43 <sanitizer invalid_char="_">
44 <valid initial="string.printable"/>
45 </sanitizer>
46 </param>
47 </inputs>
48 <outputs>
49 <data format="sbml" name="out"/>
50 </outputs>
51 <tests>
52 <test>
53
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58
59 <param name="sbml" value="toy_model.xml"/>
60
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66 <param name="tab" value="formula.tsv"/>
67
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73 <output ftype="sbml" name="out">
74
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80 <assert_contents>
81
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87 <is_valid_xml/>
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94 <has_line_matching expression=".*CH6O6.*" n="2"/>
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101 <has_line_matching expression=".*CH12O4.*" n="2"/>
102
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108 </assert_contents>
109
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115 </output>
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122 </test>
123 <test expect_failure="true">
124
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130 <param name="sbml" value="toy_model.xml"/>
131
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136
137 <param name="tab" value="formulaBad.tsv"/>
138
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144 </test>
145 </tests>
146 <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas
147 The ids must correspond between the tabulated file and the SBML file.
148 If prefix or suffix is different in the SBML file, use the -p or the -s options.
149 The formula will be written in the SBML file in two locations:+
150 - in the metabolite HTML notes (e.g. formula: C16H29O2)
151 - as a fbc attribute (e.g. fbc:chemicalFormula="C16H29O2")]]></help>
152 <citations>
153 <citation type="doi">10.1515/jib-2017-0082</citation>
154 </citations>
155 </tool>