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comparison tools/attributes/SetPathways/SetPathways.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_SetPathways" name="SetPathways" version="develop">
3 <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</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.SetPathways#if str($colp) != 'nan':
11 -cp "$colp"
12 #end if
13 #if str($sep):
14 -sep "$sep"
15 #end if
16 #if str($colid) != 'nan':
17 -ci "$colid"
18 #end if
19 $p
20 #if str($nSkip):
21 -n "$nSkip"
22 #end if
23 -i "$sbml"
24 #if str($tab) != 'None':
25 -tab "$tab"
26 #end if
27 #if str($c):
28 -c "$c"
29 #end if
30 -o "$out"
31 ]]></command>
32 <inputs>
33 <param argument="-cp" label="[2] number of the column where are the pathways" name="colp" optional="true" type="integer" value="2"/>
34 <param argument="-sep" label="[|] Separator of pathways in the tabulated file" name="sep" optional="true" type="text" value="|">
35 <sanitizer invalid_char="_">
36 <valid initial="string.printable"/>
37 </sanitizer>
38 </param>
39 <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/>
40 <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"/>
41 <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">
42 <sanitizer invalid_char="_">
43 <valid initial="string.printable"/>
44 </sanitizer>
45 </param>
46 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
47 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
48 <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="#">
49 <sanitizer invalid_char="_">
50 <valid initial="string.printable"/>
51 </sanitizer>
52 </param>
53 </inputs>
54 <outputs>
55 <data format="sbml" name="out"/>
56 </outputs>
57 <tests>
58 <test>
59
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65 <param name="sbml" value="toy_model.xml"/>
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72 <param name="tab" value="pathways.tsv"/>
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79 <output ftype="sbml" name="out">
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86 <assert_contents>
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93 <is_valid_xml/>
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100 <has_line_matching expression=".*groups:id=.*" n="3"/>
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107 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
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114 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
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121 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
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128 </assert_contents>
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135 </output>
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142 </test>
143 <test>
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150 <param name="sbml" value="toy_model.xml"/>
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157 <param name="tab" value="pathwaysOtherSep.tsv"/>
158
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164 <param name="sep" value=" + "/>
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171 <output ftype="sbml" name="out">
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178 <assert_contents>
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185 <is_valid_xml/>
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192 <has_line_matching expression=".*groups:id=.*" n="3"/>
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199 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
200
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206 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
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213 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
214
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220 </assert_contents>
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227 </output>
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234 </test>
235 </tests>
236 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways
237 The ids must correspond between the tabulated file and the SBML file.
238 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
239 Pathways will be written in the SBML file in two ways:- as reaction note (e.g. SUBSYSTEM: purine_biosynthesis)- as SBML group (see Group package specifications: https://pmc.ncbi.nlm.nih.gov/articles/PMC5451322/)]]></help>
240 <citations>
241 <citation type="doi">10.1515/jib-2016-290</citation>
242 </citations>
243 </tool>