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comparison tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml @ 0:dcd16521b969 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author metexplore
date Fri, 10 Jun 2022 10:31:34 +0000
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children 9b162ee6ff8e
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-1:000000000000 0:dcd16521b969
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.11.0">
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:0.11.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#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 "$nSkip"
22 #end if
23 -sbml "$sbml"
24 #if str($tab) != 'None':
25 -tab "$tab"
26 #end if
27 #if str($c):
28 -c "$c"
29 #end if
30 -out "$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="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
47 <param argument="-tab" format="tsv" label="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 <param name="sbml" value="toy_model.xml"/>
60 <param name="tab" value="pathways.tsv"/>
61 <output ftype="sbml" name="out">
62 <assert_contents>
63 <is_valid_xml/>
64 <has_line_matching expression=".*groups:id=.*" n="3"/>
65 <has_line_matching expression=".*groups:id=.P1.*" n="1"/>
66 <has_line_matching expression=".*groups:id=.P2.*" n="1"/>
67 <has_line_matching expression=".*groups:id=.P3.*" n="1"/>
68 </assert_contents>
69 </output>
70 </test>
71 <test>
72 <param name="sbml" value="toy_model.xml"/>
73 <param name="tab" value="pathwaysOtherSep.tsv"/>
74 <param name="sep" value=" + "/>
75 <output ftype="sbml" name="out">
76 <assert_contents>
77 <is_valid_xml/>
78 <has_line_matching expression=".*groups:id=.*" n="3"/>
79 <has_line_matching expression=".*groups:id=.P1.*" n="1"/>
80 <has_line_matching expression=".*groups:id=.P2.*" n="1"/>
81 <has_line_matching expression=".*groups:id=.P3.*" n="1"/>
82 </assert_contents>
83 </output>
84 </test>
85 </tests>
86 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways
87 The ids must correspond between the tabulated file and the SBML file.
88 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
89 Pathways will be written in the SBML file in two ways:- as reaction note (e.g. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group:
90 <groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
91 <groups:listOfMembers>
92 <groups:member groups:idRef="R_GLUPRT"/>
93 <groups:member groups:idRef="R_RNDR1b"/>
94 ...
95 ]]></help>
96 </tool>