Mercurial > repos > metexplore > met4j

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author metexplore
date Fri, 10 Jun 2022 10:31:34 +0000
parents
children 9b162ee6ff8e
comparison
equal deleted inserted replaced
-1:000000000000 0:dcd16521b969
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="0.11.0">
3 <description>Set charge 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:0.11.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan':
11 -cc "$colcharge"
12 #end if
13 #if str($colid) != 'nan':
14 -ci "$colid"
15 #end if
16 $p
17 $s
18 #if str($nSkip):
19 -n "$nSkip"
20 #end if
21 -sbml "$sbml"
22 #if str($tab) != 'None':
23 -tab "$tab"
24 #end if
25 #if str($c):
26 -c "$c"
27 #end if
28 -out "$out"
29 ]]></command>
30 <inputs>
31 <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" 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="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
41 <param argument="-tab" format="tsv" label="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 <param name="sbml" value="toy_model.xml"/>
54 <param name="tab" value="charges.tsv"/>
55 <output ftype="sbml" name="out">
56 <assert_contents>
57 <is_valid_xml/>
58 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
59 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
60 </assert_contents>
61 </output>
62 </test>
63 <test>
64 <param name="sbml" value="toy_model.xml"/>
65 <param name="tab" value="chargesWithComment.tsv"/>
66 <output ftype="sbml" name="out">
67 <assert_contents>
68 <is_valid_xml/>
69 <has_line_matching expression=".*fbc:charge=.2.*" n="0"/>
70 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
71 </assert_contents>
72 </output>
73 </test>
74 <test>
75 <param name="sbml" value="toy_model.xml"/>
76 <param name="tab" value="charges.tsv"/>
77 <param name="nSkip" value="1"/>
78 <output ftype="sbml" name="out">
79 <assert_contents>
80 <is_valid_xml/>
81 <has_line_matching expression=".*fbc:charge=.2.*" n="0"/>
82 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
83 </assert_contents>
84 </output>
85 </test>
86 <test>
87 <param name="sbml" value="toy_model.xml"/>
88 <param name="tab" value="charges.tsv"/>
89 <param name="ci" value="2"/>
90 <param name="cc" value="3"/>
91 <output ftype="sbml" name="out">
92 <assert_contents>
93 <is_valid_xml/>
94 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
95 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
96 </assert_contents>
97 </output>
98 </test>
99 <test>
100 <param name="sbml" value="XF_network.sbml"/>
101 <param name="tab" value="chargesXF.tsv"/>
102 <param name="p" value="true"/>
103 <param name="s" value="true"/>
104 <output ftype="sbml" name="out">
105 <assert_contents>
106 <is_valid_xml/>
107 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>
108 </assert_contents>
109 </output>
110 </test>
111 </tests>
112 <help><![CDATA[Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas
113 The charge must be a number. The ids must correspond between the tabulated file and the SBML file.
114 If prefix or suffix is different in the SBML file, use the -p or the -s options.
115 The charge will be written in the SBML file in two locations:+
116 - in the reaction notes (e.g. <p>charge: -1</p>)
117 - as fbc attribute (e.g. fbc:charge="1")]]></help>
118 </tool>