Mercurial > repos > metexplore > met4j_setcharges

annotate SetCharges.xml @ 3:d266101e0e48 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:32:28 +0000
parents 921a828bd368
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
2 <tool id="met4j_SetCharges" name="SetCharges" version="@TOOL_VERSION@">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
3 <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
4 <macros>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
5 <import>macros.xml</import>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
6 </macros>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
7 <expand macro="bio_tools"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
8 <expand macro="requirements"/>
1
921a828bd368 planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 6bb33ff0ff022029543e5e5ace7d16418715aa1c
metexplore
parents: 0
diff changeset
9 <command detect_errors="exit_code"><![CDATA[met4j attributes.SetCharges#if str($colcharge) != 'nan':
0
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
10 -cc "$colcharge"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
11 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
12 #if str($colid) != 'nan':
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
13 -ci "$colid"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
14 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
15 $p
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
16 $s
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
17 #if str($nSkip):
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
18 -n "$nSkip"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
19 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
20 -i "$sbml"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
21 #if str($tab) != 'None':
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
22 -tab "$tab"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
23 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
24 #if str($c):
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
25 -c "$c"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
26 #end if
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
27 -o "$out"
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
28 ]]></command>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
29 <inputs>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
30 <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
31 <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
32 <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"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
33 <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"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
34 <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">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
35 <sanitizer invalid_char="_">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
36 <valid initial="string.printable"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
37 </sanitizer>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
38 </param>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
39 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
40 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
41 <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="#">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
42 <sanitizer invalid_char="_">
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
43 <valid initial="string.printable"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
44 </sanitizer>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
45 </param>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
46 </inputs>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
47 <outputs>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
48 <data format="sbml" name="out"/>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
49 </outputs>
3
d266101e0e48 planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
metexplore
parents: 1
diff changeset
50 <tests/>
0
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
51 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
52 The charge must be a number. The ids must correspond between the tabulated file and the SBML file.
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
53 If prefix or suffix is different in the SBML file, use the -p or the -s options.
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
54 The charge will be written in the SBML file in two locations:+
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
55 - in the reaction notes (e.g. charge: -1)
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
56 - as fbc attribute (e.g. fbc:charge="1")
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
57 @ATTRIBUTION@]]></help>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
58 <citations>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
59 <citation type="doi">10.1515/jib-2017-0082</citation>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
60 </citations>
ec91516cc95f planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
61 </tool>