Mercurial > repos > metexplore > met4j_setids

annotate SetIds.xml @ 2:c0fea71f04d3 draft default tip

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 71335d4a636672d264cc4f443c07856907571928
author metexplore
date Fri, 21 Nov 2025 10:23:40 +0000
parents 6c8c9af89afe
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c362da4bccfb 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"?>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
2 <tool id="met4j_SetIds" name="SetIds" version="@TOOL_VERSION@">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
3 <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</description>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
4 <macros>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
5 <import>macros.xml</import>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
6 </macros>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
7 <expand macro="bio_tools"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
8 <expand macro="requirements"/>
1
6c8c9af89afe 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.SetIds#if str($colname) != 'nan':
0
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
10 -cnew "$colname"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
11 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
12 #if str($colid):
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
13 -ci "$colid"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
14 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
15 $p
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
16 $s
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
17 #if str($o):
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
18 -t "$o"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
19 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
20 #if str($nSkip):
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
21 -n "$nSkip"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
22 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
23 -i "$sbml"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
24 #if str($tab) != 'None':
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
25 -tab "$tab"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
26 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
27 #if str($c):
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
28 -c "$c"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
29 #end if
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
30 -o "$out"
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
31 ]]></command>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
32 <inputs>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
33 <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
34 <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
35 <sanitizer invalid_char="_">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
36 <valid initial="string.printable"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
37 </sanitizer>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
38 </param>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
39 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
40 <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"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
41 <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
42 <sanitizer invalid_char="_">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
43 <valid initial="string.printable"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
44 </sanitizer>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
45 </param>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
46 <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">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
47 <sanitizer invalid_char="_">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
48 <valid initial="string.printable"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
49 </sanitizer>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
50 </param>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
51 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
52 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
53 <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="#">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
54 <sanitizer invalid_char="_">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
55 <valid initial="string.printable"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
56 </sanitizer>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
57 </param>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
58 </inputs>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
59 <outputs>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
60 <data format="sbml" name="out"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
61 </outputs>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
62 <tests>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
63 <test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
64 <param name="sbml" value="toy_model.xml"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
65 <param name="tab" value="idMetabolites.tsv"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
66 <param name="o" value="METABOLITE"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
67 <output ftype="sbml" name="out">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
68 <assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
69 <is_valid_xml/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
70 <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
71 <has_line_matching expression=".*id=.metaboliteB.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
72 </assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
73 </output>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
74 </test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
75 <test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
76 <param name="sbml" value="toy_model.xml"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
77 <param name="tab" value="idReactions.tsv"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
78 <output ftype="sbml" name="out">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
79 <assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
80 <is_valid_xml/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
81 <has_line_matching expression=".*id=.reaction1.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
82 <has_line_matching expression=".*id=.reaction2.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
83 </assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
84 </output>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
85 </test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
86 <test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
87 <param name="sbml" value="XF_network.sbml"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
88 <param name="tab" value="idPathways.tsv"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
89 <param name="o" value="PATHWAY"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
90 <output ftype="sbml" name="out">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
91 <assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
92 <is_valid_xml/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
93 <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
94 <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
95 </assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
96 </output>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
97 </test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
98 <test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
99 <param name="sbml" value="XF_network.sbml"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
100 <param name="tab" value="idGenes.tsv"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
101 <param name="o" value="GENE"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
102 <output ftype="sbml" name="out">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
103 <assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
104 <is_valid_xml/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
105 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
106 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
107 </assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
108 </output>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
109 </test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
110 <test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
111 <param name="sbml" value="XF_network.sbml"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
112 <param name="tab" value="idCompartments.tsv"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
113 <param name="o" value="COMPARTMENT"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
114 <output ftype="sbml" name="out">
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
115 <assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
116 <is_valid_xml/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
117 <has_line_matching expression=".*id=.cytosol.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
118 <has_line_matching expression=".*id=.extra.*" n="1"/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
119 </assert_contents>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
120 </output>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
121 </test>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
122 </tests>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
123 <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
124 The ids must correspond between the tabulated file and the SBML file.
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
125 If prefix or suffix is different in the SBML file, use the -p or the -s options.
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
126 @ATTRIBUTION@]]></help>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
127 <citations/>
c362da4bccfb planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3
metexplore
parents:
diff changeset
128 </tool>