Mercurial > repos > metexplore > met4j_setids

comparison SetIds.xml @ 3:d80ba6cbcf39 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 e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:32:56 +0000
parents 6c8c9af89afe
children
comparison
equal deleted inserted replaced
2:c0fea71f04d3 3:d80ba6cbcf39
57 </param> 57 </param>
58 </inputs> 58 </inputs>
59 <outputs> 59 <outputs>
60 <data format="sbml" name="out"/> 60 <data format="sbml" name="out"/>
61 </outputs> 61 </outputs>
62 <tests> 62 <tests/>
63 <test>
64 <param name="sbml" value="toy_model.xml"/>
65 <param name="tab" value="idMetabolites.tsv"/>
66 <param name="o" value="METABOLITE"/>
67 <output ftype="sbml" name="out">
68 <assert_contents>
69 <is_valid_xml/>
70 <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>
71 <has_line_matching expression=".*id=.metaboliteB.*" n="1"/>
72 </assert_contents>
73 </output>
74 </test>
75 <test>
76 <param name="sbml" value="toy_model.xml"/>
77 <param name="tab" value="idReactions.tsv"/>
78 <output ftype="sbml" name="out">
79 <assert_contents>
80 <is_valid_xml/>
81 <has_line_matching expression=".*id=.reaction1.*" n="1"/>
82 <has_line_matching expression=".*id=.reaction2.*" n="1"/>
83 </assert_contents>
84 </output>
85 </test>
86 <test>
87 <param name="sbml" value="XF_network.sbml"/>
88 <param name="tab" value="idPathways.tsv"/>
89 <param name="o" value="PATHWAY"/>
90 <output ftype="sbml" name="out">
91 <assert_contents>
92 <is_valid_xml/>
93 <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>
94 <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>
95 </assert_contents>
96 </output>
97 </test>
98 <test>
99 <param name="sbml" value="XF_network.sbml"/>
100 <param name="tab" value="idGenes.tsv"/>
101 <param name="o" value="GENE"/>
102 <output ftype="sbml" name="out">
103 <assert_contents>
104 <is_valid_xml/>
105 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
106 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
107 </assert_contents>
108 </output>
109 </test>
110 <test>
111 <param name="sbml" value="XF_network.sbml"/>
112 <param name="tab" value="idCompartments.tsv"/>
113 <param name="o" value="COMPARTMENT"/>
114 <output ftype="sbml" name="out">
115 <assert_contents>
116 <is_valid_xml/>
117 <has_line_matching expression=".*id=.cytosol.*" n="1"/>
118 <has_line_matching expression=".*id=.extra.*" n="1"/>
119 </assert_contents>
120 </output>
121 </test>
122 </tests>
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 63 <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids
124 The ids must correspond between the tabulated file and the SBML file. 64 The ids must correspond between the tabulated file and the SBML file.
125 If prefix or suffix is different in the SBML file, use the -p or the -s options. 65 If prefix or suffix is different in the SBML file, use the -p or the -s options.
126 @ATTRIBUTION@]]></help> 66 @ATTRIBUTION@]]></help>
127 <citations/> 67 <citations/>