Mercurial > repos > metexplore > met4j_setgprs

comparison SetGprs.xml @ 3:d8b1f69da790 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 15:32:48 +0000
parents 67e93e5f08ee
children
comparison
equal deleted inserted replaced
2:67e93e5f08ee 3:d8b1f69da790
43 </param> 43 </param>
44 </inputs> 44 </inputs>
45 <outputs> 45 <outputs>
46 <data format="sbml" name="out"/> 46 <data format="sbml" name="out"/>
47 </outputs> 47 </outputs>
48 <tests> 48 <tests/>
49 <test>
50 <param name="sbml" value="toy_model.xml"/>
51 <param name="tab" value="gpr.tsv"/>
52 <output ftype="sbml" name="out">
53 <assert_contents>
54 <is_valid_xml/>
55 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
56 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
57 <has_line_matching expression=".*fbc:id=.G3.*" n="1"/>
58 <has_line_matching expression=".*fbc:id=.G4.*" n="1"/>
59 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G1.*" n="1"/>
60 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G2.*" n="1"/>
61 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G3.*" n="1"/>
62 <has_line_matching expression=".*fbc:geneProductRef fbc:geneProduct=.G4.*" n="1"/>
63 <has_line_matching expression=".*fbc:and.*" n="2"/>
64 </assert_contents>
65 </output>
66 </test>
67 </tests>
68 <help><![CDATA[Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way 49 <help><![CDATA[Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way
69 The ids must correspond between the tabulated file and the SBML file. 50 The ids must correspond between the tabulated file and the SBML file.
70 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option. 51 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
71 GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307 52 GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307
72 (The GPR will be written in the SBML file in two locations: 53 (The GPR will be written in the SBML file in two locations:
73 - in the reaction html notes (GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )) 54 - in the reaction html notes (GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 ))
74 - as fbc gene product association (see FBC package specifications: https://doi.org/10.1515/jib-2017-0082) 55 - as fbc gene product association (see FBC package specifications: https://doi.org/10.1515/jib-2017-0082)
75 @ATTRIBUTION@]]></help> 56 @ATTRIBUTION@]]></help>
76 <citations> 57 <citations>
58 <citation type="doi">10.1515/jib-2017-0082</citation>
77 <citation type="doi">10.1038/nprot.2011.308</citation> 59 <citation type="doi">10.1038/nprot.2011.308</citation>
78 <citation type="doi">10.1515/jib-2017-0082</citation>
79 </citations> 60 </citations>
80 </tool> 61 </tool>