Mercurial > repos > metexplore > met4j_setcharges

comparison SetCharges.xml @ 3:d266101e0e48 draft

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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
comparison
equal deleted inserted replaced
2:8f767bc45914 3:d266101e0e48
45 </param> 45 </param>
46 </inputs> 46 </inputs>
47 <outputs> 47 <outputs>
48 <data format="sbml" name="out"/> 48 <data format="sbml" name="out"/>
49 </outputs> 49 </outputs>
50 <tests> 50 <tests/>
51 <test>
52 <param name="sbml" value="toy_model.xml"/>
53 <param name="tab" value="charges.tsv"/>
54 <output ftype="sbml" name="out">
55 <assert_contents>
56 <is_valid_xml/>
57 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
58 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
59 </assert_contents>
60 </output>
61 </test>
62 <test>
63 <param name="sbml" value="toy_model.xml"/>
64 <param name="tab" value="chargesWithComment.tsv"/>
65 <output ftype="sbml" name="out">
66 <assert_contents>
67 <is_valid_xml/>
68 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
69 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
70 </assert_contents>
71 </output>
72 </test>
73 <test>
74 <param name="sbml" value="toy_model.xml"/>
75 <param name="tab" value="charges.tsv"/>
76 <param name="nSkip" value="1"/>
77 <output ftype="sbml" name="out">
78 <assert_contents>
79 <is_valid_xml/>
80 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
81 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
82 </assert_contents>
83 </output>
84 </test>
85 <test>
86 <param name="sbml" value="toy_model.xml"/>
87 <param name="tab" value="charges.tsv"/>
88 <param name="ci" value="2"/>
89 <param name="cc" value="3"/>
90 <output ftype="sbml" name="out">
91 <assert_contents>
92 <is_valid_xml/>
93 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
94 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
95 </assert_contents>
96 </output>
97 </test>
98 <test>
99 <param name="sbml" value="XF_network.sbml"/>
100 <param name="tab" value="chargesXF.tsv"/>
101 <param name="p" value="true"/>
102 <param name="s" value="true"/>
103 <output ftype="sbml" name="out">
104 <assert_contents>
105 <is_valid_xml/>
106 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>
107 </assert_contents>
108 </output>
109 </test>
110 </tests>
111 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges 51 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges
112 The charge must be a number. The ids must correspond between the tabulated file and the SBML file. 52 The charge must be a number. The ids must correspond between the tabulated file and the SBML file.
113 If prefix or suffix is different in the SBML file, use the -p or the -s options. 53 If prefix or suffix is different in the SBML file, use the -p or the -s options.
114 The charge will be written in the SBML file in two locations:+ 54 The charge will be written in the SBML file in two locations:+
115 - in the reaction notes (e.g. charge: -1) 55 - in the reaction notes (e.g. charge: -1)