Mercurial > repos > metexplore > met4j

comparison tools/convert/FbcToNotes/FbcToNotes.xml @ 10:6a112eaf8f38 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
comparison
equal deleted inserted replaced
9:0976a6257300 10:6a112eaf8f38
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_FbcToNotes" name="FbcToNotes" version="develop"> 2 <tool id="met4j_FbcToNotes" name="FbcToNotes" version="2.0.0">
3 <description>Convert FBC package annotations to sbml html notes</description> 3 <description>Convert FBC package annotations to sbml html notes</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath"
11 -o "$outputPath" 11 -o "$outputPath"
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
16 <outputs> 16 <outputs>
17 <data format="sbml" name="outputPath"/> 17 <data format="sbml" name="outputPath"/>
18 </outputs> 18 </outputs>
19 <tests> 19 <tests>
20 <test> 20 <test>
21
22
23
24
25
26
27
28
29
30
31
32 <param name="inputPath" value="ECOL.xml"/> 21 <param name="inputPath" value="ECOL.xml"/>
33
34
35
36
37
38
39
40
41
42
43
44 <output ftype="sbml" name="outputPath"> 22 <output ftype="sbml" name="outputPath">
45
46
47
48
49
50
51
52
53
54
55
56 <assert_contents> 23 <assert_contents>
57
58
59
60
61
62
63
64
65
66
67
68 <is_valid_xml/> 24 <is_valid_xml/>
69
70
71
72
73
74
75
76
77
78
79
80 <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/> 25 <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/>
81
82
83
84
85
86
87
88
89
90
91
92 </assert_contents> 26 </assert_contents>
93
94
95
96
97
98
99
100
101
102
103
104 </output> 27 </output>
105
106
107
108
109
110
111
112
113
114
115
116 </test> 28 </test>
117 </tests> 29 </tests>
118 <help><![CDATA[Convert FBC package annotations to sbml html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help> 30 <help><![CDATA[Convert FBC package annotations to sbml html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help>
119 <citations> 31 <citations>
120 <citation type="doi">10.1515/jib-2017-0082</citation> 32 <citation type="doi">10.1515/jib-2017-0082</citation>