Mercurial > repos > metexplore > met4j

comparison build/tools/GetGenesFromReactions/GetGenesFromReactions.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_GetGenesFromReactions" name="GetGenesFromReactions" version="develop"> 2 <tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.0">
3 <description>Get gene lists from a list of reactions and a SBML file.</description> 3 <description>Get gene lists from a list of reactions and a SBML file.</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 attributes.GetGenesFromReactions -i "$sbml" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
11 -r "$reactionFile" 11 -r "$reactionFile"
12 #if str($sep): 12 #if str($sep):
13 -sep "$sep" 13 -sep "$sep"
32 <outputs> 32 <outputs>
33 <data format="tsv" name="outputFile"/> 33 <data format="tsv" name="outputFile"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37
38
39
40
41
42
43
44
45
46
47
48 <param name="sbml" value="XF_network.sbml"/> 37 <param name="sbml" value="XF_network.sbml"/>
49
50
51
52
53
54
55
56
57
58
59
60 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 38 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
61
62
63
64
65
66
67
68
69
70
71
72 <output ftype="tsv" name="outputFile"> 39 <output ftype="tsv" name="outputFile">
73
74
75
76
77
78
79
80
81
82
83
84 <assert_contents> 40 <assert_contents>
85
86
87
88
89
90
91
92
93
94
95
96 <has_n_lines n="2"/> 41 <has_n_lines n="2"/>
97
98
99
100
101
102
103
104
105
106
107
108 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/> 42 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
109
110
111
112
113
114
115
116
117
118
119
120 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/> 43 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
121
122
123
124
125
126
127
128
129
130
131
132 </assert_contents> 44 </assert_contents>
133
134
135
136
137
138
139
140
141
142
143
144 </output> 45 </output>
145
146
147
148
149
150
151
152
153
154
155
156 </test> 46 </test>
157 </tests> 47 </tests>
158 <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help> 48 <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
159 <citations/> 49 <citations/>
160 </tool> 50 </tool>