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comparison tools/attributes/SetIds/SetIds.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
comparison
equal deleted inserted replaced
10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_SetIds" name="SetIds" version="2.0.0"> 2 <tool id="met4j_SetIds" name="SetIds" version="2.0.1">
3 <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</description> 3 <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</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:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetIds#if str($colname) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetIds#if str($colname) != 'nan':
11 -cnew "$colname" 11 -cnew "$colname"
12 #end if 12 #end if
13 #if str($colid): 13 #if str($colid):
60 <outputs> 60 <outputs>
61 <data format="sbml" name="out"/> 61 <data format="sbml" name="out"/>
62 </outputs> 62 </outputs>
63 <tests> 63 <tests>
64 <test> 64 <test>
65
65 <param name="sbml" value="toy_model.xml"/> 66 <param name="sbml" value="toy_model.xml"/>
67
66 <param name="tab" value="idMetabolites.tsv"/> 68 <param name="tab" value="idMetabolites.tsv"/>
69
67 <param name="o" value="METABOLITE"/> 70 <param name="o" value="METABOLITE"/>
71
68 <output ftype="sbml" name="out"> 72 <output ftype="sbml" name="out">
73
69 <assert_contents> 74 <assert_contents>
75
70 <is_valid_xml/> 76 <is_valid_xml/>
77
71 <has_line_matching expression=".*id=.metaboliteA.*" n="1"/> 78 <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>
79
72 <has_line_matching expression=".*id=.metaboliteB.*" n="1"/> 80 <has_line_matching expression=".*id=.metaboliteB.*" n="1"/>
81
73 </assert_contents> 82 </assert_contents>
83
74 </output> 84 </output>
85
75 </test> 86 </test>
76 <test> 87 <test>
88
77 <param name="sbml" value="toy_model.xml"/> 89 <param name="sbml" value="toy_model.xml"/>
90
78 <param name="tab" value="idReactions.tsv"/> 91 <param name="tab" value="idReactions.tsv"/>
92
79 <output ftype="sbml" name="out"> 93 <output ftype="sbml" name="out">
94
80 <assert_contents> 95 <assert_contents>
96
81 <is_valid_xml/> 97 <is_valid_xml/>
98
82 <has_line_matching expression=".*id=.reaction1.*" n="1"/> 99 <has_line_matching expression=".*id=.reaction1.*" n="1"/>
100
83 <has_line_matching expression=".*id=.reaction2.*" n="1"/> 101 <has_line_matching expression=".*id=.reaction2.*" n="1"/>
102
84 </assert_contents> 103 </assert_contents>
104
85 </output> 105 </output>
106
86 </test> 107 </test>
87 <test> 108 <test>
109
88 <param name="sbml" value="XF_network.sbml"/> 110 <param name="sbml" value="XF_network.sbml"/>
111
89 <param name="tab" value="idPathways.tsv"/> 112 <param name="tab" value="idPathways.tsv"/>
113
90 <param name="o" value="PATHWAY"/> 114 <param name="o" value="PATHWAY"/>
115
91 <output ftype="sbml" name="out"> 116 <output ftype="sbml" name="out">
117
92 <assert_contents> 118 <assert_contents>
119
93 <is_valid_xml/> 120 <is_valid_xml/>
121
94 <has_line_matching expression=".*groups:id=.CEB.*" n="1"/> 122 <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>
123
95 <has_line_matching expression=".*groups:id=.NSP.*" n="1"/> 124 <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>
125
96 </assert_contents> 126 </assert_contents>
127
97 </output> 128 </output>
129
98 </test> 130 </test>
99 <test> 131 <test>
132
100 <param name="sbml" value="XF_network.sbml"/> 133 <param name="sbml" value="XF_network.sbml"/>
134
101 <param name="tab" value="idGenes.tsv"/> 135 <param name="tab" value="idGenes.tsv"/>
136
102 <param name="o" value="GENE"/> 137 <param name="o" value="GENE"/>
138
103 <output ftype="sbml" name="out"> 139 <output ftype="sbml" name="out">
140
104 <assert_contents> 141 <assert_contents>
142
105 <is_valid_xml/> 143 <is_valid_xml/>
144
106 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> 145 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
146
107 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> 147 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
148
108 </assert_contents> 149 </assert_contents>
150
109 </output> 151 </output>
152
110 </test> 153 </test>
111 <test> 154 <test>
155
112 <param name="sbml" value="XF_network.sbml"/> 156 <param name="sbml" value="XF_network.sbml"/>
157
113 <param name="tab" value="idCompartments.tsv"/> 158 <param name="tab" value="idCompartments.tsv"/>
159
114 <param name="o" value="COMPARTMENT"/> 160 <param name="o" value="COMPARTMENT"/>
161
115 <output ftype="sbml" name="out"> 162 <output ftype="sbml" name="out">
163
116 <assert_contents> 164 <assert_contents>
165
117 <is_valid_xml/> 166 <is_valid_xml/>
167
118 <has_line_matching expression=".*id=.cytosol.*" n="1"/> 168 <has_line_matching expression=".*id=.cytosol.*" n="1"/>
169
119 <has_line_matching expression=".*id=.extra.*" n="1"/> 170 <has_line_matching expression=".*id=.extra.*" n="1"/>
171
120 </assert_contents> 172 </assert_contents>
173
121 </output> 174 </output>
175
122 </test> 176 </test>
123 </tests> 177 </tests>
124 <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids 178 <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids
125 The ids must correspond between the tabulated file and the SBML file. 179 The ids must correspond between the tabulated file and the SBML file.
126 If prefix or suffix is different in the SBML file, use the -p or the -s options. 180 If prefix or suffix is different in the SBML file, use the -p or the -s options.