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comparison build/tools/SetCharges/SetCharges.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
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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_SetCharges" name="SetCharges" version="2.0.0"> 2 <tool id="met4j_SetCharges" name="SetCharges" version="2.0.1">
3 <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description> 3 <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</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.SetCharges#if str($colcharge) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetCharges#if str($colcharge) != 'nan':
11 -cc "$colcharge" 11 -cc "$colcharge"
12 #end if 12 #end if
13 #if str($colid) != 'nan': 13 #if str($colid) != 'nan':
48 <outputs> 48 <outputs>
49 <data format="sbml" name="out"/> 49 <data format="sbml" name="out"/>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>
52 <test> 52 <test>
53
53 <param name="sbml" value="toy_model.xml"/> 54 <param name="sbml" value="toy_model.xml"/>
55
54 <param name="tab" value="charges.tsv"/> 56 <param name="tab" value="charges.tsv"/>
57
55 <output ftype="sbml" name="out"> 58 <output ftype="sbml" name="out">
59
56 <assert_contents> 60 <assert_contents>
61
57 <is_valid_xml/> 62 <is_valid_xml/>
63
58 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> 64 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
65
59 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 66 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
67
60 </assert_contents> 68 </assert_contents>
69
61 </output> 70 </output>
71
62 </test> 72 </test>
63 <test> 73 <test>
74
64 <param name="sbml" value="toy_model.xml"/> 75 <param name="sbml" value="toy_model.xml"/>
76
65 <param name="tab" value="chargesWithComment.tsv"/> 77 <param name="tab" value="chargesWithComment.tsv"/>
78
66 <output ftype="sbml" name="out"> 79 <output ftype="sbml" name="out">
80
67 <assert_contents> 81 <assert_contents>
82
68 <is_valid_xml/> 83 <is_valid_xml/>
84
69 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> 85 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
86
70 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 87 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
88
71 </assert_contents> 89 </assert_contents>
90
72 </output> 91 </output>
92
73 </test> 93 </test>
74 <test> 94 <test>
95
75 <param name="sbml" value="toy_model.xml"/> 96 <param name="sbml" value="toy_model.xml"/>
97
76 <param name="tab" value="charges.tsv"/> 98 <param name="tab" value="charges.tsv"/>
99
77 <param name="nSkip" value="1"/> 100 <param name="nSkip" value="1"/>
101
78 <output ftype="sbml" name="out"> 102 <output ftype="sbml" name="out">
103
79 <assert_contents> 104 <assert_contents>
105
80 <is_valid_xml/> 106 <is_valid_xml/>
107
81 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> 108 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
109
82 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 110 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
111
83 </assert_contents> 112 </assert_contents>
113
84 </output> 114 </output>
115
85 </test> 116 </test>
86 <test> 117 <test>
118
87 <param name="sbml" value="toy_model.xml"/> 119 <param name="sbml" value="toy_model.xml"/>
120
88 <param name="tab" value="charges.tsv"/> 121 <param name="tab" value="charges.tsv"/>
122
89 <param name="ci" value="2"/> 123 <param name="ci" value="2"/>
124
90 <param name="cc" value="3"/> 125 <param name="cc" value="3"/>
126
91 <output ftype="sbml" name="out"> 127 <output ftype="sbml" name="out">
128
92 <assert_contents> 129 <assert_contents>
130
93 <is_valid_xml/> 131 <is_valid_xml/>
132
94 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> 133 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
134
95 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> 135 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
136
96 </assert_contents> 137 </assert_contents>
138
97 </output> 139 </output>
140
98 </test> 141 </test>
99 <test> 142 <test>
143
100 <param name="sbml" value="XF_network.sbml"/> 144 <param name="sbml" value="XF_network.sbml"/>
145
101 <param name="tab" value="chargesXF.tsv"/> 146 <param name="tab" value="chargesXF.tsv"/>
147
102 <param name="p" value="true"/> 148 <param name="p" value="true"/>
149
103 <param name="s" value="true"/> 150 <param name="s" value="true"/>
151
104 <output ftype="sbml" name="out"> 152 <output ftype="sbml" name="out">
153
105 <assert_contents> 154 <assert_contents>
155
106 <is_valid_xml/> 156 <is_valid_xml/>
157
107 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> 158 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>
159
108 </assert_contents> 160 </assert_contents>
161
109 </output> 162 </output>
163
110 </test> 164 </test>
111 </tests> 165 </tests>
112 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges 166 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges
113 The charge must be a number. The ids must correspond between the tabulated file and the SBML file. 167 The charge must be a number. The ids must correspond between the tabulated file and the SBML file.
114 If prefix or suffix is different in the SBML file, use the -p or the -s options. 168 If prefix or suffix is different in the SBML file, use the -p or the -s options.