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comparison tools/convert/Tab2Sbml/Tab2Sbml.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_Tab2Sbml" name="Tab2Sbml" version="2.0.0"> 2 <tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="2.0.1">
3 <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description> 3 <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</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 convert.Tab2Sbml#if str($colid) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
11 -ci "$colid" 11 -ci "$colid"
12 #end if 12 #end if
13 #if str($colformula) != 'nan': 13 #if str($colformula) != 'nan':
74 <outputs> 74 <outputs>
75 <data format="sbml" name="sbml"/> 75 <data format="sbml" name="sbml"/>
76 </outputs> 76 </outputs>
77 <tests> 77 <tests>
78 <test> 78 <test>
79
79 <param name="in" value="toy_model.tsv"/> 80 <param name="in" value="toy_model.tsv"/>
81
80 <output ftype="sbml" name="sbml"> 82 <output ftype="sbml" name="sbml">
83
81 <assert_contents> 84 <assert_contents>
85
82 <is_valid_xml/> 86 <is_valid_xml/>
87
83 <has_line_matching expression=".*reaction .*" n="7"/> 88 <has_line_matching expression=".*reaction .*" n="7"/>
89
84 <has_line_matching expression=".*species .*" n="8"/> 90 <has_line_matching expression=".*species .*" n="8"/>
91
85 </assert_contents> 92 </assert_contents>
93
86 </output> 94 </output>
95
87 </test> 96 </test>
88 <test> 97 <test>
98
89 <param name="in" value="toy_model_otherColumns.tsv"/> 99 <param name="in" value="toy_model_otherColumns.tsv"/>
100
90 <param name="colid" value="2"/> 101 <param name="colid" value="2"/>
102
91 <param name="colformula" value="3"/> 103 <param name="colformula" value="3"/>
104
92 <output ftype="sbml" name="sbml"> 105 <output ftype="sbml" name="sbml">
106
93 <assert_contents> 107 <assert_contents>
108
94 <is_valid_xml/> 109 <is_valid_xml/>
110
95 <has_line_matching expression=".*reaction .*" n="7"/> 111 <has_line_matching expression=".*reaction .*" n="7"/>
112
96 <has_line_matching expression=".*species .*" n="8"/> 113 <has_line_matching expression=".*species .*" n="8"/>
114
97 </assert_contents> 115 </assert_contents>
116
98 </output> 117 </output>
118
99 </test> 119 </test>
100 <test> 120 <test>
121
101 <param name="in" value="toy_model_otherSigns.tsv"/> 122 <param name="in" value="toy_model_otherSigns.tsv"/>
123
102 <param name="i" value="-&gt;"/> 124 <param name="i" value="-&gt;"/>
125
103 <param name="r" value="="/> 126 <param name="r" value="="/>
127
104 <output ftype="sbml" name="sbml"> 128 <output ftype="sbml" name="sbml">
129
105 <assert_contents> 130 <assert_contents>
131
106 <is_valid_xml/> 132 <is_valid_xml/>
133
107 <has_line_matching expression=".*reaction .*" n="7"/> 134 <has_line_matching expression=".*reaction .*" n="7"/>
135
108 <has_line_matching expression=".*species .*" n="8"/> 136 <has_line_matching expression=".*species .*" n="8"/>
137
109 </assert_contents> 138 </assert_contents>
139
110 </output> 140 </output>
141
111 </test> 142 </test>
112 <test> 143 <test>
144
113 <param name="in" value="toy_model.tsv"/> 145 <param name="in" value="toy_model.tsv"/>
146
114 <param name="rp" value="true"/> 147 <param name="rp" value="true"/>
148
115 <param name="mp" value="true"/> 149 <param name="mp" value="true"/>
150
116 <param name="e" value="_e"/> 151 <param name="e" value="_e"/>
152
117 <param name="createCompartment" value="true"/> 153 <param name="createCompartment" value="true"/>
154
118 <output ftype="sbml" name="sbml"> 155 <output ftype="sbml" name="sbml">
156
119 <assert_contents> 157 <assert_contents>
158
120 <is_valid_xml/> 159 <is_valid_xml/>
160
121 <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/> 161 <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/>
162
122 <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/> 163 <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/>
164
123 <has_line_matching expression=".*id=.R_reac2.*" n="1"/> 165 <has_line_matching expression=".*id=.R_reac2.*" n="1"/>
166
124 </assert_contents> 167 </assert_contents>
168
125 </output> 169 </output>
170
126 </test> 171 </test>
127 <test> 172 <test>
173
128 <param name="in" value="toy_model.tsv"/> 174 <param name="in" value="toy_model.tsv"/>
175
129 <param name="id" value="myModel"/> 176 <param name="id" value="myModel"/>
177
130 <output ftype="sbml" name="sbml"> 178 <output ftype="sbml" name="sbml">
179
131 <assert_contents> 180 <assert_contents>
181
132 <is_valid_xml/> 182 <is_valid_xml/>
183
133 <has_line_matching expression=".*myModel.*" n="1"/> 184 <has_line_matching expression=".*myModel.*" n="1"/>
185
134 </assert_contents> 186 </assert_contents>
187
135 </output> 188 </output>
189
136 </test> 190 </test>
137 </tests> 191 </tests>
138 <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help> 192 <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help>
139 <citations/> 193 <citations/>
140 </tool> 194 </tool>