Mercurial > repos > metexplore > met4j
comparison tools/convert/Sbml2Tab/Sbml2Tab.xml @ 10:6a112eaf8f38 draft
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_Sbml2Tab" name="Sbml2Tab" version="develop"> | 2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.0"> |
| 3 <description>Create a tabulated file listing reaction attributes from a SBML file</description> | 3 <description>Create a tabulated file listing reaction attributes from 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 convert.Sbml2Tab#if str($i): | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): |
| 11 -irr "$i" | 11 -irr "$i" |
| 12 #end if | 12 #end if |
| 13 #if str($r): | 13 #if str($r): |
| 32 <outputs> | 32 <outputs> |
| 33 <data format="tsv" name="out"/> | 33 <data format="tsv" name="out"/> |
| 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="in" value="toy_model.xml"/> | 37 <param name="in" value="toy_model.xml"/> |
| 49 | |
| 50 | |
| 51 | |
| 52 | |
| 53 | |
| 54 | |
| 55 | |
| 56 | |
| 57 | |
| 58 | |
| 59 | |
| 60 <output ftype="tsv" name="out"> | 38 <output ftype="tsv" name="out"> |
| 61 | |
| 62 | |
| 63 | |
| 64 | |
| 65 | |
| 66 | |
| 67 | |
| 68 | |
| 69 | |
| 70 | |
| 71 | |
| 72 <assert_contents> | 39 <assert_contents> |
| 73 | |
| 74 | |
| 75 | |
| 76 | |
| 77 | |
| 78 | |
| 79 | |
| 80 | |
| 81 | |
| 82 | |
| 83 | |
| 84 <has_n_lines n="8"/> | 40 <has_n_lines n="8"/> |
| 85 | |
| 86 | |
| 87 | |
| 88 | |
| 89 | |
| 90 | |
| 91 | |
| 92 | |
| 93 | |
| 94 | |
| 95 | |
| 96 <has_n_columns n="9"/> | 41 <has_n_columns n="9"/> |
| 97 | |
| 98 | |
| 99 | |
| 100 | |
| 101 | |
| 102 | |
| 103 | |
| 104 | |
| 105 | |
| 106 | |
| 107 | |
| 108 <has_text text="2.0 E[c] --> D[c]"/> | 42 <has_text text="2.0 E[c] --> D[c]"/> |
| 109 | |
| 110 | |
| 111 | |
| 112 | |
| 113 | |
| 114 | |
| 115 | |
| 116 | |
| 117 | |
| 118 | |
| 119 | |
| 120 <has_text text="A[c] <==> B[c]"/> | 43 <has_text text="A[c] <==> B[c]"/> |
| 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 <test> | 47 <test> |
| 158 | |
| 159 | |
| 160 | |
| 161 | |
| 162 | |
| 163 | |
| 164 | |
| 165 | |
| 166 | |
| 167 | |
| 168 | |
| 169 <param name="in" value="toy_model.xml"/> | 48 <param name="in" value="toy_model.xml"/> |
| 170 | |
| 171 | |
| 172 | |
| 173 | |
| 174 | |
| 175 | |
| 176 | |
| 177 | |
| 178 | |
| 179 | |
| 180 | |
| 181 <param name="i" value="->"/> | 49 <param name="i" value="->"/> |
| 182 | |
| 183 | |
| 184 | |
| 185 | |
| 186 | |
| 187 | |
| 188 | |
| 189 | |
| 190 | |
| 191 | |
| 192 | |
| 193 <param name="r" value="="/> | 50 <param name="r" value="="/> |
| 194 | |
| 195 | |
| 196 | |
| 197 | |
| 198 | |
| 199 | |
| 200 | |
| 201 | |
| 202 | |
| 203 | |
| 204 | |
| 205 <output ftype="tsv" name="out"> | 51 <output ftype="tsv" name="out"> |
| 206 | |
| 207 | |
| 208 | |
| 209 | |
| 210 | |
| 211 | |
| 212 | |
| 213 | |
| 214 | |
| 215 | |
| 216 | |
| 217 <assert_contents> | 52 <assert_contents> |
| 218 | |
| 219 | |
| 220 | |
| 221 | |
| 222 | |
| 223 | |
| 224 | |
| 225 | |
| 226 | |
| 227 | |
| 228 | |
| 229 <has_n_lines n="8"/> | 53 <has_n_lines n="8"/> |
| 230 | |
| 231 | |
| 232 | |
| 233 | |
| 234 | |
| 235 | |
| 236 | |
| 237 | |
| 238 | |
| 239 | |
| 240 | |
| 241 <has_n_columns n="9"/> | 54 <has_n_columns n="9"/> |
| 242 | |
| 243 | |
| 244 | |
| 245 | |
| 246 | |
| 247 | |
| 248 | |
| 249 | |
| 250 | |
| 251 | |
| 252 | |
| 253 <has_text text="2.0 E[c] -> D[c]"/> | 55 <has_text text="2.0 E[c] -> D[c]"/> |
| 254 | |
| 255 | |
| 256 | |
| 257 | |
| 258 | |
| 259 | |
| 260 | |
| 261 | |
| 262 | |
| 263 | |
| 264 | |
| 265 <has_text text="A[c] = B[c]"/> | 56 <has_text text="A[c] = B[c]"/> |
| 266 | |
| 267 | |
| 268 | |
| 269 | |
| 270 | |
| 271 | |
| 272 | |
| 273 | |
| 274 | |
| 275 | |
| 276 | |
| 277 </assert_contents> | 57 </assert_contents> |
| 278 | |
| 279 | |
| 280 | |
| 281 | |
| 282 | |
| 283 | |
| 284 | |
| 285 | |
| 286 | |
| 287 | |
| 288 | |
| 289 </output> | 58 </output> |
| 290 | |
| 291 | |
| 292 | |
| 293 | |
| 294 | |
| 295 | |
| 296 | |
| 297 | |
| 298 | |
| 299 | |
| 300 | |
| 301 </test> | 59 </test> |
| 302 </tests> | 60 </tests> |
| 303 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> | 61 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> |
| 304 <citations/> | 62 <citations/> |
| 305 </tool> | 63 </tool> |