Mercurial > repos > greg > vsnp_get_snps
comparison vsnp_get_snps.xml @ 14:44b84d32883c draft default tip
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
| author | greg |
|---|---|
| date | Mon, 15 Nov 2021 23:14:34 +0000 |
| parents | cd636b0e4f95 |
| children |
comparison
equal
deleted
inserted
replaced
| 13:cd636b0e4f95 | 14:44b84d32883c |
|---|---|
| 129 </when> | 129 </when> |
| 130 </conditional> | 130 </conditional> |
| 131 </when> | 131 </when> |
| 132 <when value="no"/> | 132 <when value="no"/> |
| 133 </conditional> | 133 </conditional> |
| 134 <param argument="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/> | 134 <param name="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/> |
| 135 </inputs> | 135 </inputs> |
| 136 <outputs> | 136 <outputs> |
| 137 <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)"> | 137 <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)"> |
| 138 <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/> | 138 <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/> |
| 139 </collection> | 139 </collection> |
| 164 </collection> | 164 </collection> |
| 165 </param> | 165 </param> |
| 166 <param name="input_excel_param" value="no"/> | 166 <param name="input_excel_param" value="no"/> |
| 167 <param name="all_isolates" value=""/> | 167 <param name="all_isolates" value=""/> |
| 168 <output_collection name="snps" type="list" count="1"> | 168 <output_collection name="snps" type="list" count="1"> |
| 169 <element name="all_vcf" file="all_vcf.fasta" ftype="fasta" compare="contains"/> | 169 <element name="all_vcf" ftype="fasta"> |
| 170 <assert_contents> | |
| 171 <has_size value="150"/> | |
| 172 </assert_contents> | |
| 173 </element> | |
| 170 </output_collection> | 174 </output_collection> |
| 171 <output_collection name="json_avg_mq" type="list" count="1"> | 175 <output_collection name="json_avg_mq" type="list" count="1"> |
| 172 <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/> | 176 <element name="all_vcf" ftype="json"> |
| 177 <assert_contents> | |
| 178 <has_size value="551"/> | |
| 179 </assert_contents> | |
| 180 </element> | |
| 173 </output_collection> | 181 </output_collection> |
| 174 <output_collection name="json_snps" type="list" count="1"> | 182 <output_collection name="json_snps" type="list" count="1"> |
| 175 <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/> | 183 <element name="all_vcf" ftype="json"> |
| 176 </output_collection> | 184 <assert_contents> |
| 177 <output name="output_summary" file="output_summary.html" ftype="html" compare="contains"/> | 185 <has_size value="876"/> |
| 186 </assert_contents> | |
| 187 </element> | |
| 188 </output_collection> | |
| 189 <output name="output_summary" ftype="html"> | |
| 190 <assert_contents> | |
| 191 <has_size value="303"/> | |
| 192 </assert_contents> | |
| 193 </output> | |
| 178 </test> | 194 </test> |
| 179 <!-- An input collection, no excel file, all_isolates is False --> | 195 <!-- An input collection, no excel file, all_isolates is False --> |
| 180 <test expect_num_outputs="4"> | 196 <test expect_num_outputs="4"> |
| 181 <param name="input_zc_vcf_type" value="collection"/> | 197 <param name="input_zc_vcf_type" value="collection"/> |
| 182 <param name="input_zc_vcf_collection"> | 198 <param name="input_zc_vcf_collection"> |
| 194 </collection> | 210 </collection> |
| 195 </param> | 211 </param> |
| 196 <param name="input_excel_param" value="no"/> | 212 <param name="input_excel_param" value="no"/> |
| 197 <param name="all_isolates" value=""/> | 213 <param name="all_isolates" value=""/> |
| 198 <output_collection name="snps" type="list" count="1"> | 214 <output_collection name="snps" type="list" count="1"> |
| 199 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/> | 215 <element name="all_vcf" ftype="fasta"> |
| 216 <assert_contents> | |
| 217 <has_size value="5226"/> | |
| 218 </assert_contents> | |
| 219 </element> | |
| 200 </output_collection> | 220 </output_collection> |
| 201 <output_collection name="json_avg_mq" type="list" count="1"> | 221 <output_collection name="json_avg_mq" type="list" count="1"> |
| 202 <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/> | 222 <element name="all_vcf" ftype="json"> |
| 223 <assert_contents> | |
| 224 <has_size value="24332"/> | |
| 225 </assert_contents> | |
| 226 </element> | |
| 203 </output_collection> | 227 </output_collection> |
| 204 <output_collection name="json_snps" type="list" count="1"> | 228 <output_collection name="json_snps" type="list" count="1"> |
| 205 <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/> | 229 <element name="all_vcf" ftype="json"> |
| 206 </output_collection> | 230 <assert_contents> |
| 207 <output name="output_summary" file="output_summary2.html" ftype="html" compare="contains"/> | 231 <has_size value="38798"/> |
| 232 </assert_contents> | |
| 233 </element> | |
| 234 </output_collection> | |
| 235 <output name="output_summary" ftype="html"> | |
| 236 <assert_contents> | |
| 237 <has_size value="303"/> | |
| 238 </assert_contents> | |
| 239 </output> | |
| 208 </test> | 240 </test> |
| 209 <!-- An input collection, an excel file, all_isolates is False --> | 241 <!-- An input collection, an excel file, all_isolates is False --> |
| 210 <test expect_num_outputs="4"> | 242 <test expect_num_outputs="4"> |
| 211 <param name="input_zc_vcf_type" value="collection"/> | 243 <param name="input_zc_vcf_type" value="collection"/> |
| 212 <param name="input_zc_vcf_collection"> | 244 <param name="input_zc_vcf_collection"> |
| 225 </param> | 257 </param> |
| 226 <param name="input_excel_param" value="yes"/> | 258 <param name="input_excel_param" value="yes"/> |
| 227 <param name="input_excel" value="89"/> | 259 <param name="input_excel" value="89"/> |
| 228 <param name="all_isolates" value=""/> | 260 <param name="all_isolates" value=""/> |
| 229 <output_collection name="snps" type="list" count="1"> | 261 <output_collection name="snps" type="list" count="1"> |
| 230 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/> | 262 <element name="Mbovis-17" ftype="fasta"> |
| 263 <assert_contents> | |
| 264 <has_size value="749"/> | |
| 265 </assert_contents> | |
| 266 </element> | |
| 231 </output_collection> | 267 </output_collection> |
| 232 <output_collection name="json_avg_mq" type="list" count="1"> | 268 <output_collection name="json_avg_mq" type="list" count="1"> |
| 233 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> | 269 <element name="Mbovis-17" ftype="json"> |
| 270 <assert_contents> | |
| 271 <has_size value="10884"/> | |
| 272 </assert_contents> | |
| 273 </element> | |
| 234 </output_collection> | 274 </output_collection> |
| 235 <output_collection name="json_snps" type="list" count="1"> | 275 <output_collection name="json_snps" type="list" count="1"> |
| 236 <element name="Mbovis-17" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> | 276 <element name="Mbovis-17" ftype="json"> |
| 237 </output_collection> | 277 <assert_contents> |
| 238 <output name="output_summary" file="output_summary3.html" ftype="html" compare="contains"/> | 278 <has_size value="6396"/> |
| 279 </assert_contents> | |
| 280 </element> | |
| 281 </output_collection> | |
| 282 <output name="output_summary" ftype="html"> | |
| 283 <assert_contents> | |
| 284 <has_size value="1057"/> | |
| 285 </assert_contents> | |
| 286 </output> | |
| 239 </test> | 287 </test> |
| 240 <!-- An input collection, an excel file, all_isolates is True --> | 288 <!-- An input collection, an excel file, all_isolates is True --> |
| 241 <test expect_num_outputs="4"> | 289 <test expect_num_outputs="4"> |
| 242 <param name="input_zc_vcf_type" value="collection"/> | 290 <param name="input_zc_vcf_type" value="collection"/> |
| 243 <param name="input_zc_vcf_collection"> | 291 <param name="input_zc_vcf_collection"> |
| 256 </param> | 304 </param> |
| 257 <param name="input_excel_param" value="yes"/> | 305 <param name="input_excel_param" value="yes"/> |
| 258 <param name="input_excel" value="89"/> | 306 <param name="input_excel" value="89"/> |
| 259 <param name="all_isolates" value="--all_isolates"/> | 307 <param name="all_isolates" value="--all_isolates"/> |
| 260 <output_collection name="snps" type="list" count="2"> | 308 <output_collection name="snps" type="list" count="2"> |
| 261 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/> | 309 <element name="Mbovis-17" ftype="fasta"> |
| 262 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/> | 310 <assert_contents> |
| 311 <has_size value="749"/> | |
| 312 </assert_contents> | |
| 313 </element> | |
| 314 <element name="all_vcf" ftype="fasta"> | |
| 315 <assert_contents> | |
| 316 <has_size value="4920"/> | |
| 317 </assert_contents> | |
| 318 </element> | |
| 263 </output_collection> | 319 </output_collection> |
| 264 <output_collection name="json_avg_mq" type="list" count="2"> | 320 <output_collection name="json_avg_mq" type="list" count="2"> |
| 265 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> | 321 <element name="Mbovis-17" ftype="json"> |
| 266 <element name="all_vcf" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> | 322 <assert_contents> |
| 323 <has_size value="10884"/> | |
| 324 </assert_contents> | |
| 325 </element> | |
| 326 <element name="all_vcf" ftype="json"> | |
| 327 <assert_contents> | |
| 328 <has_size value="24332"/> | |
| 329 </assert_contents> | |
| 330 </element> | |
| 267 </output_collection> | 331 </output_collection> |
| 268 <output_collection name="json_snps" type="list" count="2"> | 332 <output_collection name="json_snps" type="list" count="2"> |
| 269 <element name="Mbovis-17" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> | 333 <element name="Mbovis-17" ftype="json"> |
| 270 <element name="all_vcf" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> | 334 <assert_contents> |
| 271 </output_collection> | 335 <has_size value="6396"/> |
| 272 <output name="output_summary" file="output_summary4.html" ftype="html" compare="contains"/> | 336 </assert_contents> |
| 337 </element> | |
| 338 <element name="all_vcf" ftype="json"> | |
| 339 <assert_contents> | |
| 340 <has_size value="36466"/> | |
| 341 </assert_contents> | |
| 342 </element> | |
| 343 </output_collection> | |
| 344 <output name="output_summary" ftype="html"> | |
| 345 <assert_contents> | |
| 346 <has_size value="1056"/> | |
| 347 </assert_contents> | |
| 348 </output> | |
| 273 </test> | 349 </test> |
| 274 </tests> | 350 </tests> |
| 275 <help> | 351 <help> |
| 276 **What it does** | 352 **What it does** |
| 277 | 353 |