Mercurial > repos > iuc > busco
comparison busco.xml @ 20:ea8146ee148f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 9bf18dbcef34a48d3c40150ee953706bececfdd1
| author | iuc |
|---|---|
| date | Mon, 18 Mar 2024 16:01:49 +0000 |
| parents | 2a5b8b9936bf |
| children |
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| 19:2a5b8b9936bf | 20:ea8146ee148f |
|---|---|
| 207 <conditional name="use_augustus"> | 207 <conditional name="use_augustus"> |
| 208 <param name="use_augustus_selector" value="yes" /> | 208 <param name="use_augustus_selector" value="yes" /> |
| 209 </conditional> | 209 </conditional> |
| 210 </conditional> | 210 </conditional> |
| 211 <param name="outputs" value="short_summary,missing,gff" /> | 211 <param name="outputs" value="short_summary,missing,gff" /> |
| 212 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" /> | 212 <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> |
| 213 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> | 213 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> |
| 214 <output name="busco_gff"> | 214 <output name="busco_gff"> |
| 215 <assert_contents> | 215 <assert_contents> |
| 216 <has_n_lines n="1"/> | 216 <has_n_lines n="1"/> |
| 217 <has_text text="##gff-version 3" /> | 217 <has_text text="##gff-version 3" /> |
| 231 </conditional> | 231 </conditional> |
| 232 <conditional name="busco_mode"> | 232 <conditional name="busco_mode"> |
| 233 <param name="mode" value="prot" /> | 233 <param name="mode" value="prot" /> |
| 234 </conditional> | 234 </conditional> |
| 235 <param name="outputs" value="short_summary,missing,image,gff" /> | 235 <param name="outputs" value="short_summary,missing,image,gff" /> |
| 236 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="6" /> | 236 <output name="busco_sum" file="proteome_results/short_summary" compare="re_match_multiline" /> |
| 237 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" /> | 237 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" /> |
| 238 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" /> | 238 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" /> |
| 239 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> | 239 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> |
| 240 <output name="busco_gff"> | 240 <output name="busco_gff"> |
| 241 <assert_contents> | 241 <assert_contents> |
| 252 </conditional> | 252 </conditional> |
| 253 <conditional name="busco_mode"> | 253 <conditional name="busco_mode"> |
| 254 <param name="mode" value="tran" /> | 254 <param name="mode" value="tran" /> |
| 255 </conditional> | 255 </conditional> |
| 256 <param name="outputs" value="short_summary,missing,image,gff" /> | 256 <param name="outputs" value="short_summary,missing,image,gff" /> |
| 257 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" /> | 257 <output name="busco_sum" file="transcriptome_results/short_summary" compare="re_match_multiline" /> |
| 258 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> | 258 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> |
| 259 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> | 259 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> |
| 260 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> | 260 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> |
| 261 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" /> | 261 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" /> |
| 262 </test> | 262 </test> |
| 276 <param name="augustus_species" value="human" /> | 276 <param name="augustus_species" value="human" /> |
| 277 </conditional> | 277 </conditional> |
| 278 </conditional> | 278 </conditional> |
| 279 </conditional> | 279 </conditional> |
| 280 <param name="outputs" value="short_summary,gff" /> | 280 <param name="outputs" value="short_summary,gff" /> |
| 281 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" /> | 281 <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline"/> |
| 282 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> | 282 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> |
| 283 <output name="busco_gff"> | 283 <output name="busco_gff"> |
| 284 <assert_contents> | 284 <assert_contents> |
| 285 <has_n_lines n="1"/> | 285 <has_n_lines n="1"/> |
| 286 <has_text text="##gff-version 3" /> | 286 <has_text text="##gff-version 3" /> |
| 304 <param name="augustus_model" value="local.tar.gz" ftype="augustus" /> | 304 <param name="augustus_model" value="local.tar.gz" ftype="augustus" /> |
| 305 </conditional> | 305 </conditional> |
| 306 </conditional> | 306 </conditional> |
| 307 </conditional> | 307 </conditional> |
| 308 <param name="outputs" value="short_summary,missing" /> | 308 <param name="outputs" value="short_summary,missing" /> |
| 309 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" /> | 309 <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> |
| 310 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> | 310 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> |
| 311 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" /> | 311 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" /> |
| 312 </test> | 312 </test> |
| 313 <test expect_num_outputs="5"> | 313 <test expect_num_outputs="5"> |
| 314 <param name="input" value="genome.fa" /> | 314 <param name="input" value="genome.fa" /> |
| 321 <conditional name="use_augustus"> | 321 <conditional name="use_augustus"> |
| 322 <param name="use_augustus_selector" value="no" /> | 322 <param name="use_augustus_selector" value="no" /> |
| 323 </conditional> | 323 </conditional> |
| 324 </conditional> | 324 </conditional> |
| 325 <param name="outputs" value="short_summary,missing,image,gff" /> | 325 <param name="outputs" value="short_summary,missing,image,gff" /> |
| 326 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" /> | 326 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="re_match_multiline" /> |
| 327 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" /> | 327 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" /> |
| 328 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" /> | 328 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" /> |
| 329 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> | 329 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> |
| 330 <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" /> | 330 <output name="busco_gff" ftype="gff3"> |
| 331 <assert_contents> | |
| 332 <has_n_lines n="13"/> | |
| 333 </assert_contents> | |
| 334 </output> | |
| 331 </test> | 335 </test> |
| 332 <test expect_num_outputs="5"> | 336 <test expect_num_outputs="5"> |
| 333 <param name="input" value="genome.fa" /> | 337 <param name="input" value="genome.fa" /> |
| 334 <conditional name="lineage"> | 338 <conditional name="lineage"> |
| 335 <param name="lineage_mode" value="auto_detect" /> | 339 <param name="lineage_mode" value="auto_detect" /> |
| 341 <param name="use_augustus_selector" value="no" /> | 345 <param name="use_augustus_selector" value="no" /> |
| 342 </conditional> | 346 </conditional> |
| 343 </conditional> | 347 </conditional> |
| 344 <param name="outputs" value="short_summary,missing,image,gff" /> | 348 <param name="outputs" value="short_summary,missing,image,gff" /> |
| 345 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" /> | 349 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" /> |
| 346 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" /> | 350 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="6" /> |
| 347 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" /> | 351 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" /> |
| 348 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> | 352 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> |
| 349 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" /> | 353 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" /> |
| 350 </test> | 354 </test> |
| 351 <test expect_num_outputs="2"> | 355 <test expect_num_outputs="2"> |