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comparison busco.xml @ 20:ea8146ee148f draft

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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 2babe6d5c561
comparison
equal deleted inserted replaced
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">