Mercurial > repos > iuc > funannotate_annotate

comparison funannotate_annotate.xml @ 7:b6b5cd37f2a2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 90acc0e23230b2e29e1d38a90bca4009c84c7e67
author iuc
date Fri, 20 Oct 2023 10:07:28 +0000
parents 582fd74dc2a1
children 756376aeb1ae
comparison
equal deleted inserted replaced
6:582fd74dc2a1 7:b6b5cd37f2a2
66 #if $remove: 66 #if $remove:
67 --remove '${remove}' 67 --remove '${remove}'
68 #end if 68 #end if
69 69
70 --cpus \${GALAXY_SLOTS:-2} 70 --cpus \${GALAXY_SLOTS:-2}
71
72 &&
73
74 ## funannotate sometimes leaves multiple *part.tbl and *part.sqn files
75 ## https://github.com/nextgenusfs/funannotate/issues/777
76 find output/annotate_results
77 -regex ".*part_[0-9]\+\.\(sqn\|tbl\)$"
78 -delete
71 79
72 && 80 &&
73 81
74 mv output/annotate_results/*.gbk out.gbk && 82 mv output/annotate_results/*.gbk out.gbk &&
75 mv output/annotate_results/*.annotations.txt out.annotations.txt && 83 mv output/annotate_results/*.annotations.txt out.annotations.txt &&
204 <data name='new_names_passed' format='json' label="${tool.name} on ${on_string}: Gene Name/Product new-names-passed" from_work_dir="output/annotate_results/Gene2Products.new-names-passed.txt"> 212 <data name='new_names_passed' format='json' label="${tool.name} on ${on_string}: Gene Name/Product new-names-passed" from_work_dir="output/annotate_results/Gene2Products.new-names-passed.txt">
205 <filter>outputs and 'new_names_passed' in outputs</filter> 213 <filter>outputs and 'new_names_passed' in outputs</filter>
206 </data> 214 </data>
207 </outputs> 215 </outputs>
208 <tests> 216 <tests>
209 <test> 217 <test expect_num_outputs="16">
210 <conditional name="input"> 218 <conditional name="input">
211 <param name="input_type" value="gbk" /> 219 <param name="input_type" value="gbk" />
212 <param name="genbank" value="predict_augustus/Genus_species.gbk" /> 220 <param name="genbank" value="predict_augustus/Genus_species.gbk" />
213 </conditional> 221 </conditional>
214 <param name="database" value="2021-07-20-120000" /> 222 <param name="database" value="2021-07-20-120000" />
294 <assert_contents> 302 <assert_contents>
295 <has_text text="Passed Description" /> 303 <has_text text="Passed Description" />
296 </assert_contents> 304 </assert_contents>
297 </output> 305 </output>
298 </test> 306 </test>
299 <test> 307 <test expect_num_outputs="16">
300 <conditional name="input"> 308 <conditional name="input">
301 <param name="input_type" value="gff" /> 309 <param name="input_type" value="gff" />
302 <param name="gff" value="predict_augustus/Genus_species.gff3" /> 310 <param name="gff" value="predict_augustus/Genus_species.gff3" />
303 <param name="fasta" value="genome.fa" /> 311 <param name="fasta" value="genome.fa" />
304 <param name="species" value="Genus species" /> 312 <param name="species" value="Genus species" />