Mercurial > repos > iuc > funannotate_annotate

comparison funannotate_annotate.xml @ 11:9c15ca7e764e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 9e3708d04faea0f1be4ea8918e859d6f2c7eb31d
author iuc
date Wed, 26 Jun 2024 09:41:52 +0000
parents d0336d67702b
children
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10:d0336d67702b 11:9c15ca7e764e
24 --fasta '${input.fasta}' 24 --fasta '${input.fasta}'
25 --species '${input.species}' 25 --species '${input.species}'
26 #end if 26 #end if
27 27
28 --out output 28 --out output
29 --tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"
29 30
30 --database '$database.fields.path' 31 --database '$database.fields.path'
31 32
32 #if $sbt: 33 #if $sbt:
33 --sbt '${sbt}' 34 --sbt '${sbt}'
74 75
75 ## Funannotate sometimes leaves multiple *part.tbl and *part.sqn files: 76 ## Funannotate sometimes leaves multiple *part.tbl and *part.sqn files:
76 ## https://github.com/nextgenusfs/funannotate/issues/777 77 ## https://github.com/nextgenusfs/funannotate/issues/777
77 ## The partial tbl files are combined by funannotate and are deleted below. 78 ## The partial tbl files are combined by funannotate and are deleted below.
78 ## The sqn files are discrete and are collected with discover_datasets. 79 ## The sqn files are discrete and are collected with discover_datasets.
79 find output/annotate_results 80 find output/annotate_results
80 -regex ".*part_[0-9]+\.\(tbl\)$" 81 -regex ".*part_[0-9]+\.\(tbl\)$"
81 -delete 82 -delete
82 83
83 ]]></command> 84 ]]></command>
84 <inputs> 85 <inputs>
239 <output_collection name="sqn" type="list"> 240 <output_collection name="sqn" type="list">
240 <element name="Genus_species"> 241 <element name="Genus_species">
241 <assert_contents> 242 <assert_contents>
242 <has_text text="Seq-submit" /> 243 <has_text text="Seq-submit" />
243 </assert_contents> 244 </assert_contents>
244 </element> 245 </element>
245 </output_collection> 246 </output_collection>
246 <output name="fa_scaffolds"> 247 <output name="fa_scaffolds">
247 <assert_contents> 248 <assert_contents>
248 <has_text text=">sample" /> 249 <has_text text=">sample" />
249 </assert_contents> 250 </assert_contents>
333 <output_collection name="sqn" type="list"> 334 <output_collection name="sqn" type="list">
334 <element name="Genus_species"> 335 <element name="Genus_species">
335 <assert_contents> 336 <assert_contents>
336 <has_text text="Seq-submit" /> 337 <has_text text="Seq-submit" />
337 </assert_contents> 338 </assert_contents>
338 </element> 339 </element>
339 </output_collection> 340 </output_collection>
340 <output name="fa_scaffolds"> 341 <output name="fa_scaffolds">
341 <assert_contents> 342 <assert_contents>
342 <has_text text=">sample" /> 343 <has_text text=">sample" />
343 </assert_contents> 344 </assert_contents>