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comparison arriba.xml @ 13:1d459aaa5765 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
author jjohnson
date Mon, 13 Jun 2022 12:09:32 +0000
parents 73fd7703a743
children
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12:73fd7703a743 13:1d459aaa5765
11 </macros> 11 </macros>
12 <expand macro="requirements" /> 12 <expand macro="requirements" />
13 <expand macro="version_command" /> 13 <expand macro="version_command" />
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 @GENOME_SOURCE@ 15 @GENOME_SOURCE@
16 #set $filter_list = []
17 #if $options.filters
18 #set $filter_list = $options.filters.split(',')
19 #end if
16 #if $blacklist 20 #if $blacklist
17 #if $blacklist.is_of_type('tabular.gz') 21 #if $blacklist.is_of_type('tabular.gz')
18 #set $blacklist_file = 'blacklist.tsv.gz' 22 #set $blacklist_file = 'blacklist.tsv.gz'
19 ln -sf '$blacklist' $blacklist_file && 23 ln -sf '$blacklist' $blacklist_file &&
20 #else 24 #else
21 #set $blacklist_file = $blacklist 25 #set $blacklist_file = $blacklist
22 #end if 26 #end if
23 #end if 27 #else
28 #if 'blacklist' not in $filter_list
29 #silent $filter_list.append('blacklist')
30 #end if
31 #end if
32 #set $filters = ','.join($filter_list)
24 #if $known_fusions 33 #if $known_fusions
25 #if $known_fusions.is_of_type('tabular.gz') 34 #if $known_fusions.is_of_type('tabular.gz')
26 #set $known_fusions_file = 'known_fusions.tsv.gz' 35 #set $known_fusions_file = 'known_fusions.tsv.gz'
27 ln -sf '$known_fusions' $known_fusions_file && 36 ln -sf '$known_fusions' $known_fusions_file &&
28 #else 37 #else
104 #end if 113 #end if
105 -a '$genome_assembly' 114 -a '$genome_assembly'
106 -g '$genome_annotation' 115 -g '$genome_annotation'
107 #if $blacklist 116 #if $blacklist
108 -b '$blacklist_file' 117 -b '$blacklist_file'
109 #else 118 #end if
110 -f 'blacklist' 119 #if $filters
120 -f '$filters'
111 #end if 121 #end if
112 #if $protein_domains 122 #if $protein_domains
113 -p '$protein_domains' 123 -p '$protein_domains'
114 #end if 124 #end if
115 #if $known_fusions 125 #if $known_fusions
315 <help>Comma-/space-separated list of viral contigs. 325 <help>Comma-/space-separated list of viral contigs.
316 Asterisks (*) are treated as wild-cards. 326 Asterisks (*) are treated as wild-cards.
317 Default: AC_* NC_* 327 Default: AC_* NC_*
318 </help> 328 </help>
319 </param> 329 </param>
330 <param name="filters" argument="-f" type="select" optional="true" multiple="true" label="Diable filters">
331 <help>By default all filters are enabled.</help>
332 <option value="top_expressed_viral_contigs">top_expressed_viral_contigs</option>
333 <option value="viral_contigs">viral_contigs</option>
334 <option value="low_coverage_viral_contigs">low_coverage_viral_contigs</option>
335 <option value="uninteresting_contigs">uninteresting_contigs</option>
336 <option value="no_genomic_support">no_genomic_support</option>
337 <option value="short_anchor">short_anchor</option>
338 <option value="select_best">select_best</option>
339 <option value="many_spliced">many_spliced</option>
340 <option value="long_gap">long_gap</option>
341 <option value="merge_adjacent">merge_adjacent</option>
342 <option value="hairpin">hairpin</option>
343 <option value="small_insert_size">small_insert_size</option>
344 <option value="same_gene">same_gene</option>
345 <option value="genomic_support">genomic_support</option>
346 <option value="read_through">read_through</option>
347 <option value="no_coverage">no_coverage</option>
348 <option value="mismatches">mismatches</option>
349 <option value="homopolymer">homopolymer</option>
350 <option value="low_entropy">low_entropy</option>
351 <option value="multimappers">multimappers</option>
352 <option value="inconsistently_clipped">inconsistently_clipped</option>
353 <option value="duplicates">duplicates</option>
354 <option value="homologs">homologs</option>
355 <option value="blacklist">blacklist</option>
356 <option value="mismappers">mismappers</option>
357 <option value="spliced">spliced</option>
358 <option value="relative_support">relative_support</option>
359 <option value="min_support">min_support</option>
360 <option value="known_fusions">known_fusions</option>
361 <option value="end_to_end">end_to_end</option>
362 <option value="non_coding_neighbors">non_coding_neighbors</option>
363 <option value="isoforms">isoforms</option>
364 <option value="intronic">intronic</option>
365 <option value="in_vitro">in_vitro</option>
366 <option value="intragenic_exonic">intragenic_exonic</option>
367 <option value="internal_tandem_duplication">internal_tandem_duplication</option>
368 </param>
369
320 <param name="max_evalue" argument="-E" type="float" value="" optional="true" label="Max e-value threahold"> 370 <param name="max_evalue" argument="-E" type="float" value="" optional="true" label="Max e-value threahold">
321 <help>Arriba estimates the number of fusions with a given number of supporting 371 <help>Arriba estimates the number of fusions with a given number of supporting
322 reads which one would expect to see by random chance. If the expected number 372 reads which one would expect to see by random chance. If the expected number
323 of fusions (e-value) is higher than this threshold, the fusion is 373 of fusions (e-value) is higher than this threshold, the fusion is
324 discarded by the 'relative_support' filter. Note: Increasing this 374 discarded by the 'relative_support' filter. Note: Increasing this
558 <conditional name="genome"> 608 <conditional name="genome">
559 <param name="genome_source" value="cached"/> 609 <param name="genome_source" value="cached"/>
560 <param name="arriba_ref" value="GRCh38+ENSEMBL93"/> 610 <param name="arriba_ref" value="GRCh38+ENSEMBL93"/>
561 </conditional> 611 </conditional>
562 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> 612 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
613 <param name="output_fusions_vcf" value="false"/>
563 <conditional name="visualization"> 614 <conditional name="visualization">
564 <param name="do_viz" value="no"/> 615 <param name="do_viz" value="no"/>
565 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/> 616 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
566 </conditional> 617 </conditional>
567 <output name="fusions_tsv"> 618 <output name="fusions_tsv">