Mercurial > repos > jjohnson > arriba

comparison arriba.xml @ 10:c58d1774c762 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
author jjohnson
date Fri, 11 Feb 2022 19:04:06 +0000
parents 8c4c97fd0555
children 8ed8af5836d1
comparison
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9:8c4c97fd0555 10:c58d1774c762
158 #if $options.covered_fraction 158 #if $options.covered_fraction
159 -C $options.covered_fraction 159 -C $options.covered_fraction
160 #end if 160 #end if
161 #if $options.max_itd_length 161 #if $options.max_itd_length
162 -l $options.max_itd_length 162 -l $options.max_itd_length
163 #end if
164 #if $options.min_itd_allele_fraction
165 -z $options.min_itd_allele_fraction
166 #end if
167 #if $options.min_itd_supporting_reads
168 -Z $options.min_itd_supporting_reads
163 #end if 169 #end if
164 $options.duplicate_marking 170 $options.duplicate_marking
165 $options.fill_discarded_columns 171 $options.fill_discarded_columns
166 $options.fill_the_gaps 172 $options.fill_the_gaps
167 #if str($input_params.input_source) == "use_fastq" 173 #if str($input_params.input_source) == "use_fastq"
379 </help> 385 </help>
380 </param> 386 </param>
381 <param name="covered_fraction" argument="-C" type="float" value="" min="0." max="1.0" optional="true" label="Covered fraction"> 387 <param name="covered_fraction" argument="-C" type="float" value="" min="0." max="1.0" optional="true" label="Covered fraction">
382 <help>Ignore virally associated events if the virus is not fully expressed, 388 <help>Ignore virally associated events if the virus is not fully expressed,
383 i.e., less than the given fraction of the viral contig is transcribed. 389 i.e., less than the given fraction of the viral contig is transcribed.
384 Default: 0.150000 390 Default: 0.050000
385 </help> 391 </help>
386 </param> 392 </param>
387 <param name="max_itd_length" argument="-l" type="integer" value="" min="1" optional="true" label="Maximum length of internal tandem duplications"> 393 <param name="max_itd_length" argument="-l" type="integer" value="" min="1" optional="true" label="Maximum length of internal tandem duplications">
388 <help>Note: Increasing this value beyond the default can impair performance and lead to many false positives. 394 <help>Note: Increasing this value beyond the default can impair performance and lead to many false positives.
389 Default: 100 395 Default: 100
396 </help>
397 </param>
398 <param name="min_itd_allele_fraction" argument="-z" type="float" value="" min="0." max="1.0" optional="true" label="Required fraction of supporting reads to report an internal tandem duplication">
399 <help> Default: 0.070000
400 </help>
401 </param>
402 <param name="min_itd_supporting_reads" argument="-Z" type="integer" value="" min="1" optional="true" label="Required number of supporting reads to report an internal tandem duplication">
403 <help> Default: 10
390 </help> 404 </help>
391 </param> 405 </param>
392 <param name="duplicate_marking" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Use aligners duplicate marking"> 406 <param name="duplicate_marking" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Use aligners duplicate marking">
393 <help>Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a 407 <help>Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a
394 preceding program using the BAM_FDUP flag. This makes sense when unique molecular 408 preceding program using the BAM_FDUP flag. This makes sense when unique molecular
440 <param name="input_source" value="use_star"/> 454 <param name="input_source" value="use_star"/>
441 <param name="input" ftype="sam" value="Aligned.out.sam"/> 455 <param name="input" ftype="sam" value="Aligned.out.sam"/>
442 </conditional> 456 </conditional>
443 <conditional name="genome"> 457 <conditional name="genome">
444 <param name="genome_source" value="history"/> 458 <param name="genome_source" value="history"/>
445 <param name="assembly" ftype="fasta" value="genome.fasta"/> 459 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
446 <param name="annotation" ftype="gtf" value="genome.gtf"/> 460 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
447 </conditional> 461 </conditional>
448 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> 462 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
449 <conditional name="visualization"> 463 <conditional name="visualization">
450 <param name="do_viz" value="no"/> 464 <param name="do_viz" value="no"/>
451 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/> 465 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
463 <param name="input_source" value="use_star"/> 477 <param name="input_source" value="use_star"/>
464 <param name="input" ftype="sam" value="Aligned.out.sam"/> 478 <param name="input" ftype="sam" value="Aligned.out.sam"/>
465 </conditional> 479 </conditional>
466 <conditional name="genome"> 480 <conditional name="genome">
467 <param name="genome_source" value="history"/> 481 <param name="genome_source" value="history"/>
468 <param name="assembly" ftype="fasta" value="genome.fasta"/> 482 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
469 <param name="annotation" ftype="gtf" value="genome.gtf"/> 483 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
470 </conditional> 484 </conditional>
471 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> 485 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
472 <conditional name="visualization"> 486 <conditional name="visualization">
473 <param name="do_viz" value="yes"/> 487 <param name="do_viz" value="yes"/>
474 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/> 488 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>