Mercurial > repos > jjohnson > arriba
comparison arriba.xml @ 10:c58d1774c762 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
author | jjohnson |
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date | Fri, 11 Feb 2022 19:04:06 +0000 |
parents | 8c4c97fd0555 |
children | 8ed8af5836d1 |
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9:8c4c97fd0555 | 10:c58d1774c762 |
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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"/> |