comparison reduce_reads.xml @ 7:f253357915e0 draft

Cleanup reduce_reads.xml
author Jim Johnson <jj@umn.edu>
date Tue, 06 Nov 2012 11:23:22 -0600
parents 6dd67e9fd0e0
children a14e79e7ac75
comparison
equal deleted inserted replaced
6:6dd67e9fd0e0 7:f253357915e0
477 <validator type="in_range" message="value between 0.00 and 1.00" min="0.0" max="1.0"/> 477 <validator type="in_range" message="value between 0.00 and 1.00" min="0.0" max="1.0"/>
478 </param> 478 </param>
479 <param name="dont_hardclip_adaptor_sequences" type="boolean" checked="False" truevalue="-noclip_ad" falsevalue="" label="Do not hard clip adaptor sequences" help="--dont_hardclip_adaptor_sequences / -noclip_ad Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired. The program will behave correctly in those cases."/> 479 <param name="dont_hardclip_adaptor_sequences" type="boolean" checked="False" truevalue="-noclip_ad" falsevalue="" label="Do not hard clip adaptor sequences" help="--dont_hardclip_adaptor_sequences / -noclip_ad Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired. The program will behave correctly in those cases."/>
480 </when> 480 </when>
481 </conditional> 481 </conditional>
482
483 <!--
484 java -Xmx4g -jar GenomeAnalysisTK.jar \
485 -R ref.fasta \
486 -T ReduceReads \
487 -I myData.bam \
488 -o myData.reduced.bam
489
490 Argument details
491 -+-allow_polyploid_reduction / -polyploid ( boolean with default value false )
492 . Allow the experimental polyploid-based reduction capabilities of this tool
493
494 -+-context_size / -cs ( int with default value 10 )
495 . The number of bases to keep around mismatches (potential variation)
496
497 -+-dont_compress_read_names / -nocmp_names ( boolean with default value false )
498 . Do not compress read names. By default, ReduceReads will compress read names to numbers and guarantee uniqueness and reads with similar name will still have similar compressed names. Note: If you scatter/gather there is no guarantee that read name uniqueness will be maintained -+- in this case we recommend not compressing.
499
500 -+-dont_hardclip_low_qual_tails / -noclip_tail ( boolean with default value false )
501 . Do not hard clip the low quality tails of the reads. This option overrides the argument of minimum tail quality.
502
503 -+-dont_simplify_reads / -nosimplify ( boolean with default value false )
504 . Do not simplify read (strip away all extra information of the read -+- anything other than bases, quals and read group).
505
506 -+-dont_use_softclipped_bases / -no_soft ( boolean with default value false )
507 . Do not use high quality soft-clipped bases. By default, ReduceReads will hard clip away any low quality soft clipped base left by the aligner and use the high quality soft clipped bases in it's traversal algorithm to identify variant regions. The minimum quality for soft clipped bases is the same as the minimum base quality to consider (minqual)
508
509 -+-downsample_coverage / -ds ( int with default value 250 )
510 . Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this). A value of 0 turns downsampling off.
511
512 -+-hard_clip_to_interval / -clip_int ( boolean with default value false )
513 . Optionally hard clip all incoming reads to the desired intervals. The hard clips will happen exactly at the interval border.
514
515 -mindel / -+-minimum_del_proportion_to_trigger_variant ( double with default value 0.05 )
516 . Minimum proportion of indels in a site to trigger a variant region. Anything below this will be considered consensus.
517
518 -+-minimum_mapping_quality / -minmap ( int with default value 20 )
519 . The minimum mapping quality to be considered for the consensus synthetic read. Reads that have mapping quality below this threshold will not be counted towards consensus, but are still counted towards variable regions.
520
521 -+-minimum_tail_qualities / -mintail ( byte with default value 2 )
522 . Reads have notoriously low quality bases on the tails (left and right). Consecutive bases with quality lower than this threshold will be hard clipped off before entering the reduce reads algorithm.
523
524 -minqual / -+-minimum_base_quality_to_consider ( byte with default value 20 )
525 . The minimum base quality to be considered for the consensus synthetic read. Reads that have base quality below this threshold will not be counted towards consensus, but are still counted towards variable regions.
526
527 -minvar / -+-minimum_alt_proportion_to_trigger_variant ( double with default value 0.05 )
528 . Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be considered consensus.
529
530 -noclip_ad / -+-dont_hardclip_adaptor_sequences ( boolean with default value false )
531 . Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired. The program will behave correctly in those cases.
532
533 -+-out / -o ( StingSAMFileWriter with default value stdout )
534 An output file created by the walker. Will overwrite contents if file exists.
535
536 -->
537 </inputs> 482 </inputs>
538 <outputs> 483 <outputs>
539 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" /> 484 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
540 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 485 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
541 </outputs> 486 </outputs>