# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1352222602 21600
# Node ID f253357915e0d45c97941eff217549be35162a5c
# Parent  6dd67e9fd0e09da49efacd2b3b2eabe888ca9bfb
Cleanup reduce_reads.xml

diff -r 6dd67e9fd0e0 -r f253357915e0 reduce_reads.xml
--- a/reduce_reads.xml	Tue Nov 06 10:32:16 2012 -0600
+++ b/reduce_reads.xml	Tue Nov 06 11:23:22 2012 -0600
@@ -479,61 +479,6 @@
         <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."/>
       </when>
     </conditional>
-
-    <!--
-java -Xmx4g -jar GenomeAnalysisTK.jar \
-   -R ref.fasta \
-   -T ReduceReads \
-   -I myData.bam \
-   -o myData.reduced.bam
-
-Argument details
--+-allow_polyploid_reduction / -polyploid ( boolean with default value false )
-. Allow the experimental polyploid-based reduction capabilities of this tool
-
--+-context_size / -cs ( int with default value 10 )
-. The number of bases to keep around mismatches (potential variation)
-
--+-dont_compress_read_names / -nocmp_names ( boolean with default value false )
-. 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.
-
--+-dont_hardclip_low_qual_tails / -noclip_tail ( boolean with default value false )
-. Do not hard clip the low quality tails of the reads. This option overrides the argument of minimum tail quality.
-
--+-dont_simplify_reads / -nosimplify ( boolean with default value false )
-. Do not simplify read (strip away all extra information of the read -+- anything other than bases, quals and read group).
-
--+-dont_use_softclipped_bases / -no_soft ( boolean with default value false )
-. 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)
-
--+-downsample_coverage / -ds ( int with default value 250 )
-. Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this). A value of 0 turns downsampling off.
-
--+-hard_clip_to_interval / -clip_int ( boolean with default value false )
-. Optionally hard clip all incoming reads to the desired intervals. The hard clips will happen exactly at the interval border.
-
--mindel / -+-minimum_del_proportion_to_trigger_variant ( double with default value 0.05 )
-. Minimum proportion of indels in a site to trigger a variant region. Anything below this will be considered consensus.
-
--+-minimum_mapping_quality / -minmap ( int with default value 20 )
-. 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.
-
--+-minimum_tail_qualities / -mintail ( byte with default value 2 )
-. 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.
-
--minqual / -+-minimum_base_quality_to_consider ( byte with default value 20 )
-. 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.
-
--minvar / -+-minimum_alt_proportion_to_trigger_variant ( double with default value 0.05 )
-. Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be considered consensus.
-
--noclip_ad / -+-dont_hardclip_adaptor_sequences ( boolean with default value false )
-. 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.
-
--+-out / -o ( StingSAMFileWriter with default value stdout )
-An output file created by the walker. Will overwrite contents if file exists.
-
-     -->
   </inputs>
   <outputs>
     <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />