# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1310145304 18000
# Node ID 29db8b6184eaf6a8b98f3de416ffb98533617a91
# Parent  9181ff21b48ab8c760cfcbd642d14916f92e2a0c
Default value for skipgap params should be true

diff -r 9181ff21b48a -r 29db8b6184ea mothur/tools/mothur/chimera.uchime.xml
--- a/mothur/tools/mothur/chimera.uchime.xml	Fri Jul 08 12:13:46 2011 -0500
+++ b/mothur/tools/mothur/chimera.uchime.xml	Fri Jul 08 12:15:04 2011 -0500
@@ -119,8 +119,8 @@
   <param name="minlen" type="integer" value="0" label="minlen - minimum unaligned sequence length. Default 10" help="Applies to both query and reference sequences."/>
   <param name="maxlen" type="integer" value="0" label="maxlen - maximum unaligned sequence length. Defaults 10000" help="Applies to both query and reference sequences."/>
 
-   <param name="skipgaps" type="boolean" falsevalue="--skipgaps=false" truevalue="" checked="false" label="skipgaps - columns containing gaps do not count as diffs. Default=T" help="controls how gapped columns affect counting of diffs"/>
-   <param name="skipgaps2" type="boolean" falsevalue="--skipgaps2=false" truevalue="" checked="false" label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default=T" help="controls how gapped columns affect counting of diffs"/>
+   <param name="skipgaps" type="boolean" falsevalue="--skipgaps=false" truevalue="" checked="true" label="skipgaps - columns containing gaps do not count as diffs. Default=T" help="controls how gapped columns affect counting of diffs"/>
+   <param name="skipgaps2" type="boolean" falsevalue="--skipgaps2=false" truevalue="" checked="true" label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default=T" help="controls how gapped columns affect counting of diffs"/>
 
   <param name="chimealns" type="boolean" falsevalue="" truevalue="--chimealns=true" checked="false" label="chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format. " help="Alignments show columns with differences that support or contradict a chimeric model."/>