# HG changeset patch
# User Daniel Blankenberg <dan@bx.psu.edu>
# Date 1427814675 14400
# Node ID 4fab5fce1adb0f497aa892e616924e7d48bb01fc
# Parent  d5f866df45ae65c9340fd4cdc099aa939f2e00af
Fix typo ("with with").

diff -r d5f866df45ae -r 4fab5fce1adb dependency_configs/tool_dependencies.xml
--- a/dependency_configs/tool_dependencies.xml	Thu Jan 29 15:02:01 2015 -0500
+++ b/dependency_configs/tool_dependencies.xml	Tue Mar 31 11:11:15 2015 -0400
@@ -6,6 +6,6 @@
         <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamparser_0_0_1" owner="blankenberg" changeset_revision="46bd908161b6" />
     </package>
     <package name="pyBamTools" version="0.0.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamtools_0_0_1" owner="blankenberg" changeset_revision="102e3710dbdc" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamtools_0_0_1" owner="blankenberg" changeset_revision="9116288f9d4c" />
     </package>
 </tool_dependency>
diff -r d5f866df45ae -r 4fab5fce1adb tools/naive_variant_caller.xml
--- a/tools/naive_variant_caller.xml	Thu Jan 29 15:02:01 2015 -0500
+++ b/tools/naive_variant_caller.xml	Tue Mar 31 11:11:15 2015 -0400
@@ -93,7 +93,7 @@
     <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" />
     
     <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
-    <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with with possible alternate alleles"/>
+    <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/>
     
     <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
     
@@ -174,7 +174,7 @@
 
     The number of genotype calls to make at each reported position.
 
-Only write out positions with with possible alternate alleles:
+Only write out positions with possible alternate alleles:
 
     When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.