# HG changeset patch
# User mrvollger
# Date 1418448263 18000
# Node ID fb4591a06949b342b1ded29ac35849e82ad0e016
# Parent  25dcbaaeedab527ea8c9d9871734e7746376d395
Deleted selected files

diff -r 25dcbaaeedab -r fb4591a06949 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 12 22:51:00 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-	<package name="trtr" version="1.0">
-		        <repository changeset_revision="591d4720366e" name="package_trtr_0_1" owner="mrvollger" toolshed="https://toolshed.g2.bx.psu.edu" />
-	</package>
-</tool_dependency>
diff -r 25dcbaaeedab -r fb4591a06949 trtr.xml
--- a/trtr.xml	Fri Dec 12 22:51:00 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<tool id="trtr" name="TRTR">
-	<requirements>
-		    <requirement type="package" version="1.0">trtr</requirement>
-	</requirements>
-
-	<description>Trim Reads of Tandem Repeat in a fastq file. </description>
-	
-	<command>
-		trtr $input $max_repeat $aggressive > $output
-	</command>
-	
-	<inputs>
-		<param format="fastq" name="input" type="data" label="Source file"/>
-		<param name="max_repeat" type="integer" value="10" label="Maximum repeat length" />
-		<param name="aggressive" type="integer" value="1" label="Aggressive? See description."/>
-	</inputs>
-	
-	<outputs>
-		<data format="fastq" name="output" />
-	</outputs>
-
-  <tests>
-    <test>
-      <param name="input" value="small.fastq"/>
-      <output name="output" file="smallTrimmed.fastq"/>
-    </test>
-    <test>
-      <param name="input" value="medium.fastq"/>
-      <output name="output" file="mediumTrimmed.fastq"/>
-    </test>
-  </tests>
-
-  <help>
-This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping and leading to innaccurate SNPs calls.
-
-The maximimum repeat length is adjustable (use 1 to trim only homopolymers).
-
-The "aggressive" option should not be touched in general. Setting to 0 will prevent the program from trimming to exactly 1 copy of the repeat, instead leaving between 1 and 2 copies.
-
-This could also be a useful first step before assembly. More testing needs to be done.
-  </help>
-
-</tool>