# HG changeset patch
# User mrvollger
# Date 1418442311 18000
# Node ID b28b80eb4b78808e7c1d1bc7505a15af633d922f
# Parent  08bbc7ba8f21a4a5d6b04d7ba7371266079702dc
Deleted selected files

diff -r 08bbc7ba8f21 -r b28b80eb4b78 tool_depensencies.xml
--- a/tool_depensencies.xml	Fri Dec 12 17:55:32 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 name="package_trtr_0_1" owner="mrvollger"/>
-	</package>
-</tool_dependency>
diff -r 08bbc7ba8f21 -r b28b80eb4b78 trtr.xml
--- a/trtr.xml	Fri Dec 12 17:55:32 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>