# HG changeset patch
# User mrvollger
# Date 1418424666 18000
# Node ID 6ddffb742bf1875486ab94cf6d59c89fe58153f9
# Parent  5c3ec718c26f4deb6c20ad5b79ff94f0c450128f
Deleted selected files

diff -r 5c3ec718c26f -r 6ddffb742bf1 myTools/trtr.xml
--- a/myTools/trtr.xml	Fri Dec 12 17:51:00 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>