# HG changeset patch
# User mrvollger
# Date 1418424559 18000
# Node ID af605e06357897868b72de3e295d7d415e265e6e
# Parent  071916bcee2572fb80f47b227760f1caee5fc096
Uploaded

diff -r 071916bcee25 -r af605e063578 myTools/trtr.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/myTools/trtr.xml	Fri Dec 12 17:49:19 2014 -0500
@@ -0,0 +1,43 @@
+<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>