# HG changeset patch
# User mrvollger
# Date 1418442370 18000
# Node ID ee55e3a4b53c239e84f7634ae4c957bdca819680
# Parent  d5427122db05c3fcc51cdd5bd1ba18d181db04cd
Uploaded

diff -r d5427122db05 -r ee55e3a4b53c trtr.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trtr.xml	Fri Dec 12 22:46:10 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>