# HG changeset patch
# User mrvollger
# Date 1418424905 18000
# Node ID cffb3efb1726a104dae1adebbe84cc541520eeb2
# Parent  7ad9438b07772705bcc40a7ee423e18aead12b46
Uploaded

diff -r 7ad9438b0777 -r cffb3efb1726 trtr.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trtr.xml	Fri Dec 12 17:55:05 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>