# HG changeset patch
# User ashvark
# Date 1444818282 14400
# Node ID 7ba1a5928aac05d16eb7782e1241e7f83a1ef0f5

Uploaded

diff -r 000000000000 -r 7ba1a5928aac ClipPolyA.jar
Binary file ClipPolyA.jar has changed
diff -r 000000000000 -r 7ba1a5928aac clipPolyA.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clipPolyA.xml	Wed Oct 14 06:24:42 2015 -0400
@@ -0,0 +1,41 @@
+<tool id="clippolya" name="ClipPolyA">
+	<command >
+	<![CDATA[
+			java -Xmx4g -jar /home/galaxy/galaxy-dist/tools/ngs_rna/PolyA/ClipPolyA.jar -i $input -o $output -s $minSignalLength -m $minReadLength $outputAll $threePrime $fivePrime $polyASignals $polyTSignals
+	]]>
+	</command>
+   	<inputs>
+		<param name="input" type="data" format="fastqsanger" label="Fastq file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
+		<param type="integer" value="6" name="minSignalLength" label="Min poly-A/T signal length"/>
+		<param type="integer" value="25" name="minReadLength" label="Min read length after clipping"/>
+		<param name="outputAll" type="boolean" checked="true" truevalue="-k" falsevalue="" label="Output all reads (clipped and non-clipped)" help="If not selected, only clipped sequences were written to output" />
+		<param name="threePrime" type="boolean" checked="true" truevalue="-3" falsevalue="" label="Clip from 3'-end"  />
+		<param name="fivePrime" type="boolean" checked="false" truevalue="-5" falsevalue="" label="Clip from 5'-end"  />
+		<param name="polyASignals" type="boolean" checked="true" truevalue="-a" falsevalue="" label="Poly-A signals"  />
+		<param name="polyTSignals" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Poly-T signals"  />
+ 
+	</inputs>
+	<outputs>
+		<data name="output" format="fastqsanger" label="Poly-A trimmed on ${on_string}"/>
+	</outputs>
+	 <help>
+
+Implemented by Alexander Graf
+
+**What it does**
+Poly-A and Poly-T signals are trimmed from the beginning or the ending of a read, where the signal occures at least 6 times.
+ 
+------
+
+**Input formats**
+
+FASTQ file in Sanger format
+
+------
+
+**Output**
+
+FASTQ file containing the clipped reads
+
+	</help>
+</tool>