view clipPolyA.xml @ 0:7ba1a5928aac draft default tip

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<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

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**Output**

FASTQ file containing the clipped reads

	</help>
</tool>