# HG changeset patch
# User geert-vandeweyer
# Date 1392297661 18000
# Node ID 548887c4227cf2e2655539b856621416bf90bb3f

Uploaded

diff -r 000000000000 -r 548887c4227c Paired_fastQ_trimmer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Paired_fastQ_trimmer.xml	Thu Feb 13 08:21:01 2014 -0500
@@ -0,0 +1,59 @@
+<tool id="Paired_fastQ_trimmer" name="Paired FastQ QC-Trimmer" >
+	<description></description>
+	<requirements>
+		<requirement type='package' version='1.92'>perl_module_threads</requirement>
+		<requirement type='package' version='1.46'>perl_module_threads_shared</requirement>
+		<requirement type='package' version='3.02'>perl_module_Thread_Queue</requirement>
+
+        </requirements>
+	<command interpreter="perl">Paired_fastQ_trimmer.pl -v 0 -i "$inputforward" -q "$trimq" -n "$readnames" -s "$style" -o $output1 -F $output3 -S $side -m $minlength
+		#if $IsPaired.paired=="true":
+			-I $inputreverse
+			-O $output2
+		#end if
+	</command>	
+
+	<inputs>
+		<param  name="trimq" value="30" type="integer" label="Quality Threshold (phred)" />
+		<param  name="minlength" value="18" type="integer" label="Discard Reads shorter than this value as failed" /> 
+		<param name="readnames" value="@" type="text" label="First (eg 5) characters of the read names" />
+		<param name="style" type="select" label="Trimming Style to use" >
+			<option value='simple'>Simple 1bp-window trimming</option>
+			<option value='bwa'>BWA-Style trimming (bwa -q param)</option>
+		</param>
+		<param name="side" type="select" label="Which side of the reads should be trimmed" >
+			<option value='b'>Both 5' and 3'</option>
+			<option value='3'>3' only</option>
+			<option value='5'>5' only</option>
+		</param>
+		<conditional name="IsPaired">
+		<param name="paired" type="select" label="Is the data paired-end?">
+        		<option value="false">Single-end</option>
+		        <option value="true">Paired-end</option>
+      		</param>
+		<when value='true'>
+			<param format="fastqsanger" name="inputforward" type="data" label="FASTQ file with Forward Reads" />
+			<param name='inputreverse' type='data' format='fastqsanger' label='FASTQ file with Reverse Reads' />
+		</when>
+		<when value='false'>
+			<param format="fastqsanger" name="inputforward" type="data" label="FASTQ to trim" />
+		</when>	
+		</conditional>	
+	</inputs>
+	
+	<outputs>
+		<data format='fastqsanger' name="output1" label="${tool.name} on ${on_string}: Forward reads"/>
+		<data format='fastqsanger' name='output2' label="${tool.name} on ${on_string}: Reverse reads">
+			<filter>(IsPaired['paired'] == 'true')</filter>
+		</data>
+		<data format='fastqsanger' name='output3' label="${tool.name} on ${on_string}: Removed read pairs" />
+	</outputs>
+<help>
+
+**What it does**
+
+This tool trims FASTQ files based on quality score. It handles paired-end data in a single step, supporting simple trimming and BWA-style trimming. 
+
+
+</help>
+</tool>