<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>
<citations>
	<citation type="doi">10.1111/cge.12470</citation>
</citations>
</tool>