<tool id="multiplicom_primer_trimming" name="Multiplicom Primer Trimmer" version="0.0.1">
  <description></description>
  <requirements>
    <requirement type="package" version='latest'>twoBitToFa</requirement>
  </requirements>
  <command interpreter="perl">
	multiplicom_primer_trimming.pl
	## input files
	-i $inputf
	-I $inputr
	-b $mastr
	## read length
	-r $readlength
	## output files
	-o $outf
	-O $outr
	-F $failed
	-R $report
	## reference genome
	-t "${indexes.fields.path}"
	
  </command>
  <inputs>
	<param name='inputf' type='data' format='fastq,fastqsanger' label='Forward Sequences' help='Forward Reads in fastq format' />
	<param name='inputr' type='data' format='fastq,fastqsanger' label='Reverse Sequences' help='Reverse Reads in fastq format' />
	<param name='mastr' type='data' format='bed' label='MASTR file' help='Design file of the Multiplicom MASTR assay' />
	<param name='readlength' type='integer' value='250' label='Read Length' help='Applied Readlength, per read' />
	<param name="indexes" type="select" label="Reference Genome" help="Select the correct genome build" >
		<options from_data_table="2bit" >
			<filter type="sort_by" column="2" />
			<validator type="no_options" message="No indexes are available" />
		</options>
	</param>
   </inputs>
   <outputs>
	<data format_source="inputf" name="outf" label="${tool.name} on ${on_string}: Forward Reads"/>
    	<data format_source="inputr" name="outr" label="${tool.name} on ${on_string}: Reverse Reads"/>
    	<data format_source="inputf"	name="failed" label="${tool.name} on ${on_string}: Failed Pairs"/>
    	<data format="txt" name="report" label="${tool.name} on ${on_string}: Runtime output"/>
   </outputs>
   <help>
	This tools scans paired FASTQ files for the presence of Multiplicom MASTR PCR primers. If found, primers are clipped. 	
   </help>
</tool>