<tool id="uniqprimer" name="Uniqprimer" version="0.5.0">
	<description>Design specific primers of sequences</description>
	<requirements>
		<requirement type="package" version="6.6.0">emboss</requirement>
		<requirement type="package" version="3.23">mummer</requirement>
		<requirement type="package" version="2.5.0">primer3</requirement>
	</requirements>
	<command>$__tool_directory__/uniqprimer.sh $include $exclude $product_size_range $primer_size $min_size $max_size $crossvalidate $outfile $log $fasta
#for $i in $inputs
        -i ${i.input}
#end for

</command>
	<inputs>
		<param format="fasta" name="include" type="data" label="FASTA file to include" help="Sequences for which you want design specific primer"/>
		<repeat name="inputs" title="Include FASTA file">
			<param name="input" label="Add FASTA file to include" type="data" format="fasta" />
		</repeat>
		<param format="fasta" name="exclude" type="data" label="FASTA file to exclude" help="Primers will not match these sequences"/>
                <param type="text" name="product_size_range" label="Product size range" value="100-300"/>
                <param type="text" name="primer_size" label="Optimal primer size" value="20"/>
                <param type="text" name="min_size" label="Min primer size" value="18"/>
                <param type="text" name="max_size" label="Max primer size" value="27"/>
		<param name="crossvalidate" type="select" label="Cross validate primers against exclude files for extra certainty">
			<option value="Yes">Yes</option>
			<option value="No">No</option>
		</param>
	</inputs>
	<outputs>
		<data format="txt" name="outfile" label="Primer list"/>
		<data format="fasta" name="fasta" label="Fasta for Primer3"/>
		<data format="txt" name="log" label="Logfile"/>
	</outputs>
	<help>
	

.. class:: infomark

**Program encapsulated in Galaxy by IRRI (International Rice Reasearch Institute) and South Green bioinformatics platform**

.. class:: infomark

**UniqPrimer version 0.5.0**

-----

==============
 Please cite:
==============

"".

-----

===========
 Overview:
===========

Uniqprimer designs specific primers of sequences. The goal of this tool is to accept a number of "include" FASTA files of diagnostic target genomes (draft or complete) and "exclude" files of non-target genomes, and output a list of PCR primers that will amplify target genomes but not non-target genomes.

	</help>

</tool>