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author stheil
date Thu, 15 Oct 2015 10:12:03 -0400
parents 3203097d0a70
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<tool id="readPerContig" name="readPerContig" version="1.0">
	<description>
	This script counts the number of read per contig using a Blat output.
  Output is a 2 column tabular file.
  </description>
	<command interpreter="perl">readPerContig.pl-r $reference -id $identity -cov $coverage -b blat_result -v 0 -s $statistics	-o $output</command>
	<inputs>
		<param name="reference" type="data" format="fasta" label="References."/>
		<param name="blat" type="data" format="psl" label="Blat .psl output file."/>
		<param name="identity" type="integer" value="95" label="Identity threshold."/>
		<param name="coverage" type="integer" value="60" label="Coverage threshold."/>
		<param name="statistics" type="select" label="Statistics to print">
			<option value="nb_reads">Read number</option>
			<option value="rpkm">RPKM</option>
			<option value="mean_coverage">Mean coverage</option>
		</param>
	</inputs>
	<outputs>
		<data name="output" format="tabular"/>
	</outputs>
</tool>