Mercurial > repos > stheil > readpercontig_blat
view readPerContig.xml @ 1:3203097d0a70 draft
Uploaded
author | stheil |
---|---|
date | Thu, 15 Oct 2015 09:53:48 -0400 |
parents | |
children |
line wrap: on
line source
<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>