Mercurial > repos > stheil > readpercontig_blat
diff readPerContig.xml @ 1:3203097d0a70 draft
Uploaded
| author | stheil |
|---|---|
| date | Thu, 15 Oct 2015 09:53:48 -0400 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readPerContig.xml Thu Oct 15 09:53:48 2015 -0400 @@ -0,0 +1,21 @@ +<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>