Mercurial > repos > stheil > readpercontig_blat
comparison readPerContig.xml @ 1:3203097d0a70 draft
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author | stheil |
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date | Thu, 15 Oct 2015 09:53:48 -0400 |
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0:9730db7c9ad3 | 1:3203097d0a70 |
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1 <tool id="readPerContig" name="readPerContig" version="1.0"> | |
2 <description> | |
3 This script counts the number of read per contig using a Blat output. | |
4 Output is a 2 column tabular file. | |
5 </description> | |
6 <command interpreter="perl">readPerContig.pl-r $reference -id $identity -cov $coverage -b blat_result -v 0 -s $statistics -o $output</command> | |
7 <inputs> | |
8 <param name="reference" type="data" format="fasta" label="References."/> | |
9 <param name="blat" type="data" format="psl" label="Blat .psl output file."/> | |
10 <param name="identity" type="integer" value="95" label="Identity threshold."/> | |
11 <param name="coverage" type="integer" value="60" label="Coverage threshold."/> | |
12 <param name="statistics" type="select" label="Statistics to print"> | |
13 <option value="nb_reads">Read number</option> | |
14 <option value="rpkm">RPKM</option> | |
15 <option value="mean_coverage">Mean coverage</option> | |
16 </param> | |
17 </inputs> | |
18 <outputs> | |
19 <data name="output" format="tabular"/> | |
20 </outputs> | |
21 </tool> |