Mercurial > repos > ashvark > clip_polya
comparison clipPolyA.xml @ 0:7ba1a5928aac draft default tip
Uploaded
author | ashvark |
---|---|
date | Wed, 14 Oct 2015 06:24:42 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:7ba1a5928aac |
---|---|
1 <tool id="clippolya" name="ClipPolyA"> | |
2 <command > | |
3 <![CDATA[ | |
4 java -Xmx4g -jar /home/galaxy/galaxy-dist/tools/ngs_rna/PolyA/ClipPolyA.jar -i $input -o $output -s $minSignalLength -m $minReadLength $outputAll $threePrime $fivePrime $polyASignals $polyTSignals | |
5 ]]> | |
6 </command> | |
7 <inputs> | |
8 <param name="input" type="data" format="fastqsanger" label="Fastq file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> | |
9 <param type="integer" value="6" name="minSignalLength" label="Min poly-A/T signal length"/> | |
10 <param type="integer" value="25" name="minReadLength" label="Min read length after clipping"/> | |
11 <param name="outputAll" type="boolean" checked="true" truevalue="-k" falsevalue="" label="Output all reads (clipped and non-clipped)" help="If not selected, only clipped sequences were written to output" /> | |
12 <param name="threePrime" type="boolean" checked="true" truevalue="-3" falsevalue="" label="Clip from 3'-end" /> | |
13 <param name="fivePrime" type="boolean" checked="false" truevalue="-5" falsevalue="" label="Clip from 5'-end" /> | |
14 <param name="polyASignals" type="boolean" checked="true" truevalue="-a" falsevalue="" label="Poly-A signals" /> | |
15 <param name="polyTSignals" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Poly-T signals" /> | |
16 | |
17 </inputs> | |
18 <outputs> | |
19 <data name="output" format="fastqsanger" label="Poly-A trimmed on ${on_string}"/> | |
20 </outputs> | |
21 <help> | |
22 | |
23 Implemented by Alexander Graf | |
24 | |
25 **What it does** | |
26 Poly-A and Poly-T signals are trimmed from the beginning or the ending of a read, where the signal occures at least 6 times. | |
27 | |
28 ------ | |
29 | |
30 **Input formats** | |
31 | |
32 FASTQ file in Sanger format | |
33 | |
34 ------ | |
35 | |
36 **Output** | |
37 | |
38 FASTQ file containing the clipped reads | |
39 | |
40 </help> | |
41 </tool> |