Mercurial > repos > ashvark > clip_polya
changeset 0:7ba1a5928aac draft default tip
Uploaded
| author | ashvark |
|---|---|
| date | Wed, 14 Oct 2015 06:24:42 -0400 |
| parents | |
| children | |
| files | ClipPolyA.jar clipPolyA.xml |
| diffstat | 2 files changed, 41 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clipPolyA.xml Wed Oct 14 06:24:42 2015 -0400 @@ -0,0 +1,41 @@ +<tool id="clippolya" name="ClipPolyA"> + <command > + <![CDATA[ + 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 + ]]> + </command> + <inputs> + <param name="input" type="data" format="fastqsanger" label="Fastq file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param type="integer" value="6" name="minSignalLength" label="Min poly-A/T signal length"/> + <param type="integer" value="25" name="minReadLength" label="Min read length after clipping"/> + <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" /> + <param name="threePrime" type="boolean" checked="true" truevalue="-3" falsevalue="" label="Clip from 3'-end" /> + <param name="fivePrime" type="boolean" checked="false" truevalue="-5" falsevalue="" label="Clip from 5'-end" /> + <param name="polyASignals" type="boolean" checked="true" truevalue="-a" falsevalue="" label="Poly-A signals" /> + <param name="polyTSignals" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Poly-T signals" /> + + </inputs> + <outputs> + <data name="output" format="fastqsanger" label="Poly-A trimmed on ${on_string}"/> + </outputs> + <help> + +Implemented by Alexander Graf + +**What it does** +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. + +------ + +**Input formats** + +FASTQ file in Sanger format + +------ + +**Output** + +FASTQ file containing the clipped reads + + </help> +</tool>