Mercurial > repos > rnateam > segemehl
changeset 2:dc63d59e7bf8 draft
Uploaded
author | bgruening |
---|---|
date | Sat, 18 Jan 2014 05:43:29 -0500 |
parents | 468b59eae694 |
children | e1d38fef6dd5 |
files | segemehl.xml |
diffstat | 1 files changed, 13 insertions(+), 10 deletions(-) [+] |
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--- a/segemehl.xml Sat Jan 18 05:26:31 2014 -0500 +++ b/segemehl.xml Sat Jan 18 05:43:29 2014 -0500 @@ -110,24 +110,27 @@ <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" /> <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" /> </repeat> - <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end) (default:5000)" /> + <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000 (-I)" /> </when> </conditional> - <param name="minsize" type="integer" value="12" size="5" label="Minimum size of queries (default:12)"> + <param name="minsize" type="integer" value="12" size="5" label="Minimum size of queries" help="default: 12 (-m)"> <validator type="in_range" min="1"/> </param> - <param name="accuracy" type="integer" value="85" size="5" label="Min percentage of matches per read in semi-global alignment (default:85)" > + <param name="accuracy" type="integer" value="85" size="5" label="Min percentage of matches per read in semi-global alignment" help="default: 85 (-A)" > <validator type="in_range" min="1" max="100"/> </param> - <param name="hitstrategy" type="integer" value="1" size="5" label="report only best scoring hits (=1) or all (=0) (default:1)" /> - <param name="prime5" type="text" size="80" label="add 5' adapter (default:none)" /> - <param name="prime3" type="text" size="80" label="add 3' adapter (default:none)" /> - <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail"/> - <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter"/> - <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping"/> - <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position (might take a while!)"/> + <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)"> + <option value="1">report only best scoring hits</option> + <option value="0">report all scoring hits</option> + </param> + <param name="prime5" type="text" size="80" label="add 5' adapter" help="default: none (-Q)" /> + <param name="prime3" type="text" size="80" label="add 3' adapter" help="default: none (-P)"/> + <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" help="(-T)"/> + <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/> + <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="-C"/> + <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/> </inputs> <outputs>