Mercurial > repos > john-mccallum > pcr_markers
view patman.xml @ 2:ea2117a7b363 draft
Uploaded CAPS marker design workflow for 454 Data
author | john-mccallum |
---|---|
date | Sun, 09 Sep 2012 23:16:56 -0400 |
parents | a0689dc29b7f |
children |
line wrap: on
line source
<?xml version="1.0"?> <tool id="patman_1" name="search for patterns in DNA using PatMaN"> <description>search for approximate patterns in DNA libraries</description> <command>patman -a -e $edits -g $gaps -D $inputfastaFile -P $inputPatfile | sort | uniq > $patman_outputfile </command> <inputs> <param name="edits" type="integer" label="max N mismatches and or gaps" value="0" size="1" /> <param name="gaps" type="integer" label="max N gaps" value="0" size="1"/> <param format="fasta" name="inputfastaFile" type="data" label="Multifasta target file" /> <param format="fasta" name="inputPatfile" type="data" label="Pattern fasta" /> </inputs> <outputs> <data format="tabular" name="patman_outputfile" /> </outputs> <help> This is a Galaxy wrapper for PatMaN: a DNA pattern matcher for short sequences * Website https://bioinf.eva.mpg.de/patman/ * PubMed Citation_ *Inputs* * Patterns in fasta format (create from tabular using tabular-to-fasta tool) * Multifasta file of target sequences *Output* * 6 Column tabular interval data * Columns Chrom, Pattern Name, Start, End, strand, N mismatches :: isotig05934 ACP818 368 389 + 0 isotig05934 ACP859 377 396 + 0 isotig06765 ACP822 448 468 + 0 isotig07088 ACP825 49 75 + 0 isotig07652 ACP830 199 218 + 0 isotig07652 ACP831 257 276 + 0 isotig10333 ACP837 474 497 + 0 isotig10393 ACP838 10 34 + 0 .. _Citation: http://www.ncbi.nlm.nih.gov/pubmed/18467344?dopt=Abstract </help> </tool>