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First upload of PCR Marker tools
author john-mccallum
date Thu, 14 Jun 2012 19:29:26 -0400
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children a0689dc29b7f
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-1:000000000000 0:21053f7f9ed1
1 <?xml version="1.0"?>
2 <tool id="patman_1" name="search for patterns in DNA using PatMaN">
3 <description>search for approximate patterns in DNA libraries</description>
4 <command>patman -a -e $edits -g $gaps -D $inputfastaFile -P $inputPatfile | sort | uniq > $patman_outputfile </command>
5 <inputs>
6 <param name="edits" type="integer" label="max N mismatches and or gaps" value="0" size="1" />
7 <param name="gaps" type="integer" label="max N gaps" value="0" size="1"/>
8 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta target file" />
9 <param format="fasta" name="inputPatfile" type="data" label="Pattern fasta" />
10
11 </inputs>
12 <outputs>
13 <data format="tabular" name="patman_outputfile" />
14 </outputs>
15 <help>
16
17
18
19 This is a Galaxy wrapper for PatMaN: a DNA pattern matcher for short sequences
20
21 * Website https://bioinf.eva.mpg.de/patman/
22 * PubMed Citation_
23
24 *Inputs*
25
26 * Patterns in fasta format (create from tabular using tabular-to-fasta tool)
27 * Multifasta file of target sequences
28
29 *Output*
30
31 * 6 Column tabular interval data
32 * Columns Chrom, Pattern Name, Start, End, strand, N mismatches
33
34 ::
35
36 isotig05934 ACP818 368 389 + 0
37 isotig05934 ACP859 377 396 + 0
38 isotig06765 ACP822 448 468 + 0
39 isotig07088 ACP825 49 75 + 0
40 isotig07652 ACP830 199 218 + 0
41 isotig07652 ACP831 257 276 + 0
42 isotig10333 ACP837 474 497 + 0
43 isotig10393 ACP838 10 34 + 0
44
45
46
47 .. _Citation: http://www.ncbi.nlm.nih.gov/pubmed/18467344?dopt=Abstract
48
49
50 </help>
51 </tool>