<?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>