<?xml version="1.0"?>
<tool id="CAPS_Marker_Design_2" name="CAPS Detection">
  <description>identify SNPs that condition restriction polymorphisms</description>
  <command interpreter="python">find_CAPS.py $inputFasta $inputSNPGff3File >  $outputfile</command>
  <inputs>
    <param format="gff3" name="inputSNPGff3File" type="data" label="GFF3 file containing SNP data"/>
    <param format="fasta" name="inputFasta" type="data" label="fasta source file" />
  </inputs>
  <outputs>
     <data format="interval" name="outputfile" />
  </outputs>
  <tests>
        <test>
                <param name="inputSNPGff3File" value="targets.gff" ftype="gff3"/>
                <param name="inputFasta" value="targets.fasta" ftype="fasta"/>
                <output name="outputfile" file="find_caps_output.txt"/>
        </test>
  </tests>
<help>
.. class:: infomark
	
**TIP**

This tool identifies SNPs that condition restriction polymorphisms.

Currently it utilizes a fixed list of robust enzymes known to work well in PCR buffers

 AluI,ApaI,BamHI,BbrPI,BfrI,ClaI,DpnI,DraI,EcoRI,HaeIII,HindII,HinfI,HpaI,PvuII,RsaI,SacI,Sau3AI,SmaI,TaqI

It produces a tabular output in interval format

record ID,  start, stop, feature ID,enzyme, phase (ie whether it cuts reference or variant sequence)





**Example**



*input GFF3*

::

	JR843866	gsmapper	SNP	63	63	.	.	.	ID=JR843866:gsmapperSNP:63;Reference_seq=T;Variant_seq=C;Total_reads=22;Variant_reads=20
	JR843866	gsmapper	SNP	146	146	.	.	.	ID=JR843866:gsmapperSNP:146;Reference_seq=T;Variant_seq=C;Total_reads=26;Variant_reads=10
	JR843866	gsmapper	SNP	258	258	.	.	.	ID=JR843866:gsmapperSNP:258;Reference_seq=T;Variant_seq=G;Total_reads=4;Variant_reads=3
	JR848320	gsmapper	SNP	157	157	.	.	.	ID=JR848320:gsmapperSNP:157;Reference_seq=C;Variant_seq=T;Total_reads=10;Variant_reads=10
	JR848554	gsmapper	SNP	54	54	.	.	.	ID=JR848554:gsmapperSNP:54;Reference_seq=T;Variant_seq=G;Total_reads=5;Variant_reads=5
	JR848554	gsmapper	SNP	74	74	.	.	.	ID=JR848554:gsmapperSNP:74;Reference_seq=C;Variant_seq=T;Total_reads=7;Variant_reads=7
	JR848554	gsmapper	SNP	123	123	.	.	.	ID=JR848554:gsmapperSNP:123;Reference_seq=T;Variant_seq=A;Total_reads=11;Variant_reads=11
	JR848554	gsmapper	SNP	147	147	.	.	.	ID=JR848554:gsmapperSNP:147;Reference_seq=T;Variant_seq=C;Total_reads=13;Variant_reads=13
	JR848554	gsmapper	SNP	161	161	.	.	.	ID=JR848554:gsmapperSNP:161;Reference_seq=C;Variant_seq=T;Total_reads=13;Variant_reads=13



*output columnar data*

::

	JR843866	63	64	JR843866:gsmapperSNP:63		HaeIII	variant
	JR848320	157	158	JR848320:gsmapperSNP:157	TaqI	variant
	JR848320	157	158	JR848320:gsmapperSNP:157	HinfI	variant
	JR848554	162	163	JR848554:gsmapperSNP:162	TaqI	variant
	JR848554	162	163	JR848554:gsmapperSNP:162	ClaI	variant
	JR848554	306	307	JR848554:gsmapperSNP:306	TaqI	variant
	JR848554	652	653	JR848554:gsmapperSNP:652	TaqI	variant


-------------------------------------------------------------------------------


*If you use this tool please cite:*

A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
(2012)

Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum





</help>
</tool>