--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_CAPS.xml	Thu Jun 14 19:29:26 2012 -0400
@@ -0,0 +1,81 @@
+<?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>
+<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 GFF*
+
+::
+
+	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>