diff GVF_Features_Extracter.xml @ 0:21053f7f9ed1 draft

First upload of PCR Marker tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GVF_Features_Extracter.xml	Thu Jun 14 19:29:26 2012 -0400
@@ -0,0 +1,54 @@
+<?xml version="1.0"?>
+<tool id="GVF Features  Extracter_1" name="GVF Feature ID Extracter">
+  <description>Extract unique feature IDs from a GVF/GFF3 file </description>
+  <command >awk '!/^#/ {print $1":"$2":"$3":"$4}'   $inputgff3File | sort | uniq >  $column_outputfile</command>
+  <inputs>
+    <param format="gff3" name="inputgff3File" type="data" label="GVF/Gff3 File"/>
+  </inputs>
+  <outputs>
+     <data format="tabular"  name="column_outputfile" />
+  </outputs>
+<help>
+
+.. class:: infomark
+
+**TIP**
+
+This tool extracts a unique feature identifier from  GVF/GFF3 format, primarily to enable downstream analysis of SNPs or marker design
+
+
+----
+
+**Example**
+
+*input GFF3*
+
+::
+
+ ##gff-version 3
+ 1119927 gsMapper        SNP     434     434     .       .       .       ID=1119927:gsMapper:SNP:434;Reference_seq=G;Variant_seq=A;Total_reads=10;Variant_freq=100;Enzyme=AluI;Phase=variant
+ 1120709 gsMapper        SNP     361     361     .       .       .       ID=1120709:gsMapper:SNP:361;Reference_seq=T;Variant_seq=C;Total_reads=22;Variant_freq=68;Enzyme=TaqI;Phase=variant
+ 1120709 gsMapper        SNP     704     704     .       .       .       ID=1120709:gsMapper:SNP:704;Reference_seq=A;Variant_seq=G;Total_reads=20;Variant_freq=90;Enzyme=RsaI;Phase=variant
+
+*output tabular text*
+
+::
+
+ 1119927:gsMapper:SNP:434
+ 1120709:gsMapper:SNP:361
+ 1120709:gsMapper:SNP:704
+
+ -----------------------------------------------------
+ 
+*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>