# HG changeset patch
# User mcharles
# Date 1402913474 14400
# Node ID 428799b670075be850e638026d342e4695276c4c
# Parent  2e27d068d9b04cef1343995ab5c000d2ca0346ad
Uploaded

diff -r 2e27d068d9b0 -r 428799b67007 filtersamunique/filtersamunique.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filtersamunique/filtersamunique.pl	Mon Jun 16 06:11:14 2014 -0400
@@ -0,0 +1,20 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n");
+while (my $line=<IN>){
+	if ($line =~ /^\@/){
+		#Header conservation
+		print $line;
+	}
+	else {
+		#Optionnal flag verification
+		if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){
+			print $line;
+		}
+	}
+}
+
+
+close (IN);
\ No newline at end of file
diff -r 2e27d068d9b0 -r 428799b67007 filtersamunique/filtersamunique.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filtersamunique/filtersamunique.xml	Mon Jun 16 06:11:14 2014 -0400
@@ -0,0 +1,18 @@
+<tool id="filtersamunique" name="filtersamunique" version="0.01">
+<description>Filter SAM file for uniquelly match reads</description>
+<command interpreter="perl">
+    filtersamunique.pl $input_sam_file > $output_file 
+</command>
+<inputs>
+<param name="input_sam_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="sam" label="${tool.name} on ${on_string}"/>
+</outputs>
+
+<help>
+
+
+
+</help>
+</tool>
diff -r 2e27d068d9b0 -r 428799b67007 filtersamunique/test.tar.bz2
Binary file filtersamunique/test.tar.bz2 has changed