changeset 4:a8eccdcc0800 draft

Deleted selected files

--- a/fastq_paired_reads_convention.pl	Thu May 10 16:36:55 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-#! /usr/bin/perl -w
-
-use strict;
-use warnings;
-
-# fastq_paired_reads_convention2.pl [input file] [left output file] [right output file]
-
-die "Check arguments" unless @ARGV == 3;
-
-#open (LEFT, '>data/left2.fastq') or die "Cannot create $ARGV[1]: $!\n";
-#open (RIGHT, '>data/right2.fastq') or die "Cannot create $ARGV[2]: $!\n";
-#open (INPUT, '<data/interlaced.fastq') or die "Cannot open $ARGV[0]: $!\n";
-
-open (LEFT, '>', $ARGV[1]) or die "Cannot create $ARGV[1]: $!\n";
-open (RIGHT, '>', $ARGV[2]) or die "Cannot create $ARGV[2]: $!\n";
-open (INPUT, '<', $ARGV[0]) or die "Cannot open $ARGV[0]: $!\n";
-
-my $which = 0;
-my $current_id;
-
-while(<INPUT>) {
-	chomp;
-	if(/ 1\S*/){
-		$_ =~ s/ 1\S*//;
-		$_.='/1';
-		$current_id = substr $_, 1;
-		$which = 1;
-	}
-	if(/ 2\S*/){
-		$_ =~ s/ 2\S*//;
-		$_.='/2';
-		$current_id = substr $_, 1;
-		$which = 2;
-	}
-	
-	if($_ eq '+'){
-		$_.=$current_id;
-	}
-	
-	if($which == 1){
-		print LEFT "$_\n";
-	}
-	if($which == 2){
-		print RIGHT "$_\n";
-	}
-}
-
-close (LEFT);
-close (RIGHT);
-close (INPUT);
\ No newline at end of file

--- a/fastq_paired_reads_convention.xml	Thu May 10 16:36:55 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<tool id="FASTQPairedReadsConvention" name="Convert paired reads format">
-	<description>to conventional (/1 and /2)</description>
-	<command interpreter="perl">fastq_paired_reads_convention.pl $input $left_out $right_out</command>
-	<inputs>
-		<param name="input" type="data" label="FASTQ file" format="fastqsanger, fastqcssanger"></param></inputs>
-	<outputs>
-		<data format="input" name="left_out"></data>
-		<data format="input" name="right_out"></data></outputs>
-	<help>
-	
-	**What it does**
-	
-	This tool takes a paired ends fastq file (with the first format below) and produces a left and right fastq file (with the second format below).
-	
-	-----
-	
-	**Example**
-	
-	Data like this::
-	
-    <![CDATA[
-	@M00325:2:000000000-A0DG1:1:1:15761:1554 1:N:0:1
-	NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG
-	+
-	#+14:A?DAD1<;EBD@C3C33:C0)))8'5::69=6';;;/58<>335'898(:0&&&0&070&&05085-55538<<-5>999-550--5&559>9<8<<(&&)&(+(((&&0&(+(&)&&&)(&((((((((+(&&((+++(((+((&
-    ]]>
-	
-	will produce an empty right file and a left file with one entry like this::
-	
-    <![CDATA[
-	@M00325:2:000000000-A0DG1:1:1:15761:1554/1
-	NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG
-	+M00325:2:000000000-A0DG1:1:1:15761:1554/1
-	#+14:A?DAD1<;EBD@C3C33:C0)))8'5::69=6';;;/58<>335'898(:0&&&0&070&&05085-55538<<-5>999-550--5&559>9<8<<(&&)&(+(((&&0&(+(&)&&&)(&((((((((+(&&((+++(((+((&
-    ]]>
-	
-	</help></tool>