#6 Change file type test to work with a Galaxy wrapper

[Oleksandr Moskalenko]

Please take a look at the following patch. I had to make the following changes to be able to get ribopicker work the Galaxy wrapper as without it a "-p destination: Broken pipe" message was output to the stderr preventing the Galaxy wrapper from working. The wrapper can be checked out from "hg clone http://malex@toolshed.g2.bx.psu.edu/repos/malex/ribopicker".

--- ribopicker-standalone-0.4.3/ribopicker.pl 2011-12-01 18:06:44.000000000 -0500
+++ ../0.4.3/bin/ribopicker_galaxy.pl 2012-10-16 18:32:03.512372941 -0400
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl

#===============================================================================
# Author: Robert SCHMIEDER, Computational Science Research Center @ SDSU, CA
@@ -422,10 +422,12 @@
$count = 3;
$fasta = $fastq = $qual = 0;
$format = 'unknown';
-

• open(FILE,"perl -p -e 's/\r/\n/g;s/\n\n/\n/g' < $file |") or die "ERROR: Could not open file $file: $! \n";
• open(FILE,'<', $file) or die "ERROR: Could not open file $file: $! \n";
  while (<file>) {
  chomp();</file>
• s/^\s+//g;
  next unless(length($_));
  if($count-- == 0) {
  last;