Galaxy |

Changeset 10:f0bdf862ba39 (2012-12-31)

Previous changeset 9:cb6deaad121f (2012-12-31) Next changeset 11:52c5e53aff28 (2013-01-02)

Commit message:
Simplified perl wrapper.

modified:
flexbar.pl

diff -r cb6deaad121f -r f0bdf862ba39 flexbar.pl
--- a/flexbar.pl Mon Dec 31 00:50:58 2012 +0100
+++ b/flexbar.pl Mon Dec 31 18:40:01 2012 +0100

[

@@ -5,38 +5,29 @@
use warnings;
use strict;

-my $flexbarDir = "";
-
-my $pwd = $ENV{PWD};
+my $format  = pop @ARGV;
+my $folder  = pop @ARGV;
+my $id      = pop @ARGV;
+my $outFile = pop @ARGV;

-my $lastIdx = $#ARGV;
-my $format  = $ARGV[$lastIdx];
-my $folder  = $ARGV[$lastIdx - 1];
-my $id      = $ARGV[$lastIdx - 2];
-my $outFile = $ARGV[$lastIdx - 3];
+my $call = join " ", @ARGV;

-my $call = join " ", @ARGV[0..($lastIdx - 4)];
+system $call .' --target reads > '. $outFile and exit 1;

-system $flexbarDir . $call .' --target reads > '. $outFile;

-foreach(<$pwd ."/reads"*>){
+foreach(<reads*>){

- if(/^\.\//){
- my $file = $pwd ."/". $_;
-
- s/^\.\///;
- my $fileType;
-
- $fileType = $1         if /\.(\w+)$/;
- $fileType = $format    if /\.\w+fast\w$/;
- $fileType = 'tabular'  if $fileType eq 'lengthdist';
-
- s/_//g;
-
- my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
-
- rename $file, $name;
- rename $name, $folder;
- }
+ my $fileType;
+
+ $fileType = $1         if /\.(\w+)$/;
+ $fileType = $format    if /\.\w+fast\w$/;
+ $fileType = 'tabular'  if $fileType eq 'lengthdist';
+
+ s/_//g;
+
+ my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
+
+ rename $_, $name;
+ rename $name, $folder;
}