diff glang-galaxy-conf/kbws/emboss_single_outputfile_wrapper.pl @ 2:8947fca5f715 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/emboss_single_outputfile_wrapper.pl	Fri Jun 26 05:21:44 2015 -0400
@@ -0,0 +1,27 @@
+#! /usr/bin/perl -w
+use strict;
+use File::Copy;
+
+my $cmd_string = join (" ",@ARGV);
+my $results = `$cmd_string`;
+my @files = split("\n",$results);
+my $fileNameOut = $ARGV[6];
+my ($drive, $outputDir, $file) = File::Spec->splitpath( $fileNameOut );
+my $destination = $fileNameOut;
+
+foreach my $thisLine (@files)
+  {
+      if ($thisLine =~ /Created /)
+        {
+            $thisLine =~ /[\w|\.]+$/;
+            $thisLine =$&;
+            #print "outfile: $thisLine\n";
+            #there is only one file to move, so we can quit after finding it
+            move($drive.$outputDir.$thisLine,$fileNameOut);
+            exit(1);
+        }
+      else
+        {
+            print $thisLine,"\n";
+        }
+  }