Hi Hans, Thanks for the reply. I called the perl script with the 3rd argument because I don't understand the galaxy part of it, on command line I call it with just 2 arguments. How does the galaxy work with the output that is just a file ? What is the right way to handle the output with galaxy? In short: I can't even seem to get a command line working program working under galaxy without some proper manual, even google is not my best friend here when it comes to galaxy framework. //Michel On Tue, 2009-12-01 at 16:03 +0100, Hotz, Hans-Rudolf wrote:
Michel
I am not sure, whether I do understand your e-mail correctly, but something looks strange to me:
you call a perl script with 3 arguments :
###########40################ <tool id="GAPSS_FASTA_to_FASTQ" name="GAPSS - FASTA to FASTQ"> <description>converter</description> <command interpreter="perl">GAPSS_FASTA2FASTQ.v2.pl $input $score $output</command>
but you never use "$ARGV[2]" in your 'PERl script job 40'
Have you tried
my $fastq_output_file_name = $ARGV[2];
instead of " my $fastq_output_file_name = $file_to_convert.".fastq"; "
Hans