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