From e120767d06b10ed97769bc031190da2aedfd0917 Mon Sep 17 00:00:00 2001 From: Toshiro Nishimura Date: Mon, 28 Mar 2011 16:55:20 -0700 Subject: [PATCH] ratio.pl args/docs --- ratio.pl | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/ratio.pl b/ratio.pl index 2b6d7d7..5f50d15 100755 --- a/ratio.pl +++ b/ratio.pl @@ -16,7 +16,9 @@ use Launch; -pod2usage(-verbose => 99,-sections => [qw/NAME SYNOPSIS OPTIONS/]) if $opt_help; +pod2usage(-verbose => 99,-sections => [qw/NAME SYNOPSIS OPTIONS/]) +unless $opt_output_directory && $opt_reference_a && $opt_reference_b && $opt_raw && $opt_ecotype_a && $opt_ecotype_b && scalar %opt_splice; + my $conf=qq/ log4perl.logger = DEBUG, Print @@ -60,11 +62,6 @@ sub _gen_files { ####################################################################### # Handle options - -$logger->logdie("-o -r, -ra, -rb, -ea, -eb, -s required") -unless $opt_output_directory && -$opt_reference_a && $opt_reference_b && $opt_raw && $opt_ecotype_a && $opt_ecotype_b && scalar %opt_splice; - $logger->info("raw file: $opt_raw"); $logger->info("reference A: $opt_reference_a"); $logger->info("reference B: $opt_reference_b"); @@ -238,7 +235,7 @@ =head1 SYNOPSIS Usage examples: -ratio.pl [options]... + ratio.pl -r raw.fastq -ea Col -b Ler -ra genome-a.fasta -rb genome-b.fasta -l 100 -m 2 -s 1 50 -o outdir -b basename =head1 REQUIRED ARGUMENTS @@ -294,7 +291,7 @@ =head1 OPTIONS =item -m | --bowtie-mismatches -Number of mismatches to allow in bowtie +Number of mismatches to allow in bowtie. =for Euclid num.default: 2 @@ -302,7 +299,7 @@ =head1 OPTIONS =item -o | --output-directory -Output Directory +Output Directory. =item -b | --basename