From d8a9a7c0930453938cbded5cdd1378f168d8dcb3 Mon Sep 17 00:00:00 2001
From: zhangyong <zhangyong19971019@gmail.com>
Date: Mon, 20 Nov 2023 14:56:17 +0800
Subject: [PATCH] Modified help message.

---
 config/config.txt               |  1 +
 gaep                            |  4 ++--
 scripts/breakpoint_detection.pl |  3 ++-
 scripts/pipeline.pl             |  2 +-
 scripts/run_busco5.pl           | 18 +++++++-----------
 scripts/run_merqury.pl          |  4 ++--
 scripts/stat_accuracy_base.pl   |  4 ++--
 7 files changed, 17 insertions(+), 19 deletions(-)

diff --git a/config/config.txt b/config/config.txt
index 619511e..2d11d9f 100644
--- a/config/config.txt
+++ b/config/config.txt
@@ -52,4 +52,5 @@ metaeuk=
 {hmmsearch}
 hmmsearch=
 {bbtools}
+#path to stat.sh
 bbtools=
diff --git a/gaep b/gaep
index 506f692..e0f131a 100755
--- a/gaep
+++ b/gaep
@@ -9,11 +9,11 @@ use FindBin qw ($RealBin);
 my $task = 'gaep';
 my $mode = 0;
 
-my $command      =  shift ;
+my $command =  shift ;
 
 my $usage = qq(
 Program: gaep
-Version: V1.1.1
+Version: V1.2.3
 
 Pipeline to assess genome assembly.
 
diff --git a/scripts/breakpoint_detection.pl b/scripts/breakpoint_detection.pl
index ba0a595..077eb9f 100755
--- a/scripts/breakpoint_detection.pl
+++ b/scripts/breakpoint_detection.pl
@@ -14,8 +14,9 @@
 my $mode = 0;
 
 my $usage = <<USAGE;
-Program: $task
+Program: gaep bkp
 
+Usage:   gaep bkp <-r fasta_file> [options]
 Options:
          -r <FILE>           genome assembly in a fasta file
          -i <FILE>           Fastq file. Can be set more than one time.
diff --git a/scripts/pipeline.pl b/scripts/pipeline.pl
index ed3dbe8..62a566c 100755
--- a/scripts/pipeline.pl
+++ b/scripts/pipeline.pl
@@ -3,7 +3,7 @@
 =head1 Description
 
  GAEP: Genome Assembly Evaluating Pipeline
- Version: V1.1.1
+ Version: V1.2.3
 
 =head1 Usage
 
diff --git a/scripts/run_busco5.pl b/scripts/run_busco5.pl
index 62e2f9c..8ec7b48 100755
--- a/scripts/run_busco5.pl
+++ b/scripts/run_busco5.pl
@@ -10,10 +10,10 @@
 my $mode = 0;
 
 my $usage = <<USAGE;
-Program: $task
+Program: gaep busco
 
 Command: 
-    $task -r assembly [options]
+    gaep busco <-r assembly> [options]
 
 Options: 
     -d <PATH>       output directory
@@ -53,7 +53,7 @@
 	"h"              => \$help,
 );
 
-die $usage if $help || (!$assembly && !$lineage);
+die $usage if $help || (!$assembly || !$lineage);
 
 $lineage = "./$lineage" if $lineage !~ /\//;
 if (-e "$lineage/dataset.cfg") {
@@ -78,7 +78,10 @@
 		die "[$task]Error! Can't make directory:\"$dir\"\n";
 	}
 }
-$prefix_out   = "busco_output" unless $prefix_out;
+#elsif(!$dir) {
+#	$dir='./run_busco5_output';
+#}
+$prefix_out = "busco_output" unless $prefix_out;
 
 #$ENV{PATH} = "$ENV{PATH}".":".dirname($config->{'augustus'});
 #my $AUGUSTUS_CONFIG_PATH = dirname($config->{'augustus'})."/../config";
@@ -108,13 +111,6 @@
 sub create_config {
 	my $config  = shift;
 	my $def_con = shift;
-	#$config->{'tblastn'}              = dirname($config->{'tblastn'});
-	#$config->{'makeblastdb'}          = $config->{'tblastn'};
-	#$config->{'augustus'}             = dirname($config->{'augustus'});
-	#$config->{'etraining'}            = $config->{'augustus'};
-	#$config->{'gff2gbSmallDNA.pl'}    = $config->{'augustus'};
-	#$config->{'new_species.pl'}       = $config->{'augustus'};
-	#$config->{'optimize_augustus.pl'} = $config->{'augustus'};
 	if (lc($domain) eq 'eukaryota') {
 		$config->{metaeuk} = $config->{metaeuk} ? check_software("metaeuk", $config->{metaeuk}) : check_software("metaeuk");
 		die "[$task] Error! Can't find metaeuk.\nPlease input a correct path or add it to environment.\n" if $config->{'metaeuk'} eq "-1"; 
diff --git a/scripts/run_merqury.pl b/scripts/run_merqury.pl
index 8f163d2..e2de06c 100755
--- a/scripts/run_merqury.pl
+++ b/scripts/run_merqury.pl
@@ -9,9 +9,9 @@
 my $mode = 0;
 
 my $usage = qq(
-Program: $task
+Program: gaep kacc
 
-Usage:   $task <-r fasta> <-i fastq> [<-i fastq>] [options]
+Usage:   gaep kacc <-r fasta> <-i fastq> [<-i fastq>] [options]
 Options:
          -r          Genome assembly in a fasta file
          -g          Total length of assembly
diff --git a/scripts/stat_accuracy_base.pl b/scripts/stat_accuracy_base.pl
index f06711f..0c14b0a 100755
--- a/scripts/stat_accuracy_base.pl
+++ b/scripts/stat_accuracy_base.pl
@@ -10,9 +10,9 @@
 my $mode = 0;
 
 my $usage = qq(
-Program: $task
+Program: gaep macc
 
-Usage:   $task 
+Usage:   gaep macc <-r fasta_file> [options]
 Options:
          -r <FILE>           Genome assembly in a fasta file
          -i <FILE>           Fastq1 file. Can be set more than one time