Add -seqtype param

bioperl · Sep 30, 2011 · 4173eae · 4173eae
1 parent f2c95e1
commit 4173eae
Showing 1 changed file with 23 additions and 24 deletions.
diff --git a/lib/Bio/Tools/Run/Alignment/Muscle.pm b/lib/Bio/Tools/Run/Alignment/Muscle.pm
@@ -1,4 +1,3 @@
-# $Id$
 #
 # BioPerl module for Bio::Tools::Run::Alignment::Muscle
 #
@@ -126,7 +125,7 @@ use Bio::Tools::Run::WrapperBase;
 
 BEGIN {
     %DEFAULTS = ( 'AFORMAT' => 'fasta' );
-    @MUSCLE_PARAMS = qw(IN OUT TREE1 LOG LOGA SCOREFILE GAPOPEN 
+    @MUSCLE_PARAMS = qw(IN OUT TREE1 LOG LOGA SCOREFILE GAPOPEN SEQTYPE
 			MAXMB MAXHOURS MAXITERS KBAND IN1 IN2 USETREE USETREE_NOWARN);
     @MUSCLE_SWITCHES = qw(QUIET DIAGS REFINE STABLE GROUP 
 			  CLW CLWSTRICT MSF);
@@ -524,36 +523,36 @@ sub _setinput {
 
 sub _setparams {
     my ($self) = @_;
-    my ($attr, $value,$param_string);
+    my ( $attr, $value, $param_string );
     $param_string = '';
     my $laststr;
-    for  $attr ( @MUSCLE_PARAMS ) {
-	$value = $self->$attr();
-	next unless (defined $value);	
-	my $attr_key = lc $attr;
-        $attr_key = ' -'.$attr_key;
-        $param_string .= $attr_key .' '.$value;
 
+    for $attr (@MUSCLE_PARAMS) {
+        $value = $self->$attr();
+        next unless ( defined $value );
+        my $attr_key = lc $attr;
+        $attr_key = ' -' . $attr_key;
+        $param_string .= $attr_key . ' ' . $value;
     }
-    for  $attr ( @MUSCLE_SWITCHES) {
- 	$value = $self->$attr();
- 	next unless ($value);
- 	my $attr_key = lc $attr; #put switches in format expected by tcoffee
- 	$attr_key = ' -'.$attr_key;
- 	$param_string .= $attr_key ;
+    for $attr (@MUSCLE_SWITCHES) {
+        $value = $self->$attr();
+        next unless ($value);
+        my $attr_key = lc $attr;    # put switches in format expected by tcoffee
+        $attr_key = ' -' . $attr_key;
+        $param_string .= $attr_key;
     }
 
     # Set default output file if no explicit output file selected
-    unless ($self->outfile_name ) {	
-	my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir());
-	close($tfh);
-	undef $tfh;
-	$self->outfile_name($outfile);
+    unless ( $self->outfile_name ) {
+        my ( $tfh, $outfile ) = $self->io->tempfile( -dir => $self->tempdir() );
+        close($tfh);
+        undef $tfh;
+        $self->outfile_name($outfile);
     }
-    $param_string .= " -out ".$self->outfile_name;
-    
-    if ($self->quiet() || $self->verbose < 0) { 
-	$param_string .= ' 2> /dev/null';
+    $param_string .= " -out " . $self->outfile_name;
+
+    if ( $self->quiet() || $self->verbose < 0 ) {
+        $param_string .= ' 2> /dev/null';
     }
     return $param_string;
 }