Add missing arguments and a test

bioperl · Jan 4, 2012 · a39249e · a39249e
1 parent 7be4a04
commit a39249e
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Showing 2 changed files with 17 additions and 7 deletions.
diff --git a/lib/Bio/Tools/Run/Phylo/FastTree.pm b/lib/Bio/Tools/Run/Phylo/FastTree.pm
@@ -82,13 +82,14 @@ use Bio::Root::IO;
 
 use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
 
-our @FastTree_PARAMS = qw(log cat n intree intree1 constraints sprlength topm close 
-    refresh constraintWeight);
-our @FastTree_SWITCHES = qw(quiet nopr nt fastest slow nosupport pseudo gtr wag quote noml 
-    nome mllen gamma spr nni sprlength mlnni mllen slownni nocat notoo 2nd no2nd nj bionj
-);
+our @FastTree_PARAMS =
+  qw(log cat n intree intree1 constraints sprlength topm close
+  refresh constraintWeight spr mlacc nni mlnni seed matrix gtrrates gtrfreq makematrix );
+our @FastTree_SWITCHES =
+  qw(quiet nopr nt fastest slow nosupport pseudo gtr wag quote noml
+  nome mllen gamma sprlength mllen slownni nocat notoo 2nd no2nd nj bionj top notop
+  nomatrix rawdist );
 our $PROGRAM_NAME = 'FastTree';
-#our $PROGRAM_DIR = Bio::Root::IO->catfile($ENV{FastTreeDIR}) if $ENV{FastTreeDIR};
 
 =head2 new
 

diff --git a/t/FastTree.t b/t/FastTree.t
@@ -8,7 +8,7 @@ use strict;
 BEGIN {
     use Bio::Root::Test;
     test_begin(
-        -tests => 8,
+        -tests => 9,
     );
     use_ok('Bio::Root::IO');
     use_ok('Bio::Tools::Run::Phylo::FastTree');
@@ -41,6 +41,15 @@ SKIP: {
     $tree = $fastft->run($alignfile);
     ok( defined($tree), "Tree is defined" );
 
+    my $slowft = Bio::Tools::Run::Phylo::FastTree->new(
+        -quiet   => 1,
+        -mlacc   => 2,
+        -slownni => 1,
+        -spr     => 4
+    );
+    $tree = $slowft->run($alignfile);
+    ok( defined($tree), "Tree is defined" );
+
     # Input is protein sequence alignment
     $alignio = Bio::AlignIO->new(
         -format => 'msf',