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Add missing arguments and a test

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1 parent 7be4a04 commit a39249e40203e7aae225494491c8b1cfef261776 @bosborne bosborne committed Jan 4, 2012
Showing with 17 additions and 7 deletions.
  1. +7 −6 lib/Bio/Tools/Run/Phylo/FastTree.pm
  2. +10 −1 t/FastTree.t
@@ -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
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@@ -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',

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