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Add missing arguments and a test

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commit a39249e40203e7aae225494491c8b1cfef261776 1 parent 7be4a04
bosborne bosborne authored

Showing 2 changed files with 17 additions and 7 deletions. Show diff stats Hide diff stats

  1. +7 6 lib/Bio/Tools/Run/Phylo/FastTree.pm
  2. +10 1 t/FastTree.t
13 lib/Bio/Tools/Run/Phylo/FastTree.pm
@@ -82,13 +82,14 @@ use Bio::Root::IO;
82 82
83 83 use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
84 84
85   -our @FastTree_PARAMS = qw(log cat n intree intree1 constraints sprlength topm close
86   - refresh constraintWeight);
87   -our @FastTree_SWITCHES = qw(quiet nopr nt fastest slow nosupport pseudo gtr wag quote noml
88   - nome mllen gamma spr nni sprlength mlnni mllen slownni nocat notoo 2nd no2nd nj bionj
89   -);
  85 +our @FastTree_PARAMS =
  86 + qw(log cat n intree intree1 constraints sprlength topm close
  87 + refresh constraintWeight spr mlacc nni mlnni seed matrix gtrrates gtrfreq makematrix );
  88 +our @FastTree_SWITCHES =
  89 + qw(quiet nopr nt fastest slow nosupport pseudo gtr wag quote noml
  90 + nome mllen gamma sprlength mllen slownni nocat notoo 2nd no2nd nj bionj top notop
  91 + nomatrix rawdist );
90 92 our $PROGRAM_NAME = 'FastTree';
91   -#our $PROGRAM_DIR = Bio::Root::IO->catfile($ENV{FastTreeDIR}) if $ENV{FastTreeDIR};
92 93
93 94 =head2 new
94 95
11 t/FastTree.t
@@ -8,7 +8,7 @@ use strict;
8 8 BEGIN {
9 9 use Bio::Root::Test;
10 10 test_begin(
11   - -tests => 8,
  11 + -tests => 9,
12 12 );
13 13 use_ok('Bio::Root::IO');
14 14 use_ok('Bio::Tools::Run::Phylo::FastTree');
@@ -41,6 +41,15 @@ SKIP: {
41 41 $tree = $fastft->run($alignfile);
42 42 ok( defined($tree), "Tree is defined" );
43 43
  44 + my $slowft = Bio::Tools::Run::Phylo::FastTree->new(
  45 + -quiet => 1,
  46 + -mlacc => 2,
  47 + -slownni => 1,
  48 + -spr => 4
  49 + );
  50 + $tree = $slowft->run($alignfile);
  51 + ok( defined($tree), "Tree is defined" );
  52 +
44 53 # Input is protein sequence alignment
45 54 $alignio = Bio::AlignIO->new(
46 55 -format => 'msf',

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