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revision 1.12, Sat Jun 4 16:49:03 2011 UTC revision 1.13, Wed Jul 6 17:02:21 2011 UTC
# Line 3  Line 3 
3  #  #
4    
5  #  #
6  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2011 University of Chicago and Fellowship
7  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
8  #  #
9  # This file is part of the SEED Toolkit.  # This file is part of the SEED Toolkit.
# Line 37  Line 37 
37    
38         -a   alias_file    - relabel tips using aliases        # table: [id alias]         -a   alias_file    - relabel tips using aliases        # table: [id alias]
39         -b                 - show bootstrap/branch support values         -b                 - show bootstrap/branch support values
40           -bar               - show scale bar
41         -c   tax|role|file - color tips by taxonomy, roles,         -c   tax|role|file - color tips by taxonomy, roles,
42                              or groups specified in a file     # table: [id group]                              or groups specified in a file     # table: [id group]
43         -d   desc_file     - add description to each tip       # table: [id description]         -d   desc_file     - add description to each tip       # table: [id description]
# Line 51  Line 52 
52         -s   show_list     - preferred tips to show when collapsing subtrees         -s   show_list     - preferred tips to show when collapsing subtrees
53                              (D = Woese' list of 69 common organisms)                              (D = Woese' list of 69 common organisms)
54         -t   title         - title for html page         -t   title         - title for html page
55           -units label       - units label for scale bar; implies -bar
56         -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)         -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)
57         -y   dy            - vertical separation of consecutive tips (D = 1)         -y   dy            - vertical separation of consecutive tips (D = 1)
58    
# Line 83  Line 85 
85  shown in percent for internal nodes of the tree. min_dx and dy are set  shown in percent for internal nodes of the tree. min_dx and dy are set
86  to 2 unless they are explicitly specified.  to 2 unless they are explicitly specified.
87    
88    =item -bar
89    
90    Include a scale bar on the drawing.
91    
92  =item -c tax | role | group_file  =item -c tax | role | group_file
93    
94  The value for the -c option can be a string ('tax' or 'role') or the  The value for the -c option can be a string ('tax' or 'role') or the
# Line 145  Line 151 
151    
152  This title of the HTML page.  This title of the HTML page.
153    
154    =item -units scale_bar_units
155    
156    Include a scale bar with the specified units (inplies -bar).
157    
158  =item -x n  =item -x n
159    
160  Specifies the minimum length of a distance between two nodes. (D = 1)  Specifies the minimum length of a distance between two nodes. (D = 1)
# Line 206  Line 216 
216    
217         -a   alias_file    - relabel tips using aliases        # file: [id alias]         -a   alias_file    - relabel tips using aliases        # file: [id alias]
218         -b                 - show bootstrap/branch support values         -b                 - show bootstrap/branch support values
219           -bar               - show scale bar
220         -c   tax|role|file - color tips by taxonomy, roles,         -c   tax|role|file - color tips by taxonomy, roles,
221                              or groups specified in a file     # file: [id group]                              or groups specified in a file     # file: [id group]
222         -d   desc_file     - add description to each tip       # file: [id description]         -d   desc_file     - add description to each tip       # file: [id description]
# Line 220  Line 231 
231         -s   show_list     - preferred tips to show when collapsing subtrees         -s   show_list     - preferred tips to show when collapsing subtrees
232                              (D = Woese' list of 69 common organisms)                              (D = Woese' list of 69 common organisms)
233         -t   title         - title for html page         -t   title         - title for html page
234           -units label       - units label for scale bar; implies -bar
235         -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)         -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)
236         -y   dy            - vertical separation of consecutive tips (D = 1)         -y   dy            - vertical separation of consecutive tips (D = 1)
237         -anno              - use the annotator's SEED for URLs         -anno              - use the annotator's SEED for URLs
# Line 233  Line 245 
245    
246  my ($help, $url, $alias_file, $focus_file, $branch, $collapse_by, $show_file,  my ($help, $url, $alias_file, $focus_file, $branch, $collapse_by, $show_file,
247      $desc_file, $keep_file, $link_file, $text_link, $popup_file, $id_file, $title,      $desc_file, $keep_file, $link_file, $text_link, $popup_file, $id_file, $title,
248      $min_dx, $dy, $ncolor, $color_by, $anno, $gray, $pseed, $ppseed, $raw);      $min_dx, $dy, $ncolor, $color_by, $anno, $gray, $pseed, $ppseed, $raw,
249        $scale_bar, $scale_lbl);
250    
251  GetOptions("h|help"         => \$help,  GetOptions("h|help"         => \$help,
252             "a|alias=s"      => \$alias_file,             "a|alias=s"      => \$alias_file,
253               "bar"            => \$scale_bar,    # include a scale bar
254             "b|branch"       => \$branch,             "b|branch"       => \$branch,
255             "c|color=s"      => \$color_by,             "c|color=s"      => \$color_by,
256             "d|desc=s"       => \$desc_file,             "d|desc=s"       => \$desc_file,
# Line 250  Line 264 
264             "p|collapse=s"   => \$collapse_by,             "p|collapse=s"   => \$collapse_by,
265             "s|show=s"       => \$show_file,             "s|show=s"       => \$show_file,
266             "t|title=s"      => \$title,             "t|title=s"      => \$title,
267               "units=s"        => \$scale_lbl,    # units label for scale bar
268             "x|dx=i"         => \$min_dx,             "x|dx=i"         => \$min_dx,
269             "y|dy=i"         => \$dy,             "y|dy=i"         => \$dy,
270             "anno"           => \$anno,             "anno"           => \$anno,
# Line 260  Line 275 
275    
276  $help and die $usage;  $help and die $usage;
277    
278  my $opts;  my $opts = {};
279    
280  $opts->{show_branch}   = $branch;  $opts->{show_branch}   = $branch;
281  $opts->{color_by}      = $color_by;  $opts->{color_by}      = $color_by;
# Line 283  Line 298 
298  $opts->{title}         = $title;  $opts->{title}         = $title;
299  $opts->{anno}          = $anno;  $opts->{anno}          = $anno;
300  $opts->{raw}           = $raw;  $opts->{raw}           = $raw;
301    $opts->{scale_bar}     = $scale_bar if $scale_bar;
302    $opts->{scale_lbl}     = $scale_lbl if defined $scale_lbl;
303    
304  $opts->{color_by}      ||= $raw ? 'none' : 'taxonomy';  $opts->{color_by}      ||= $raw ? 'none' : 'taxonomy';
305  $opts->{collapse_by}   ||= $raw ? 'none' : 'genus';  $opts->{collapse_by}   ||= $raw ? 'none' : 'genus';

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