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comparison alignment/gblocks.pl @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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-1:000000000000 0:5b9a38ec4a39
1 #! /usr/bin/perl -w
2
3 use strict;
4 use warnings;
5 #gblocks.pl [fasta file]
6
7 my $infile=shift(@ARGV);
8 my $datatype=shift(@ARGV);
9 my $gaps=shift(@ARGV);
10 my $size=shift(@ARGV);
11 my $outfileloc=shift(@ARGV);
12 my $htmlfileloc=shift(@ARGV);
13
14
15
16
17 ##For debugging command line pass, uncomment next
18 #for (my $i=0; $i < @ARGV; $i++){
19 # print "Parameter #$i ".$ARGV[$i]."\n\n";
20 #}
21
22 system "Gblocks $infile $datatype $gaps -b4=$size";
23
24 #Gblocks requires output from $input.fas to be written to $input.fas-gb
25 #Copy that file to gout where galaxy expects to find the output
26 my $outfile = $infile."-gb";
27 my $htmlfile = $outfile.".htm";
28 system "cat $outfile > $outfileloc";
29 system "cat $htmlfile > $htmlfileloc";
30 exit;