Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison alignment/fasconcat.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
2
3 use strict;
4
5 my $fasconcatPath = '/home/galaxy/galaxy_dist/tools/fasconcat/FASconCAT_v1.0.pl';
6
7 my $outputFormat = $ARGV[0];
8 my $limit = $ARGV[1];
9 my $outFormat;
10 my @inputFiles;
11
12 for(my $i = 2; $i <= $limit; $i++) {
13 $inputFiles[$i] = " -f ";
14 $inputFiles[$i] = $inputFiles[$i].$ARGV[$i];
15 }
16
17 if($outputFormat == "0") {
18 $outFormat = "";
19 }
20 elsif($outputFormat == "1") {
21 $outFormat = " -p -p";
22 }
23 else {
24 $outFormat = " -n -n";
25 }
26
27 my $run = qx/$fasconcatPath -s -i "@inputfiles" $outFormat /;
28
29 if($outputFormat == "0") {
30 qx/cp FcC_smatrix.fas output/;
31 }
32 elsif($outputFormat == "1") {
33 qx/cp FcC_smatrix.phy output/;
34 }
35 else {
36 qx/cp FcC_smatrix.nex output/;
37 }