diff velvet/velvetg_jgi_wrapper.pl @ 0:4afe13ac23b6 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/velvet/velvetg_jgi_wrapper.pl	Tue Jun 07 17:52:16 2011 -0400
@@ -0,0 +1,66 @@
+#!/usr/bin/env perl
+
+# Conventience wrapper for velvetg; copies outfiles to galaxy-specified destinations.
+# Please email bugs/feature requests to Edward Kirton ([e-mail])
+#
+# History:
+# - 2010/03/04 : file created
+# - 2001/02/05 : added new options, outfiles; renamed to velvetg_jgi to avoid collision with the other velvetg tool
+
+use strict;
+use warnings;
+use File::Copy;
+
+# shift wrapper args
+my $velveth_path=shift @ARGV or die;
+my $velvetg_path=shift @ARGV or die;
+my $velvetg_outfile=shift @ARGV or die;
+my $contigs_outfile=shift @ARGV or die;
+my $stats_outfile=shift @ARGV or die;
+my $lastgraph_outfile=shift @ARGV or die;
+my $unused_reads_outfile=shift @ARGV or die;
+my $amos_outfile=shift @ARGV or die;
+
+# setup velvetg folder
+die("Velveth folder does not exist: $velveth_path\n") unless -d $velveth_path;
+-d $velvetg_path or mkdir($velvetg_path) or die("Unable to create output folder, $velvetg_path: $!\n");
+die("velveth Sequences file does not exist: $velveth_path/Sequences") unless -f "$velveth_path/Sequences";
+symlink("$velveth_path/Sequences", "$velvetg_path/Sequences");
+die("velveth Roadmaps file does not exist: $velveth_path/Roadmaps") unless -f "$velveth_path/Roadmaps";
+symlink("$velveth_path/Roadmaps", "$velvetg_path/Roadmaps");
+die("velveth Log file does not exist: $velveth_path/Log") unless -f "$velveth_path/Log";
+copy("$velveth_path/Log", "$velvetg_path/Log");
+
+# run command (remaining args, starting with exe path)
+open (VELVETG, "@ARGV|") or die("Unable to run velvetg\n");
+open (OUT, ">$velvetg_outfile") or die("Unable to open outfile, $velvetg_outfile: $!\n");
+while (<VELVETG>) {
+    print OUT $_;
+    print if /^Final graph/;
+}
+close VELVETG;
+close OUT;
+
+# process output
+unlink($contigs_outfile);
+move("$velvetg_path/contigs.fa", $contigs_outfile);
+unlink($stats_outfile);
+move("$velvetg_path/stats.txt", $stats_outfile);
+
+unlink($lastgraph_outfile);
+if ( -f "$velvetg_path/LastGraph") {
+    move("$velvetg_path/LastGraph", $lastgraph_outfile);
+} elsif ( -f "$velvetg_path/Graph2") {
+    move("$velvetg_path/Graph2", $lastgraph_outfile);
+} else {
+    open(OUT, ">$lastgraph_outfile") or die($!);
+    print OUT "ERROR: $velvetg_path/LastGraph not found!\n";
+    close OUT;
+}
+unlink($unused_reads_outfile);
+move("$velvetg_path/UnusedReads.fa", $unused_reads_outfile);
+if ( $amos_outfile ne 'None' ) {
+    unlink($amos_outfile);
+    move("$velvetg_path/velvet_asm.afg", $amos_outfile);
+}
+exit;