diff ComMet_wrapper.pl @ 0:dfdfbdd47b32 default tip

migrate from GitHub

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ComMet_wrapper.pl	Sun Apr 19 20:55:17 2015 +0900
@@ -0,0 +1,56 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use FindBin;
+
+print STDOUT "The tool script is called with:\n", join(" ", ($0, @ARGV)), "\n\n";
+
+my ($in, $outdmc, $outdmr) = ("", "", "");
+my $default_option = "";
+#my $default_option = "--nobeta --nodual";
+
+my $tooldir = shift(@ARGV);
+$tooldir = $FindBin::Bin;
+my $intype_mapper = shift(@ARGV);
+
+if ($intype_mapper eq "bsf-call") {
+    my $in1 = shift(@ARGV);
+    my $in2 = shift(@ARGV);
+    my $tmp = "ComMet.tmp.$$";
+    ($outdmc, $outdmr) = @ARGV;
+    &invoke_command("$tooldir/bin/Bsf2ComMetIn.pl $in1 $in2 > $tmp");
+    &invoke_command("$tooldir/bin/ComMet $default_option $tmp $outdmc $outdmr");
+}
+elsif ($intype_mapper eq "commet") {
+    ($in, $outdmc, $outdmr) = @ARGV;
+    &invoke_command("$tooldir/bin/ComMet $default_option $in $outdmc $outdmr");
+}
+else {
+    die "never reach here\n";
+}
+
+sub invoke_command {
+    my ($command) = @_;
+    print "invoking: $command\n";
+    system($command);
+}
+
+=pod
+<!--
+    <conditional name="advancedset">
+      <param name="advancedset_use" type="select" label="use advanced setting">
+        <option value="No" selected="true">No</option>
+        <option value="Yes">Yes</option>
+      </param>
+      <when value="No">
+      </when>
+      <when value="Yes">
+        <param name="beta" type="boolean" falsevalue="--nobeta" label="use beta mixture distributions"/>
+        <param name="dual" type="boolean" falsevalue="--nodual" label="use dual HMM architectures"/>
+        <param name="cpg" type="boolean" falsevalue="--noncpg" label="input files contain cytosine sites only in CpG context"/>
+      </when>
+    </conditional>    
+-->
+=cut