Mercurial > repos > nml > bundle_collections

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bundle_collection.pl	Fri Nov 20 10:23:17 2015 -0500
@@ -0,0 +1,120 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use File::Copy;
+use File::Basename;
+use Getopt::Long;
+use Pod::Usage;
+
+my ($html_file, $html_path, @args, %information, $folder);
+
+Getopt::Long::Configure('bundling');
+GetOptions(
+	'i|input=s'	=> \@args,
+	'h|html=s'	=> \$html_file,
+	'p|path=s'	=> \$html_path
+	);
+
+pod2usage(1) unless @args && $html_file && $html_path;
+
+#At this point, the output directory does not exist yet. So we have to make it
+mkdir $html_path or die "Could not make directory $!";
+
+#Now make a folder for all our files
+my $data_folder = $html_path."/Bundled_Collection";
+mkdir $data_folder or die "Could not make directory $!";
+
+#Go through each list item
+foreach my $entry (@args)
+{
+	#Get key and value. Remove any spaces
+	my ($info, $file) = split /=/, $entry;
+	my ($name, $ext) = split /,/, $info;
+	$name=~s/ /_/g;
+	my $full_name = $name.".".$ext;
+
+	#We store this for later to make the html file
+	$information{$name}{$ext}=1;
+
+	#copy each file to its directory
+
+	my $file_path = $data_folder."/".$full_name;
+
+	copy($file,$file_path) or die "Could not copy $file to $file_path: $!";
+}
+
+#Write out the html file
+open my $out, ">", $html_file or die "Could not open html file: $!";
+
+my $num_keys = scalar(keys %information);
+my $num_vals = scalar(@args);
+
+printf $out "<!DOCTYPE html>
+<html>
+<style type=\"text/css\">
+
+body {
+        font-family: sans-serif;
+        color: #000;
+        }
+
+table {
+        margin-left: 3em;
+        text-align: center;
+        }
+th {
+        text-align:center;
+        background-color: #000080;
+        color: #FFF;
+        padding: 0.4em;
+        }
+td {
+        font-family: monospace;
+        text-align: left;
+        background-color: #EEE;
+        color: #000;
+        padding: 0.4em;
+        }
+h2 {
+        color: #800000;
+        padding-bottom: 0;
+        margin-bottom: 0;
+        clear: left;
+        }
+</style></head>
+
+  <body>
+
+<h2 id=\"M0\">Bundle Collection Summary</h2><br><br>
+
+Number of keys: $num_keys<br>
+Number of values: $num_vals<br><br>
+
+<table border=\"1\"><tr><th>File name</th><th>File type</th></tr>";
+
+foreach my $key (sort(keys %information))
+{
+
+	foreach my $val (keys %{$information{$key}} )
+	{
+		printf $out "<tr><td>$key</td><td>$val</td></tr>";
+	}
+}
+
+printf $out "</table></body></html>";
+
+close $out;
+
+__END__
+
+=head1 name
+
+		bundle_collection.pl - Downloads a collection from Galaxy
+
+=head1 SYNOPSIS
+
+	bundle_collection.pl -h html_file -p output_path -o "key=value"
+
+=back
+=cut
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bundle_collection.xml	Fri Nov 20 10:23:17 2015 -0500
@@ -0,0 +1,28 @@
+<tool id="bundle_collection" name="Bundle Collection" version="1.0.1">
+	<description>Download a collection of files</description>
+	<command interpreter="perl">bundle_collection.pl -h $html_file -p $html_file.files_path
+		#for $f in $input.keys
+			-i "$f,$input[$f].ext=$input[$f]"
+			#if $input[$f].metadata.bam_index and $input[$f].metadata.bam_index != "None"
+				#set $bamind = $f+","+$input[$f].ext+".bai="+$input[$f].metadata.bam_index
+				-i "$bamind"
+			#end if
+		#end for
+	</command>
+
+	<inputs>
+		<param name="input" type="data_collection" label="Data Collection" collection_type="list"/>
+	</inputs>
+
+	<outputs>
+		<data name="html_file" format="html" label="Bundled Collection" />
+	</outputs>
+	<help>
+		***What it does**
+
+		This tool will bundle up files in a list collection into a downloadable zip file
+
+		Author: Mariam Iskander and Jen Cabral
+	</help>
+
+</tool>