<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>