<tool id="bundle_collection" name="Bundle Collection" version="1.2.1">
	<description>Download a collection of files</description>
	<stdio>
  	<exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
  </stdio>
	<command interpreter="perl">bundle_collection.pl -h $html_file -p $html_file.files_path

        #if $singles_or_list.type == "list":

                #if $singles_or_list.input:
               	    #for $f in $singles_or_list.input.keys
		    -i "$f,$singles_or_list.input[$f].ext=$singles_or_list.input[$f]"
		    #if $singles_or_list.input[$f].metadata.bam_index and $singles_or_list.input[$f].metadata.bam_index != "None"
		        #set $bamind = $f+","+$singles_or_list.input[$f].ext+".bai="+$singles_or_list.input[$f].metadata.bam_index
		        -i "$bamind"
	            #end if
		    #end for
                #end if
      #elif $singles_or_list.type == "singles":
                #for $dataset in $singles_or_list.single_files
                    #if $dataset.single_file:
                        -i "$dataset.single_file.name,$dataset.single_file.ext=$dataset.single_file"
                    #end if

		    #if $dataset.single_file.metadata.bam_index and $dataset.single_file.metadata.bam_index != "None"
		        #set $bamind = $dataset.single_file.name+","+$dataset.single_file.ext+".bai="+$dataset.single_file.metadata.bam_index
		        -i "$bamind"
	            #end if
                    
                #end for
      #end if
	</command>

	<inputs>
          <conditional name="singles_or_list">
            <param name="type" type="select" label="Bundle type">
              <option value="singles">Individual datasets</option>
              <option value="list">List Collection </option>
            </param>
            <when value="singles">
              <repeat name='single_files' title='Single dataset(s)'>
                <param name="single_file" label="Dataset to add the bundle" type="data" format='data' optional='False'/>
              </repeat>              
            </when>
            <when value="list">
              <param name="input" type="data_collection" label="Data Collection" collection_type="list" optional='False'/>
            </when>
          </conditional>
	</inputs>

	<outputs>
		<data name="html_file" format="html" label="Bundled Collection" />
	</outputs>
	<tests>
		<test>
		  <output/>
		</test>
	</tests>

	<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>

	<citations>
  </citations>

</tool>