mkdir input;

#set $in_= 'input'


#if '__ob__' in str($semantic_type):
	#set $type_temp = str($semantic_type).replace('__ob__', '[')
	#set $type_temp = str($type_temp).replace('__cb__', ']')
	#set $semantic_type = $type_temp
#end if

#def is_fastq($f_test)
	#set $f = open($f_test, 'rb')
	#if str($f.readline()[0]) == '@'
		#$f.close()
		#return True
	#end if

	#$f.close()
	#return False
#end def


## Symlinks creation or On the fly creation of a combo file
#if $input_type.type == 'list_list'
	## Symlinks creation or On the fly creation of a combo file
	#for $f in $input_type.list_list:

		#set $is_fastq_file = $is_fastq(str($f))

		#if $is_fastq_file:
			#set $file_for_processing = "'input/" + $f.name + '.gz' + "'"
			gzip -c ${f} > $file_for_processing;
		#else
			#set $file_for_processing = "'input/" + $f.name + "'"
			ln -s ${f}  $file_for_processing;
		#end if
	#end for
	#if 'SingleEndFastqManifestPhred' in str($inputformat):
			#set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt"
			#set $m_file = open(str($cwd), 'w')
			$m_file.write("sample-id,absolute-filepath,direction\n")
			#for $f in $input_type.list_list:
				$m_file.write(str($f.name).split("_")[0]+",$PWD/input/"+str($f.name)+".gz,forward\n")
			#end for
			$m_file.close()
			#set $in_= str($cwd)
		#end if
	

#elif $input_type.type == 'list_paired_collection':
  
	#set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt"
	#set $m_file = open(str($cwd), 'w')
	$m_file.write("sample-id,absolute-filepath,direction\n")	

	#for $pair in $input_type.list_paired_collection:
		#set $forward_is_fastq_file = $is_fastq(str($pair.forward))
		#set $reverse_is_fastq_file = $is_fastq(str($pair.reverse))
		
		#if $forward_is_fastq_file:
	 		gzip -c ${pair.forward} > input/${pair.name}_R1_001.fastq.gz;
	 		$m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n")
		#else
	  		ln -s ${pair.forward} input/${pair.name}_R1_001.fastq.gz;
			$m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n")
        #end if

	 	#if $reverse_is_fastq_file:
	 		gzip -c ${pair.reverse} > input/${pair.name}_R2_001.fastq.gz;
			$m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n")
        #else
	  		ln -s ${pair.reverse} input/${pair.name}_R2_001.fastq.gz;
			$m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n")
	  	#end if
	#end for

	
	$m_file.close()
	#if 'PairedEndFastqManifestPhred' in str($inputformat):
		#set $in_= str($cwd)
	#elif  'Casava' in str($inputformat):
		#set $in_= 'input'
	#end if

#else
	#set $res = $is_fastq(str($file))

	#if $res
		gzip -c ${file} > ${file.name}.gz;
		#set $in_= $file.name + '.gz'

	#else
		#set $in_= str($file)
	#end if
   
   #if "MultiplexedSingleEndBarcodeInSequence" in str($semantic_type):      
 			mv *_R1_* forward.fastq.gz;
	    #set $in_= 'forward.fastq.gz';
   #end if 

#end if


## rename files to predefined names for "MultiplexedPairedEndBarcodeInSequence"
#if "MultiplexedPairedEndBarcodeInSequence" in str($semantic_type):
		mv input/*_R1_* input/forward.fastq.gz;
		mv input/*_R2_* input/reverse.fastq.gz;
#end if


qiime tools import

--input-path=$in_

#if str($inputformat) != 'None':
	#if '__ob__' in str($inputformat):
  		#set $inputformat_temp = str($inputformat).replace('__ob__', '[')
		#set $inputformat_temp = str($inputformat_temp).replace('__cb__', ']')
  		#set $inputformat = $inputformat_temp
	#end if
 --input-format="$inputformat"
#end if

--type="$semantic_type"

--output-path=outputpath.qza

;
cp outputpath.qza $outputpath