#if $input.ext.endswith(".gz")
            gunzip -c '$input' > input &&
        #else
            ln -s '$input' input &&
        #end if
    
        obiclean
        --without-progress-bar
        #if $distance
            -d '$distance'
        #end if
        #if $key
            -s '$key'
        #end if
        #if $ratio
            -r '$ratio'
        #end if
        ${head}
        
        #if $input_format_options.options_inputtype
            $input_format_options.options_inputtype
        #else
            #if $input.ext.startswith("fasta")
                --fasta
            #else if $input.ext.startswith("fastqsolexa")
                ## input file is in fastq nucleic format produced by solexa sequencer
                --solexa
            #else
                ## input file is in sanger fastq nucleic format (standard fastq)
                --sanger
            #end if
        #end if
        #if $input_format_options.options_seqtype
            $input_format_options.options_seqtype
        #end if
    
        
        #if $out_format
            --${out_format}-output
        #end if
    
        input 
        
        #if $input.ext.endswith(".gz")
        | gzip -c 
    #end if
    
        >'$output'
        
        #import json

        #try:
            #silent $outputs[0]
        #except 
            #set outputs = [("output", $output)]
        #end try

        #if $input.ext.startswith("fastq")
            #set ext = "fastqsanger"
        #else if $input.ext.startswith("fasta")
            #set ext = "fasta"
        #end if

        #try
            #if $out_format == "fasta"
                #set ext = "fasta"
            #else if $out_format == "fastq"
                #set ext = "fastqsanger"
            #end if
        #except
            #set ext = "fasta"
        #end try

        #if $input.ext.endswith(".gz")
            #set ext = ext + ".gz"
        #end if

        #set gxy_json = {}
        #for oname, o in $outputs
            #silent gxy_json[oname] = {"ext": ext}
        #end for
        && echo '${json.dumps(gxy_json)}' >> galaxy.json