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<tool id="kraken" name="kraken">
	<description>taxonomic sequence classifier</description>
	<requirements>
	  <requirement type="package" version="2.7">python</requirement>
	  <requirement type="package" version="0.10.5">kraken</requirement>
	</requirements>
	<command interpreter="python">kraken.py 
		--dbtype="${databaseChoice.database}"
		#if $databaseChoice.database == "builtinDB":
		  --db="${databaseChoice.builtinDatabases.fields.path}"
		#else:
		  --db="NOT_SUPPORTED_YET"
		#end if

		--in1="${dataFormat.input1}"
		#if $dataFormat.inputFormat == "pairedFastQ" or $dataFormat.inputFormat == "pairedFastA":
		  --in2="${dataFormat.input2}"
		#end if

		#if $dataFormat.inputFormat == "singleFastQ" or $dataFormat.inputFormat == "pairedFastQ":
		  --input-format="fq"
		#else:
		  --input-format="fa"
		#end if

                #if $quickMode.useQuickMode == "useQuick":
                  --quick
                  --min-hits="${quickMode.minHits.value}"
                #end if

	<!--		$output -->
                $kraken_summary_tsv
                <!-- $classified_seqs_fq
                $unclassified_seqs_fq -->
		</command>
	<inputs>
		<conditional name="databaseChoice">
			<param name="database" type="select" label="Do you want to use your own kraken database or use the built-in ktest database?">
				<option value="builtinDB">Use built-in db</option>
				<option value="myownDB">Use a db from my history</option>
			</param>
			<when value="builtinDB">
				<param name="builtinDatabases" type="select" label="Select a built-in kraken database">
					<options from_data_table="krakenDBs">
						<filter type="sort_by" column="2" />
						<validator type="no_options" message="No databases are available" />
					</options>
				</param>
			</when>
			<when value="myownDB">
				<param name="myownDB" type="data" format="fasta" metadata_name="dbkey" label="Select database" />
			</when>
		</conditional>

		<conditional name="quickMode">
			<param name="useQuickMode" type="select" label="Use Quick operation? (use first hit or hits)">
				<option value="useQuick">Use Quick operation</option>
				<option value="dontUseQuick">Do not use Quick operation</option>
			</param>
			<when value="useQuick">
				<param name="minHits" type="integer" label="Minimum number of hits required for classification (default:1)" value="1" default="1" />
			</when>
		</conditional>

<!--		<conditional name="libraryType">
			<param name="libtype" type="select" label="Is this library single- or paired-end?">
				<option value="single">Single-end</option>
				<option value="paired">Paired-end</option>
			</param>
			<when value="single">
				<param name="input1" type="data" format="fasta,fastq,fasta.gz,fasta.bz2,fa.gz,fq.gz,fa,fq" label="Fasta/Fastq file" />
			</when>
			<when value="paired">
				<param name="input1" type="data" format="fasta,fastq,fasta.gz,fasta.bz2,fa.gz,fq.gz,fa,fq" label="Left Fasta/Fastq file" />
				<param name="input2" type="data" format="fasta,fastq,fasta.gz,fasta.bz2,fa.gz,fq.gz,fa,fq" label="Right Fasta/Fastq file" />
			</when>
		</conditional> -->
		<conditional name="dataFormat">
			<param name="inputFormat" type="select" label="Please select input file type and library type."> 
				<option value="singleFastQ">Single-end FastQ</option>
				<option value="pairedFastQ">Paired-end FastQ</option>
				<option value="singleFastA">Single-end FastA</option>
				<option value="pairedFastA">Paired-end FastA</option>
			</param>
			<when value="singleFastQ">
				<param name="input1" type="data" format="fastq,fastqillumina,fastqsanger,fq" label="FastQ file" />
			</when>
			<when value="pairedFastQ">
				<param name="input1" type="data" format="fastq,fastqillumina,fastqsanger,fq" label="Forward/Left FastQ file" />
				<param name="input2" type="data" format="fastq,fastqillumina,fastqsanger,fq" label="Reverse/Right FastQ file" />
			</when>
			<when value="singleFastA">
				<param name="input1" type="data" format="fasta, fa" label="FastA file" />
			</when>
			<when value="pairedFastA">
				<param name="input1" type="data" format="fasta, fa" label="Forward/Left FASTA file" />
				<param name="input2" type="data" format="fasta, fa" label="Reverse/Right FASTA file" />
			</when>
		</conditional>


	</inputs>
	<outputs>
		<data format="tabular" name="kraken_summary_tsv" label="${tool.name} output summary of ${on_string}" />
		<!-- <data name="classified_seqs_fq" format_source="input1" label="${tool.name}-classified sequences from ${on_string}" />
		<data name="unclassified_seqs_fq" format_source="input1" label="${tool.name}-unclassified sequences from ${on_string}" /> -->
	</outputs>

	<help>
	This tool wraps the kraken taxonomic sequence classifier.
	</help>
</tool>