view kraken_filter.xml @ 14:fd27c97c8366 draft default tip

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<tool id="kraken_filter" name="kraken_filter">
	<description>kraken result filter</description>
	<requirements>
	  <requirement type="package" version="2.7">python</requirement>
	</requirements>
	<command interpreter="python">kraken_filter.py 
		--dbtype="${databaseChoice.database}"
		#if $databaseChoice.database == "builtinDB":
		  --db="${databaseChoice.builtinDatabases.fields.path}"
		#else:
		  --db="NOT_SUPPORTED_YET"
		#end if
	
		--in1="${dataFormat.input1}"
		--out1="${kraken_filtered_r1}"        

		#if $dataFormat.inputFormat == "pairedFastQ" or $dataFormat.inputFormat == "pairedFastA":
		  --in2="${dataFormat.input2}"
		  --out2="${kraken_filtered_r2}"
		#end if

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

		#if $whichFilter.whichFilterp == "filterClassified":
		  --taxid="${whichFilter.taxonID}"
		#else:
		  --taxid="0"
		#end if

                --kraken-results="${kraken_classification}"
        
                --logfile="${kraken_filter_log}"
	</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 (ktest)</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="whichFilter">
			<param name="whichFilterp" type="select" label="Filter classified or unclassified reads?">
				<option value="filterClassified">Filter classified reads</option>
				<option value="filterUnclassified">Filter unclassified reads</option>
			</param>
			<when value="filterClassified">
				<param name="taxonID" type="integer" label="Taxonomy ID of root taxon (default:1 - 'all')" value="1" default="1" />				
			</when>
                </conditional>

		<param name = "kraken_classification" type="data" format="tabular" label="Kraken classification output" />
<!--
		<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>
-->
<!-- new -->

		<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,fq.gz,fq" label="FASTQ file" />
			</when>
			<when value="pairedFastQ">
				<param name="input1" type="data" format="fastq,fq.gz,fq" label="Forward/Left FASTQ file" />
				<param name="input2" type="data" format="fastq,fq.gz,fq" label="Reverse/Right FASTQ file" />
			</when>
			<when value="singleFastA">
				<param name="input1" type="data" format="fasta,fasta.gz,fasta.bz2,fa.gz" label="FASTA file" />
			</when>
			<when value="pairedFastA">
				<param name="input1" type="data" format="fasta,fasta.gz,fasta.bz2,fa.gz" label="Forward/Left FASTA file" />
				<param name="input2" type="data" format="fasta,fasta.gz,fasta.bz2,fa.gz" label="Reverse/Right FASTA file" />
			</when>
		</conditional>

<!-- new -->

	</inputs>
	<outputs>
                <data format="input1" name="kraken_filtered_r1" label="${tool.name} filtered fwd-reads of ${on_string}" />
                <data format="input2" name="kraken_filtered_r2" label="${tool.name} filtered rev-reads of ${on_string}">
                	<filter>inputFormat == "pairedFastQ" or inputFormat == "pairedFastA</filter>

                </data>
                <data format="txt" name="kraken_filter_log" label="${tool.name} logfile (${on_string})" />
	</outputs>

	<help>
	This tool is a downstream filter for kraken-classified sequences. 
	</help>
</tool>