view kraken_combine.xml @ 14:fd27c97c8366 draft default tip

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<tool id="kraken_combine" name="kraken_combine">
	<description>extract unique and common sequences from two kraken runs</description>
	<requirements>
		<requirement type="package" version="2.7">python</requirement>
	</requirements>
	<command interpreter="python">kraken_combine.py
		--in1="${dataFormat.input1}"
		--set1-output-left=${set1OutputLeft}
		--set2-output-left=${set2OutputLeft}
		--unclassified-output-left=${unclassifiedOutputLeft}
		--intersection-output-left=${intersectionOutputLeft}
		--kraken-results1="${classificationSet1}"
		--kraken-results2="${classificationSet2}"

		#if $dataFormat.inputFormat == "pairedFASTQ" or $dataFormat.inputFormat == "pairedFASTA":
			--in2="${dataFormat.input2}"
			--set1-output-right=${set1OutputRight}
			--set2-output-right=${set2OutputRight}
			--unclassified-output-right=${unclassifiedOutputRight}
			--intersection-output-right=${intersectionOutputRight}
		#end if

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



	</command>
	<inputs>
		<param name="classificationSet1" type="data" format="tabular" label="Kraken classification output set1" />
		<param name="classificationSet2" type="data" format="tabular" label="Kraken classification output set2" />
	
		<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>
	</inputs>

	<outputs>
		<data format="input1" name="set1OutputLeft" label="Taxonomy1-unique sequences (R1) of ${on_string}" />
		<data format="input1" name="set2OutputLeft" label="Taxonomy2-unique sequences (R1) of ${on_string}" />
		<data format="input1" name="intersectionOutputLeft" label="Common sequences (R1) of ${on_string}" />
		<data format="input1" name="unclassifiedOutputLeft" label="Unclassified sequences (R1) of ${on_string}" />

		<data format="input2" name="set1OutputRight" label="Taxonomy1-unique sequences (R2) of ${on_string}">
			<filter>inputFormat == "pairedFASTQ" or inputFormat == "pairedFASTA"</filter>
		</data>
		<data format="input2" name="set2OutputRight" label="Taxonomy2-unique sequences (R2) of ${on_string}">
			<filter>inputFormat == "pairedFASTQ" or inputFormat == "pairedFASTA"</filter>
		</data>
		<data format="input2" name="intersectionOutputRight" label="Common sequences (R2) of ${on_string}">
			<filter>inputFormat == "pairedFASTQ" or inputFormat == "pairedFASTA"</filter>
		</data>
		<data format="input2" name="unclassifiedOutputRight" label="Unclassified sequences (R2) of ${on_string}">
			<filter>inputFormat == "pairedFASTQ" or inputFormat == "pairedFASTA"</filter>
		</data>
	</outputs>

	<help>
	This tool compares the classification results on a dataset using two different kraken-databases.
	</help>
</tool>