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<?xml version="1.0"?>

<tool id='nextseq_transfer_convert' name="Transfer and convert NextSeq run" version="1.0.0" hidden="false">
	
	<description>
		Transfer and convert a NextSeq run
	</description>

	<command interpreter="perl">
		copyNextSeq.pl $__tool_data_path__ --run $run_name --user $__user_email__ --toolDir $__tool_data_path__ --out $html_file.files_path --html $html_file --samplesheet $samplesheet --archive $sav_archive
	</command>
	
	<inputs>
		<param name="run_name" type="text" size="40" label="Run Name or Illumina Cartridge Identifier" 
		       help="A text string unique enough to unambiguously identify the autogenerated run name from the sequencer, such as the cartridge barcode (e.g. H35VJBGXX)"/>
		<param name="samplesheet" type="data" format="tabular" label="Illumina Sample Sheet"
		       help="A comma separated spreadsheet with Header, Reads, Settings and Data sections defining the experimental setup, as generated using BaseSpace or Illumina Experiment Manager (IEM) v1.8.2, or later"/> 
	</inputs>

	<outputs>
	       <data format="html" name="html_file" label="FAST QC Web report" />
	       <data format="zip" name="sav_archive" label="SAV files archive" />
	</outputs>
	<help>This tools downloads a NextSeq run from the local machine and performs base call to fastq conversion, followed by QC reports on sample data, including a zipped archive with all the files required to view metrics in Illumina's SAV software.</help>
</tool>