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author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:43:47 -0600
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1 <?xml version="1.0"?>
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2
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3 <tool id='nextseq_transfer_convert' name="Transfer and convert NextSeq run" version="1.0.0" hidden="false">
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4
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5 <description>
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6 Transfer and convert a NextSeq run
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7 </description>
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8
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9 <command interpreter="perl">
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10 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
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11 </command>
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12
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13 <inputs>
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14 <param name="run_name" type="text" size="40" label="Run Name or Illumina Cartridge Identifier"
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15 help="A text string unique enough to unambiguously identify the autogenerated run name from the sequencer, such as the cartridge barcode (e.g. H35VJBGXX)"/>
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16 <param name="samplesheet" type="data" format="tabular" label="Illumina Sample Sheet"
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17 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"/>
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18 </inputs>
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19
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20 <outputs>
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21 <data format="html" name="html_file" label="FAST QC Web report" />
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22 <data format="zip" name="sav_archive" label="SAV files archive" />
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23 </outputs>
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24 <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>
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25 </tool>