Mercurial > repos > yusuf > transfer_convert_nextseq
comparison transfer_convert_nextseq.xml @ 0:d4ac6e05c96c default tip
initial commit
| author | Yusuf Ali <ali@yusuf.email> |
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| date | Wed, 25 Mar 2015 13:43:47 -0600 |
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| -1:000000000000 | 0:d4ac6e05c96c |
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| 1 <?xml version="1.0"?> | |
| 2 | |
| 3 <tool id='nextseq_transfer_convert' name="Transfer and convert NextSeq run" version="1.0.0" hidden="false"> | |
| 4 | |
| 5 <description> | |
| 6 Transfer and convert a NextSeq run | |
| 7 </description> | |
| 8 | |
| 9 <command interpreter="perl"> | |
| 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 | |
| 11 </command> | |
| 12 | |
| 13 <inputs> | |
| 14 <param name="run_name" type="text" size="40" label="Run Name or Illumina Cartridge Identifier" | |
| 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)"/> | |
| 16 <param name="samplesheet" type="data" format="tabular" label="Illumina Sample Sheet" | |
| 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"/> | |
| 18 </inputs> | |
| 19 | |
| 20 <outputs> | |
| 21 <data format="html" name="html_file" label="FAST QC Web report" /> | |
| 22 <data format="zip" name="sav_archive" label="SAV files archive" /> | |
| 23 </outputs> | |
| 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> | |
| 25 </tool> |