| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.1+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.0 |
| cshl_fastx_barcode_splitter |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| fastx_toolkit | 0.0.14 | package |
| Additional information about this tool |
mkdir split &&
#if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
gunzip -c -f '$input' |
#elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
bzcat -f '$input' |
#else:
cat '$input' |
#end if
'$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE'
--prefix 'split/'
--suffix
#if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
'.fastqsanger'
#elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2'):
'.fastqsolexa'
#elif $input.is_of_type('fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
'.fastqillumina'
#elif $input.is_of_type('fasta', 'fasta.gz'):
'.fasta'
#else:
'.$input.extension'
#end if
--mismatches $mismatches
--partial $partial
#if $refBarcodeLocation.barcodeLocation == "idxfile":
--idxfile '$refBarcodeLocation.idxfile'
--idxidstrip $refBarcodeLocation.idxidstrip
#else:
$refBarcodeLocation.EOL
#end if
> '$summary'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
BARCODE: fastx_barcode_splitter1.txt input: fastx_barcode_splitter1.fastq refBarcodeLocation|barcodeLocation: bol mismatches: 2 partial: 0 |
name: value |
fastx_barcode_splitter1.txt fastx_barcode_splitter1.fastq value |
| Test-2 |
BARCODE: fastx_barcode_splitter1.txt input: fastx_barcode_splitter1.fastq.gz refBarcodeLocation|barcodeLocation: bol mismatches: 2 partial: 0 |
name: value |
fastx_barcode_splitter1.txt fastx_barcode_splitter1.fastq.gz value |
| Test-3 |
BARCODE: fastx_barcode_splitter1.txt input: fastx_barcode_splitter1.fastq refBarcodeLocation|idxfile: fastx_barcode_splitter_index.fastq refBarcodeLocation|barcodeLocation: idxfile mismatches: 2 partial: 0 |
name: value |
fastx_barcode_splitter1.txt fastx_barcode_splitter1.fastq fastx_barcode_splitter_index.fastq value |