| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/1.2.1 |
| toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/1.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/1.1 |
| toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/1.0 |
| je_markdupes |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| je-suite | 1.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
repeat_slots_1|SLOTS: -2 barcodes|BARCODE_FILE: markdupes_umis.txt adv_options|validation_stringency: LENIENT remove_duplicates: True adv_options|read_name_regex: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. MAX_N: 1 repeat_slots_0|SLOTS: -1 adv_options|comments_0|comment: test-run assume_sorted: True MM: 2 adv_options|optical_duplicate_pixel_distance: 100 adv_options|duplicate_scoring_strategy: SUM_OF_BASE_QUALITIES barcodes|barcode_list_type_con: file inputFile: markdupes_DNase_sorted.bam |
outFile: markdupes_DNase_sorted_marked.bam metrics_file: markdupes_metrics.txt |
markdupes_DNase_sorted.bam markdupes_umis.txt markdupes_DNase_sorted_marked.bam markdupes_metrics.txt |