| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/varscan_copynumber/varscan_copynumber/2.4.3.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/varscan_copynumber/varscan_copynumber/2.4.3.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/varscan_copynumber/varscan_copynumber/2.4.3.0 |
| varscan_copynumber |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| varscan | 2.4.3 | package |
| Additional information about this tool |
varscan copynumber
#if $pileup.pileup_select == 'separated'
'${pileup.normal_pileup}'
'${pileup.tumor_pileup}'
galaxy_out
#else:
'${pileup.combined_pileup}'
galaxy_out
--mpileup 1
#end if
--min-coverage ${min_coverage}
--min-base-qual ${min_base_qual}
--min-map-qual ${min_map_qual}
--min-segment-size ${min_segment_size}
--max-segment-size ${max_segment_size}
--p-value ${p_value}
--data-ratio ${data_ratio}
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
pileup|normal_pileup: N_Region_Chr1_CDKN2C.pileup.gz pileup|tumor_pileup: T_Region_Chr1_CDKN2C.pileup.gz pileup|pileup_select: separated |
name: value |
N_Region_Chr1_CDKN2C.pileup.gz T_Region_Chr1_CDKN2C.pileup.gz value |
| Test-2 |
pileup|combined_pileup: NT.pileup.gz pileup|pileup_select: combined |
name: value |
NT.pileup.gz value |