| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.15.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.9+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.9 |
| toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.4.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.3.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.3.0 |
| bcftools_view |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bcftools | 1.10 | package |
| htslib | 1.10 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_file: view.vcf sec_subset|samples: NA00002 sec_filter|min_ac: 1 sec_filter|max_ac: 1 sec_filter|types: snps output_type: v |
name: value |
view.vcf value |
| Test-2 |
input_file: view.bcf sec_subset|samples: NA00002 sec_filter|min_ac: 1 sec_filter|max_ac: 1 sec_filter|types: snps output_type: v |
name: value |
view.bcf value |
| Test-3 |
input_file: view.vcf sec_restrict|regions|regions_0|chrom: Y sec_restrict|regions|regions_0|start: 20 sec_restrict|regions|regions_src: regions sec_subset|samples: NA00003 sec_filter|known_or_novel: --novel sec_filter|private: --exclude-private output_type: v |
name: value |
view.vcf value |
| Test-4 |
input_file: view.vcf sec_restrict|apply_filters: PASS sec_subset|samples: NA00003 sec_filter|known_or_novel: --known sec_filter|private: --exclude-private output_type: v |
name: value |
view.vcf value |
| Test-5 |
input_file: view.vcf sec_subset|samples: NA00003 sec_filter|private: --private output_type: v |
name: value |
view.vcf value |
| Test-6 |
input_file: view.vcf sec_restrict|include: QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2 output_type: v |
name: value |
view.vcf value |
| Test-7 |
input_file: view.vcf sec_filter|phased: --phased output_type: v |
name: value |
view.vcf value |
| Test-8 |
input_file: view.vcf sec_filter|phased: --exclude-phased output_type: v |
name: value |
view.vcf value |
| Test-9 |
input_file: view.vcf sec_filter|min_alleles: 2 sec_filter|max_alleles: 2 sec_filter|min_af: 0.3 sec_filter|max_af: 0.7 sec_output|header: --header-only output_type: v |
name: value |
view.vcf value |
| Test-10 |
input_file: view.vcf sec_filter|uncalled: --uncalled sec_output|header: --no-header output_type: v |
name: value |
view.vcf value |
| Test-11 |
input_file: view.vcf sec_filter|exclude_types: snps sec_output|drop_genotypes: True output_type: v |
name: value |
view.vcf value |
| Test-12 |
input_file: view.vcf sec_filter|select_genotype: ^het sec_filter|phased: --phased output_type: v |
name: value |
view.vcf value |