| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/plink/plink/1.90b6.21+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/plink/plink/1.90b6.21+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/plink/plink/1.9.b618+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/plink/plink/1.9.b618+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/plink/plink/1.9.b618+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/plink/plink/1.9.b618+galaxy0 |
| plink |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| plink | 1.90b6.21 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputs|inputs|bed: inputs|inputs|filetype: bfile functions|id_list|file: 1.tabular functions|id_list|func: remove functions|extraction|file: testing.txt functions|extraction|range: True functions|extraction|ex_func: exclude functions|snps_exclusives: --snps-only functions|ranges|window|from: snp0 functions|ranges|window|to: snp3 functions|ranges|window|type: variant functions|ranges|single_multi: single functions|thinning|thin_count: 4 functions|thinning|thinning: Yes functions|geno_rates|geno: 0.02 functions|geno_rates|mind: 0.02 functions|allele_freq|maf: 0.01 functions|hwe|hwe_val: 1e-50 functions|hwe|modifiers: ['midp', 'include-nonctrl'] functions|hwe|hwe: Yes functions|sex_founder_filter|sex_select: --filter-cases functions|sex_founder_filter|no_sex_select: --allow-no-sex functions|sex_founder_filter|nonfounders: True functions|sex_founder_filter|filter: Yes functions|func: filtering |
name: value name: value |
1.tabular testing.txt value |
| Test-2 |
inputs|inputs|bed: inputs|inputs|filetype: bfile functions|bmerge|bed: functions|bmerge|set: Yes functions|recode: True functions|template: @asd#123 functions|length: 23 functions|update_cols|input: update_cols.txt functions|update_cols|col_num: 1 functions|update_cols|var_col: 2 functions|update_cols|skip: a functions|update_cols|set: update_name functions|func: data_manage |
name: value name: value name: value name: value |
update_cols.txt value |
| Test-3 |
inputs|inputs|input: test.vcf inputs|inputs|filetype: vcf |
name: value name: value |
test.vcf value |
| Test-4 |
inputs|inputs|bed: inputs|inputs|filetype: bfile functions|freq: True functions|hardy: True functions|missing: True functions|het: True functions|sex|mode|female_max: 0.2 functions|sex|mode|male_min: 0.8 functions|sex|mode|female_max_obvs: 10 functions|sex|mode|male_min_obvs: 200 functions|sex|mode|mode: ycount functions|sex|sex_stats: --check-sex functions|func: stats |
name: value name: value name: value name: value name: value name: value name: value name: value |
value |
| Test-5 |
inputs|inputs|bed: inputs|inputs|filetype: bfile functions|set_indep|window: 51 functions|set_indep|step: 6 functions|set_indep|r2: 0.3 functions|set_indep|choice: Yes functions|func: link |
name: value name: value name: value |
value |
| Test-6 |
inputs|inputs|bed: inputs|inputs|filetype: bfile functions|read_genome: plink.genome functions|cluster|modifiers: ['cc', 'group-avg'] functions|cluster|mds|dimensions: 10 functions|cluster|mds|modifiers: ['eigendecomp', 'eigvals'] functions|cluster|mds|mds_scaling: Yes functions|cluster|cluster: Yes functions|func: stratification |
name: value name: value name: value name: value name: value name: value name: value |
plink.genome value |
| Test-7 |
inputs|inputs|bed: inputs|inputs|filetype: bfile functions|assoc|perm|value: 10000 functions|assoc|perm|perm: mperm functions|assoc|fisher: fisher-midp functions|assoc|assoc: Yes functions|adjust|tests: ['gc', 'log10', 'qq-plot'] functions|adjust|adjust: Yes functions|logistic|perm|perm: perm functions|logistic|genedrop: True functions|logistic|perm_count: True functions|logistic|dominance: dominant functions|logistic|hide_covar: True functions|logistic|beta: True functions|logistic|intercept: True functions|logistic|logistic: Yes functions|lambda: 1.0 functions|func: association |
name: value name: value |
value |
| Test-8 |
inputs|inputs|bed: inputs|inputs|filetype: bfile functions|genome|min: 0.1 functions|genome|max: 0.9 functions|genome|modifiers: ['full', 'unbounded', 'nudge'] functions|genome|output_genome: Yes functions|func: ibd |
name: value name: value |
value |