| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/beagle/beagle/5.2_21Apr21.304+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/beagle/beagle/5.2_21Apr21.304+galaxy0 |
| beagle |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| beagle | 5.2_21Apr21.304 | package |
| Additional information about this tool |
#set out_prefix='out'
#if $optional_inputs.ref
ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext &&
#end if
beagle
gt='${gt}'
#if $optional_inputs.ref
ref=ref.$optional_inputs.ref.ext
#end if
#if $optional_inputs.map
map='${optional_inputs.map}'
#end if
#if $chrom
chrom='${chrom}'
#end if
#if $optional_inputs.excludesamples
excludesamples='${optional_inputs.excludesamples}'
#end if
#if $optional_inputs.excludemarkers
excludemarkers='${optional_inputs.excludemarkers}'
#end if
ne=$ne
window=$window
overlap=$overlap
#if $seed
seed=$seed
#end if
#if $err
err=$err
#end if
burnin=$phasing_parameters.burnin
iterations=$phasing_parameters.iterations
phase-states=$phasing_parameters.phase_states
impute=$imputation_parameters.impute
imp-states=$imputation_parameters.imp_states
imp-segment=$imputation_parameters.imp_segment
imp-step=$imputation_parameters.imp_step
cluster=$imputation_parameters.cluster
ap=$imputation_parameters.ap
gp=$imputation_parameters.gp
out=$out_prefix
nthreads=\${GALAXY_SLOTS:-1}
&& gunzip 'out.vcf.gz'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
gt: test.vcf.gz chrom: 22:100- ne: 1000000 window: 40.0 overlap: 2.0 err: 0.02 seed: 1 output_log: True phasing_parameters|burnin: 3 phasing_parameters|iterations: 12 phasing_parameters|phase_states: 280 |
name: value name: value |
test.vcf.gz value |
| Test-2 |
gt: test.vcf.gz optional_inputs|map: plink.map ne: 1000000 window: 30.0 overlap: 3.0 output_log: True phasing_parameters|burnin: 4 phasing_parameters|iterations: 10 phasing_parameters|phase_states: 250 |
name: value name: value |
test.vcf.gz plink.map value |
| Test-3 |
gt: target.vcf.gz optional_inputs|ref: ref.vcf.gz ne: 1000000 window: 40.0 overlap: 2.0 output_log: True imputation_parameters|impute: True imputation_parameters|imp_states: 1600 imputation_parameters|imp_segment: 6.0 imputation_parameters|imp_step: 0.1 imputation_parameters|cluster: 0.005 imputation_parameters|ap: True imputation_parameters|gp: True |
name: value name: value |
target.vcf.gz ref.vcf.gz value |
| Test-4 |
gt: target.vcf.gz optional_inputs|ref: ref.bref3 ne: 1000000 window: 40.0 overlap: 2.0 imputation_parameters|impute: True imputation_parameters|imp_states: 1600 imputation_parameters|imp_segment: 6.0 imputation_parameters|imp_step: 0.1 imputation_parameters|cluster: 0.005 imputation_parameters|ap: True imputation_parameters|gp: True |
name: value |
target.vcf.gz ref.bref3 value |