beagle: beagle.xml annotate

annotate beagle.xml @ 3:d93346789db9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 56eb8eaa7ffcdd9a4de1b9c7fb6459a049c7a416

author	iuc
date	Fri, 16 May 2025 18:50:59 +0000
parents	ab97b3b44590
children

rev	line source
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	1 <tool id='beagle' name='Beagle' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='23.0'>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	2 <description>phasing genotypes and imputing ungenotyped markers</description>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	3 <macros>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	4 <import>macros.xml</import>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	5 </macros>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	6 <expand macro='edam_ontology' />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	7 <expand macro='requirements' />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	8 <command detect_errors='exit_code'><![CDATA[
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	9 #set out_prefix='out'
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	10 #if $optional_inputs.ref
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	11 ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext &&
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	12 #end if
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	13 #if $gt.ext=="vcf_bgzip"
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	14 ln -s '$gt' tmp.gz &&
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	15 #end if
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	16 beagle
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	17 #if $gt.ext=="vcf_bgzip"
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	18 gt=tmp.gz
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	19 #else
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	20 gt='${gt}'
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	21 #end if
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	22 #if $optional_inputs.ref
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	23 ref=ref.$optional_inputs.ref.ext
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	24 #end if
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	25 #if $optional_inputs.map
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	26 map='${optional_inputs.map}'
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	27 #end if
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	28 #if $chrom
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	29 chrom='${chrom}'
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	30 #end if
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	31 #if $optional_inputs.excludesamples
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	32 excludesamples='${optional_inputs.excludesamples}'
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	33 #end if
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	34 #if $optional_inputs.excludemarkers
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	35 excludemarkers='${optional_inputs.excludemarkers}'
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	36 #end if
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	37 ne=$ne
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	38 window=$window
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	39 overlap=$overlap
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	40 #if $seed
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	41 seed=$seed
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	42 #end if
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	43 #if $err
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	44 err=$err
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	45 #end if
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	46 burnin=$phasing_parameters.burnin
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	47 iterations=$phasing_parameters.iterations
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	48 phase-states=$phasing_parameters.phase_states
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	49 impute=$imputation_parameters.impute
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	50 imp-states=$imputation_parameters.imp_states
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	51 imp-segment=$imputation_parameters.imp_segment
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	52 imp-step=$imputation_parameters.imp_step
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	53 cluster=$imputation_parameters.cluster
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	54 ap=$imputation_parameters.ap
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	55 gp=$imputation_parameters.gp
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	56 out=$out_prefix
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	57 nthreads=\${GALAXY_SLOTS:-1}
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	58 #if $out_format == "vcf_bgzip"
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	59 && mv out.vcf.gz '$vcf_file'
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	60 #else
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	61 && echo "decompressing beagle output"
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	62 && gunzip 'out.vcf.gz'
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	63 && mv out.vcf '$vcf_file'
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	64 #end if
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	65 ]]> </command>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	66 <inputs>
3 d93346789db9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 56eb8eaa7ffcdd9a4de1b9c7fb6459a049c7a416 iuc parents: 2 diff changeset	67 <param argument="gt" type="data" format="vcf,vcf_bgzip" label="VCF file"
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	68 help="It specifies a VCF file containing genotypes for the study samples.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	69 Each VCF record must contain a GT (genotype) format field"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	70 <section name="optional_inputs" title="Optional input files" expanded="true">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	71 <param argument="ref" type="data" format="vcf,bref3" optional="true" label="Bref3 or VCF file with phased genotypes"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	72 help="Each genotype must have two phased, non-missing alleles. If a VCF file is specified, the
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	73 phased allele separator must be used '\|'"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	74 <param argument="map" type="data" format="txt" optional="true" label="PLINK map file with cM units"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	75 help="Beagle uses linear interpolation to estimate genetic positions between map positions. If
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	76 no genetic map is specified, Beagle assumes a constant recombination rate of 1 cM per Mb"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	77 <param argument="excludesamples" type="data" format="txt" optional="true" label="Samples to exclude"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	78 help="It specifies a file containing samples (one sample identifier per line) to be excluded
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	79 from the analysis" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	80 <param argument="excludemarkers" type="data" format="txt" optional="true" label="Markers to exclude"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	81 help="It specifies a file containing markers (one marker per line) to be excluded from the
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	82 analysis. Each line of the file can be either an identifier from a VCF record’s ID field
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	83 or a genomic coordinate in the format: CHROM:POS" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	84 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	85 <param argument="chrom" type="text" optional="true" label="Specify a chromosome interval"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	86 help="Input format: [chrom]:[start]-[end]. The entire chromosome, the beginning, or the end may be
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	87 specified by chrom=[chrom], chrom=[chrom]:-[end], and chrom=[chrom]:[start]-, respectively">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	88 <sanitizer invalid_char="">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	89 <valid initial="string.letters,string.digits">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	90 <add value=":" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	91 <add value="-" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	92 </valid>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	93 </sanitizer>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	94 <validator type="regex">[0-9a-zA-Z:-]+</validator>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	95 </param>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	96 <param argument="ne" type="integer" min="0" value="1000000" label="Effective population size"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	97 help="The default value is suitable for a large, outbred population. It is needed to specify an
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	98 appropriate effective populations size if you are imputing ungenotyped markers in a small
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	99 or inbred population"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	100 <param argument="window" type="float" min="0" value="40.0" label="Window length in cM"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	101 help="The window parameter must be at least 1.1 times as large as the overlap parameter.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	102 The window parameter controls the amount of memory required for the analysis"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	103 <param argument="overlap" type="float" min="0" value="2.0" label="Window overlap in cM"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	104 help="It specifies the cM length of overlap between adjacent sliding windows"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	105 <param argument="err" type="float" min="0" max="1" optional="true"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	106 label="Allele mismatch probability for the hidden Markov model"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	107 help="If no err parameter is specified, the err parameter will be set equal 𝜃/(2(𝜃 + 𝐻))
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	108 where 𝜃 = 1/(0.5 + ln 𝐻) and 𝐻 is the number of haplotypes"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	109 <param argument="seed" type="integer" value="" optional="true" label="Random seed"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	110 help="A random seed is a number used to initialize a pseudorandom number generator" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	111 <param name="output_log" type="boolean" checked="false" label="Output a log file"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	112 <section name="phasing_parameters" title="Phasing parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	113 <param argument="burnin" type="integer" min="0" value="3" label="Max burnin iterations"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	114 help="It is the maximum number of burnin iterations used to estimate an initial haplotype
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	115 frequency model for inferring genotype phase" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	116 <param argument="iterations" type="integer" min="0" value="12" label="Phasing iterations"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	117 help="It is the number of iterations used to estimate genotype phase. Increasing this
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	118 parameter will trade increased computation time for increased phasing accuracy" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	119 <param argument="phase-states" type="integer" min="0" value="280" label="Model states for phasing"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	120 help="It is the number of model states used to estimate genotype phase" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	121 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	122 <section name="imputation_parameters" title="Imputation parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	123 <param argument="impute" type="boolean" truevalue="true" falsevalue="false"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	124 checked="true" label="Impute ungenotyped markers"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	125 help="It specifies whether markers that are present in the reference panel but absent in
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	126 that target will be imputed. This option has no effect if no reference panel is specified"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	127 <param argument="imp-states" type="integer" min="0" value="1600" label="Model states for imputation"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	128 help="It is the number of model states used to impute ungenotyped markers" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	129 <param argument="imp-segment" type="float" min="0" value="6.0" label="Minimum cM length of haplotype segments"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	130 help="It is the minimum cM length of haplotype segments that will be incorporated in the HMM state
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	131 space for a target haplotype." />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	132 <param argument="imp-step" type="float" min="0" value="0.1" label="Length in cM for detecting short IBS segments"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	133 help="It is the length in cM of the step used for detecting short IBS segments" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	134 <param argument="cluster" type="float" min="0" value="0.005" label="Max cM in a marker cluster"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	135 help="It specifies the maximum cM distance between individual markers that are combined
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	136 into an aggregate marker when imputing ungenotyped markers" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	137 <param argument="ap" type="boolean" truevalue="true" falsevalue="false"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	138 checked="false" label="Include posterior allele probabilities"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	139 help="It specifies whether AP1 and AP2 (allele probability) fields will be included in the output
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	140 VCF file when imputing ungenotyped markers" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	141 <param argument="gp" type="boolean" truevalue="true" falsevalue="false"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	142 checked="false" label="Include posterior genotype probabilities"
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	143 help="It specifies whether a GP (genotype probability) format field will be included in the output
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	144 VCF file when imputing ungenotyped markers. Genotype probabilities are calculated from allele
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	145 probabilities assuming Hardy-Weinberg Equilibrium. Consequently, the alleles in the genotype
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	146 with highest genotype probability may occasionally be different than the genotype obtained by
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	147 taking the allele with highest probability on each haplotype, which is the genotype reported
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	148 in the GT format field" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	149 </section>
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	150 <param name="out_format" type="select" label="Output data type ">
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	151 <option value="vcf" selected="true">VCF</option>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	152 <option value="vcf_bgzip">Compressed VCF (bgzip)</option>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	153 </param>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	154 </inputs>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	155 <outputs>
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	156 <data name="vcf_file" format="vcf" label="${tool.name} on ${on_string}: VCF file">
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	157 <change_format>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	158 <when input="out_format" value="vcf_bgzip" format="vcf_bgzip" />
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	159 </change_format>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	160 </data>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	161 <data name="log_file" format="txt" from_work_dir="out.log" label="${tool.name} on ${on_string}: log file">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	162 <filter>output_log</filter>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	163 </data>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	164 </outputs>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	165 <tests>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	166 <!-- Test default values -->
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	167 <test expect_num_outputs="2">
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	168 <param name="gt" value="test.vcf.gz" ftype="vcf"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	169 <param name="chrom" value="22:100-"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	170 <param name="ne" value="1000000"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	171 <param name="window" value="40.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	172 <param name="overlap" value="2.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	173 <param name="err" value="0.02"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	174 <param name="seed" value="1"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	175 <param name="output_log" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	176 <section name="phasing_parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	177 <param name="burnin" value="3"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	178 <param name="iterations" value="12"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	179 <param name="phase_states" value="280"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	180 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	181 <output name="vcf_file" file="test_output.vcf" ftype="vcf" lines_diff="3"/>
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	182 <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16">
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	183 <assert_contents>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	184 <has_text text="WARNING" negate="true"/>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	185 </assert_contents>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	186 </output>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	187 </test>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	188 <!-- Test plink file-->
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	189 <test expect_num_outputs="2">
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	190 <param name="gt" value="test.vcf.gz" ftype="vcf"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	191 <param name="ne" value="1000000"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	192 <param name="window" value="30.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	193 <param name="overlap" value="3.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	194 <param name="output_log" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	195 <section name="optional_inputs">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	196 <param name="map" value="plink.map"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	197 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	198 <section name="phasing_parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	199 <param name="burnin" value="4"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	200 <param name="iterations" value="10"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	201 <param name="phase_states" value="250"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	202 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	203 <output name="vcf_file" ftype="vcf">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	204 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	205 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	206 <has_size value="181410"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	207 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	208 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	209 <output name="log_file" ftype="txt">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	210 <assert_contents>
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	211 <has_text text="Study markers: 223"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	212 <has_size value="1696" delta="100"/>
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	213 <has_text text="WARNING" negate="true"/>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	214 <has_text_matching expression="beagle.*jar finished"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	215 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	216 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	217 </test>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	218 <!-- Test ref VCF input -->
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	219 <test expect_num_outputs="2">
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	220 <param name="gt" value="target.vcf.gz" ftype="vcf"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	221 <param name="ne" value="1000000"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	222 <param name="window" value="40.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	223 <param name="overlap" value="2.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	224 <param name="output_log" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	225 <section name="optional_inputs">
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	226 <param name="ref" value="ref.vcf.gz" ftype="vcf"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	227 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	228 <section name="imputation_parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	229 <param name="impute" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	230 <param name="imp_states" value="1600"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	231 <param name="imp_segment" value="6.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	232 <param name="imp_step" value="0.1"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	233 <param name="cluster" value="0.005"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	234 <param name="ap" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	235 <param name="gp" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	236 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	237 <output name="vcf_file" ftype="vcf">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	238 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	239 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	240 <has_size value="18773"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	241 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	242 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	243 <output name="log_file" ftype="txt">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	244 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	245 <has_text text="Reference markers: 223"/>
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	246 <has_size value="1754" delta="100"/>
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	247 <has_text text="WARNING" negate="true"/>
d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	248 <has_text_matching expression="beagle.*jar finished"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	249 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	250 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	251 </test>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	252 <!-- Test ref bref3 input -->
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	253 <test expect_num_outputs="1">
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	254 <param name="gt" value="target.vcf.gz" ftype="vcf"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	255 <param name="ne" value="1000000"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	256 <param name="window" value="40.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	257 <param name="overlap" value="2.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	258 <section name="optional_inputs">
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	259 <param name="ref" value="ref.bref3" ftype="bref3"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	260 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	261 <section name="imputation_parameters">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	262 <param name="impute" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	263 <param name="imp_states" value="1600"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	264 <param name="imp_segment" value="6.0"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	265 <param name="imp_step" value="0.1"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	266 <param name="cluster" value="0.005"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	267 <param name="ap" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	268 <param name="gp" value="true"/>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	269 </section>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	270 <output name="vcf_file" ftype="vcf">
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	271 <assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	272 <has_text text='ID=GT,Number=1,Type=String,Description="Genotype"'/>
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	273 <has_size value="18773"/>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	274 </assert_contents>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	275 </output>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	276 </test>
2 ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	277 <!-- Test vcf_bgzip output -->
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	278 <test expect_num_outputs="1">
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	279 <param name="gt" value="test.vcf.gz" ftype="vcf"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	280 <param name="chrom" value="22:100-"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	281 <param name="ne" value="1000000"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	282 <param name="window" value="40.0"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	283 <param name="overlap" value="2.0"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	284 <param name="err" value="0.02"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	285 <param name="seed" value="1"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	286 <section name="phasing_parameters">
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	287 <param name="burnin" value="3"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	288 <param name="iterations" value="12"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	289 <param name="phase_states" value="280"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	290 </section>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	291 <param name="out_format" value="vcf_bgzip"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	292 <output name="vcf_file" ftype="vcf_bgzip" file="test_output.vcf.gz" compare="sim_size" delta="500"/>
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	293
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8 iuc parents: 1 diff changeset	294 </test>
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	295 </tests>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	296 <help><![CDATA[
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	297 .. class:: infomark
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	298
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	299 Purpose
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	300
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	301 Beagle is a program for phasing and imputing missing genotypes. Sporadic missing
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	302 genotypes are imputed during phasing. If a reference panel of phased genotypes is specified
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	303 with the ref argument, ungenotyped markers that are present in the reference panel can also
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	304 be imputed.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	305
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	306 Beagle version 5.2 provides significantly faster genotype phasing than version 5.1.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	307 Recent versions of Beagle do not infer genotypes from genotype likelihood input data, but
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	308 Beagle versions 4.0 and 4.1 have this capability.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	309
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	310 ----
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	311
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	312 .. class:: infomark
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	313
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	314 HapMap genetic maps
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	315
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	316 HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available
1 d0a6954d0a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8 iuc parents: 0 diff changeset	317 in `this links <https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_
0 117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	318
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	319 ----
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	320
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	321 .. class:: infomark
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	322
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	323 Input files
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	324
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	325 Beagle uses `Variant Call Format <http://faculty.washington.edu/browning/beagle/intro-to-vcf.html>`_
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	326 (VCF) 4.3 for input and output genotype data. Pseuodoautosomal and non-pseudoautosomal
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	327 X-chromosome genotypes must be in separate input files and analysed separately unless male
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	328 haploid genotypes are coded as homozygous diploid genotypes.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	329
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	330 In the VCF file, if any heterozygote genotype is unphased (with "/" allele separator) in a marker window,
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	331 it will consider all heterozygote genotypes to be unphased, regardless of the allele separator used ("\|" or "/").
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	332 Beagle assumes that an the VCF file has a name ending in ".gz" is compressed with gzip or bgzip,
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	333 and that a reference VCF file that has a name ending in “.bref3” is compressed with bref version 3.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	334
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	335 ----
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	336
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	337 .. class:: infomark
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	338
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	339 Output files
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	340
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	341 There are two output files. The log file gives a summary of the analysis that includes the
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	342 Beagle version, the command line arguments, and compute time.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	343
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	344 The vcf.gz file is a bgzip-compressed VCF file that contains phased, non-missing
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	345 genotypes for all non-reference samples. The output vcf.gz file can be uncompressed with the
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	346 unix gunzip utility.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	347
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	348 If a reference panel is specified and ungenotyped markers are imputed, the VCF INFO
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	349 field will contain:
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	350
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	351 ::
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	352
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	353 - A "DR2" subfield with the estimated squared correlation between the estimated allele dose and the true allele dose.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	354 - An "AF" subfield with the estimated alternate allele frequencies in the target samples.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	355 - The "IMP" flag if the marker is imputed.
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	356
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	357 ]]> </help>
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	358 <expand macro="citations" />
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" iuc parents: diff changeset	359 </tool>

Mercurial > repos > iuc > beagle

annotate beagle.xml @ 3:d93346789db9 draft default tip