Mercurial > repos > avowinkel > gatk
view haplotype_caller.xml @ 0:b80ff7f43ad1 draft default tip
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
author | avowinkel |
---|---|
date | Thu, 24 Sep 2015 12:10:01 -0400 |
parents | |
children |
line wrap: on
line source
<macros> <xml name="HaplotypeCallerParameters" tokens="tag"> <expand macro="macro_bam_input" tag="@TAG@" /> <conditional name="cond_usage"> <param name="cond_usage_selector" type="select" label="Select usage"> <option value="GVCF">Single-sample all-sites calling on DNAseq (GVCF mode)</option> </param> <when value="GVCF"> <expand macro="HaplotypeCallerGVCF" /> </when> </conditional> <expand macro="macro_optional_parameters"> <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,‑‑sample_ploidy &lt;sample_ploidy&gt;" /> </expand> </xml> <xml name="HaplotypeCallerOutput"> <data format="vcf" name="hc_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string} (gVCF)"> <yield /> </data> </xml> <template name="HaplotypeCallerPreprocessing"> <![CDATA[ @token_bam_input_pre@ ]]> </template> <template name="HaplotypeCallerOptions"> <![CDATA[ --out output.g.vcf @token_bam_input@ #set $optionals = $analysis_type.optional_parameters #if $optionals.optional_parameters_enabled --sample_ploidy $optionals.sample_ploidy #end if #set $usage_selector = $analysis_type.cond_usage.cond_usage_selector #set $usage = $analysis_type.cond_usage #if str($usage_selector) == 'GVCF' --emitRefConfidence "GVCF" #end if ]]> </template> <xml name="HaplotypeCallerGVCF"> <param name="emitRefConfidence" type="select" optional="true" label="Mode for emitting reference confidence scores" help="-ERC,‑‑emitRefConfidence &lt;emitRefConfidence&gt;"> <option value="GVCF">GVCF (Reference model emitted with condensed non-variant blocks)</option> </param> </xml> </macros>