Mercurial > repos > avowinkel > gatk
comparison 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 |
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| children |
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| -1:000000000000 | 0:b80ff7f43ad1 |
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| 1 <macros> | |
| 2 <xml name="HaplotypeCallerParameters" tokens="tag"> | |
| 3 | |
| 4 <expand macro="macro_bam_input" tag="@TAG@" /> | |
| 5 | |
| 6 <conditional name="cond_usage"> | |
| 7 <param name="cond_usage_selector" type="select" label="Select usage"> | |
| 8 <option value="GVCF">Single-sample all-sites calling on DNAseq (GVCF mode)</option> | |
| 9 </param> | |
| 10 <when value="GVCF"> | |
| 11 <expand macro="HaplotypeCallerGVCF" /> | |
| 12 </when> | |
| 13 </conditional> | |
| 14 | |
| 15 <expand macro="macro_optional_parameters"> | |
| 16 | |
| 17 <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;" /> | |
| 18 | |
| 19 </expand> | |
| 20 | |
| 21 </xml> | |
| 22 | |
| 23 <xml name="HaplotypeCallerOutput"> | |
| 24 <data format="vcf" name="hc_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string} (gVCF)"> | |
| 25 <yield /> | |
| 26 </data> | |
| 27 </xml> | |
| 28 | |
| 29 <template name="HaplotypeCallerPreprocessing"> | |
| 30 <![CDATA[ | |
| 31 @token_bam_input_pre@ | |
| 32 ]]> | |
| 33 </template> | |
| 34 | |
| 35 <template name="HaplotypeCallerOptions"> | |
| 36 <![CDATA[ | |
| 37 --out output.g.vcf | |
| 38 | |
| 39 @token_bam_input@ | |
| 40 | |
| 41 #set $optionals = $analysis_type.optional_parameters | |
| 42 #if $optionals.optional_parameters_enabled | |
| 43 --sample_ploidy $optionals.sample_ploidy | |
| 44 #end if | |
| 45 | |
| 46 #set $usage_selector = $analysis_type.cond_usage.cond_usage_selector | |
| 47 #set $usage = $analysis_type.cond_usage | |
| 48 | |
| 49 #if str($usage_selector) == 'GVCF' | |
| 50 --emitRefConfidence "GVCF" | |
| 51 #end if | |
| 52 ]]> | |
| 53 </template> | |
| 54 | |
| 55 | |
| 56 | |
| 57 <xml name="HaplotypeCallerGVCF"> | |
| 58 <param name="emitRefConfidence" type="select" optional="true" label="Mode for emitting reference confidence scores" help="-ERC,‑‑emitRefConfidence &lt;emitRefConfidence&gt;"> | |
| 59 <option value="GVCF">GVCF (Reference model emitted with condensed non-variant blocks)</option> | |
| 60 </param> | |
| 61 </xml> | |
| 62 | |
| 63 </macros> | |
| 64 | |
| 65 |