Mercurial > repos > avowinkel > gatk

annotate haplotype_caller.xml @ 0:b80ff7f43ad1 draft default tip

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author avowinkel
date Thu, 24 Sep 2015 12:10:01 -0400
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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1 <macros>
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2 <xml name="HaplotypeCallerParameters" tokens="tag">
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4 <expand macro="macro_bam_input" tag="@TAG@" />
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6 <conditional name="cond_usage">
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7 <param name="cond_usage_selector" type="select" label="Select usage">
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8 <option value="GVCF">Single-sample all-sites calling on DNAseq (GVCF mode)</option>
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9 </param>
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10 <when value="GVCF">
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11 <expand macro="HaplotypeCallerGVCF" />
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12 </when>
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13 </conditional>
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15 <expand macro="macro_optional_parameters">
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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,&#8209;&#8209;sample_ploidy &amp;lt;sample_ploidy&amp;gt;" />
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19 </expand>
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21 </xml>
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23 <xml name="HaplotypeCallerOutput">
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24 <data format="vcf" name="hc_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string} (gVCF)">
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25 <yield />
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26 </data>
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27 </xml>
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29 <template name="HaplotypeCallerPreprocessing">
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30 <![CDATA[
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31 @token_bam_input_pre@
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32 ]]>
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33 </template>
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35 <template name="HaplotypeCallerOptions">
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36 <![CDATA[
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37 --out output.g.vcf
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39 @token_bam_input@
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41 #set $optionals = $analysis_type.optional_parameters
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42 #if $optionals.optional_parameters_enabled
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43 --sample_ploidy $optionals.sample_ploidy
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44 #end if
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46 #set $usage_selector = $analysis_type.cond_usage.cond_usage_selector
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47 #set $usage = $analysis_type.cond_usage
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49 #if str($usage_selector) == 'GVCF'
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50 --emitRefConfidence "GVCF"
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51 #end if
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52 ]]>
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53 </template>
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57 <xml name="HaplotypeCallerGVCF">
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58 <param name="emitRefConfidence" type="select" optional="true" label="Mode for emitting reference confidence scores" help="-ERC,‑‑emitRefConfidence &amp;lt;emitRefConfidence&amp;gt;">
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59 <option value="GVCF">GVCF (Reference model emitted with condensed non-variant blocks)</option>
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60 </param>
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61 </xml>
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63 </macros>
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