Mercurial > repos > iuc > strelka_somatic

annotate strelka_somatic.xml @ 0:c06e033242df draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
author iuc
date Wed, 27 Jan 2021 14:46:27 +0000
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c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
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1 <?xml version="1.0"?>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
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2 <tool id="strelka_somatic" name="Strelka Somatic" version="@TOOL_VERSION@+@GALAXY_VERSION@">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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3 <description>@DESCRIPTION@ for somatic variation in tumor/normal sample pairs</description>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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4 <macros>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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5 <import>macros.xml</import>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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6 </macros>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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7 <expand macro="requirements"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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8 <command detect_errors="exit_code"><![CDATA[
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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9 ## initialize
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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10 #if $normalBam.is_of_type('bam')
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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11 ln -s '$normalBam' './input_normal.bam' &&
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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12 ln -s '$normalBam.metadata.bam_index' './input_normal.bam.bai' &&
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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13 #elif $normalBam.is_of_type('cram')
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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14 ln -s '$normalBam' './input_normal.cram' &&
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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15 ln -s '$normalBam.metadata.cram_index' './input_normal.cram.crai' &&
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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16 #end if
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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17 #if $tumorBam.is_of_type('bam')
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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18 ln -s '$tumorBam' './input_tumor.bam' &&
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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19 ln -s '$tumorBam.metadata.bam_index' './input_tumor.bam.bai' &&
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
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20 #elif $tumorBam.is_of_type('cram')
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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21 ln -s '$tumorBam' './input_tumor.cram' &&
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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22 ln -s '$tumorBam.metadata.cram_index' './input_tumor.cram.crai' &&
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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23 #end if
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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24 @INIT@
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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25
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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26 ## create workflow
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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27 configureStrelkaSomaticWorkflow.py
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
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28 #if $normalBam.is_of_type('bam')
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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29 --normalBam ./input_normal.bam
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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30 #elif $normalBam.is_of_type('cram')
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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31 --normalBam ./input_normal.cram
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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32 #end if
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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33 #if $tumorBam.is_of_type('bam')
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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34 --tumorBam ./input_tumor.bam
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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35 #elif $tumorBam.is_of_type('cram')
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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36 --tumorBam ./input_tumor.cram
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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37 #end if
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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38 $oo.outputCallableRegions
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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39 @CREATE@
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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40
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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41 ## run workflow
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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42 @RUN@
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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43
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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44 ## decompress results if needed and move everything to final destinations
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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45 #if $oo.vcf_type == "decompressed"
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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46 && bgzip -d results/results/variants/somatic.indels.vcf.gz
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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47 && bgzip -d results/results/variants/somatic.snvs.vcf.gz
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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48 && mv results/results/variants/somatic.indels.vcf '$out_indels'
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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49 && mv results/results/variants/somatic.snvs.vcf '$out_snvs'
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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50 #else
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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51 && mv results/results/variants/somatic.indels.vcf.gz '$out_indels'
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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52 && mv results/results/variants/somatic.snvs.vcf.gz '$out_snvs'
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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53 #end if
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
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54 #if $oo.outputCallableRegions
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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55 && bgzip -d results/results/regions/somatic.callable.regions.bed.gz
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
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56 && mv results/results/regions/somatic.callable.regions.bed '$out_callable'
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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57 #end if
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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58
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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59 ]]></command>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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60 <configfiles>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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61 <configfile name="config_file">
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62 ## parser cannot handle indents
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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63 [StrelkaSomatic]
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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64 depthFilterMultiple = $strelka.depthFilterMultiple
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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65 snvMaxFilteredBasecallFrac = $strelka.snvMaxFilteredBasecallFrac
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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66 snvMaxSpanningDeletionFrac = $strelka.snvMaxSpanningDeletionFrac
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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67 indelMaxWindowFilteredBasecallFrac = $strelka.indelMaxWindowFilteredBasecallFrac
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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68 ssnvPrior = $strelka.ssnvPrior
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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69 sindelPrior = $strelka.sindelPrior
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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70 ssnvNoise = $strelka.ssnvNoise
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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71 sindelNoiseFactor = $strelka.sindelNoiseFactor
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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72 ssnvNoiseStrandBiasFrac = $strelka.ssnvNoiseStrandBiasFrac
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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73 minTier1Mapq = $strelka.minTier1Mapq
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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74 minTier2Mapq = $strelka.minTier2Mapq
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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75 ssnvQuality_LowerBound = $strelka.ssnvQuality_LowerBound
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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76 sindelQuality_LowerBound = $strelka.sindelQuality_LowerBound
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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77 ssnvContamTolerance = $strelka.ssnvContamTolerance
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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78 indelContamTolerance = $strelka.indelContamTolerance
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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79 @CONFIG@
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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80 </configfile>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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81 </configfiles>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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82 <inputs>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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83 <param argument="--normalBam" type="data" format="bam,cram" multiple="false" label="Select normal sample file" help="In bam or cram format."/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
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84 <param argument="--tumorBam" type="data" format="bam,cram" multiple="false" label="Select tumor sample file" help="In bam or cram format."/>
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85 <expand macro="input_required"/>
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86 <expand macro="calling_model" />
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87 <expand macro="calling_model_expert" />
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88 <expand macro="regions_select" />
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89
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90 <section name="oo" title="Output options" expanded="false">
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91 <expand macro="input_output"/>
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92 <param argument="--outputCallableRegions" type="boolean" checked="false" truevalue="--outputCallableRegions" falsevalue="" label="Generate bed file describing somatic callable regions of the genome" help=""/>
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93 </section>
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94
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95 <section name="strelka" title="Strelka run configuration" expanded="false">
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96 <expand macro="input_strelka"/>
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97 <param argument="depthFilterMultiple" type="float" value="3.0" label="Set depthFilterMultiple" help="If the depth filter is not skipped, all variants which occur at a depth greater than depthFilterMultiple*chromosome mean depth will be filtered out."/>
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98 <param argument="snvMaxFilteredBasecallFrac" type="float" value="0.4" min="0.0" max="1.0" label="Set snvMaxFilteredBasecallFrac" help="Somatic SNV calls are filtered at sites where greater than this fraction of basecalls have been removed by the mismatch density filter in either sample."/>
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99 <param argument="snvMaxSpanningDeletionFrac" type="float" value="0.75" min="0.0" max="1.0" label="Set snvMaxSpanningDeletionFrac" help="Somatic SNV calls are filtered at sites where greater than this fraction of overlapping reads contain deletions which span the SNV call site."/>
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100 <param argument="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" min="0.0" max="1.0" label="Set indelMaxWindowFilteredBasecallFrac" help="Somatic indel calls are filtered if greater than this fraction of basecalls in a window extending 50 bases to each side of an indel's call position have been removed by the mismatch density filter."/>
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101 <param argument="ssnvPrior" type="float" value="0.0001" min="0.0" label="Set ssnvPrior" help="Prior probability of a somatic snv or indel."/>
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102 <param argument="sindelPrior" type="float" value="0.000001" min="0.0" label="Set sindelPrior" help="Prior probability of a somatic snv or indel."/>
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103 <param argument="ssnvNoise" type="float" value="0.0000000005" min="0.0" label="Set ssnvNoise" help="Probability of an snv or indel noise allele NB: in the calling model a noise allele is shared in tumor and normal samples, but occurs at any frequency."/>
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104 <param argument="sindelNoiseFactor" type="float" value="2.2" label="Set sindelNoiseFactor" help="Somatic indel noise factor."/>
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105 <param argument="ssnvNoiseStrandBiasFrac" type="float" value="0.0" min="0.0" max="1.0" label="Set ssnvNoiseStrandBiasFrac" help="Fraction of snv noise attributed to strand-bias. It is not recommended to change this setting. However, if it is essential to turn the strand bias penalization off, the following is recommended: Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5, (1) set ssnvNoiseStrandBiasFrac = 0 (2) divide the current ssnvNoise value by 2."/>
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106 <param argument="minTier1Mapq" type="integer" value="20" label="Set minTier1Mapq" help="Minimum MAPQ score for reads at tier1."/>
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107 <param argument="minTier2Mapq" type="integer" value="0" label="Set minTier2Mapq" help="Minimum MAPQ score for reads at tier2."/>
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108 <param argument="ssnvQuality_LowerBound" type="integer" value="15" label="Set ssnvQuality_LowerBound" help="Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are marked as filtered."/>
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109 <param argument="sindelQuality_LowerBound" type="integer" value="40" label="Set sindelQuality_LowerBound" help="Somatic quality score (QSI_NT, NT=ref) below which somatic indels are marked as filtered."/>
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110 <param argument="ssnvContamTolerance" type="float" value="0.15" min="0.0" max="1.0" label="Set ssnvContamTolerance" help="Tolerance of tumor contamination in the normal sample."/>
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111 <param argument="indelContamTolerance" type="float" value="0.15" min="0.0" max="1.0" label="Set indelContamTolerance" help="Tolerance of tumor contamination in the normal sample."/>
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112 </section>
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113 </inputs>
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114 <outputs>
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115 <data name="out_indels" format="vcf" label="${tool.name} on ${on_string}, Indels, vcf">
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116 <change_format>
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117 <when input="oo.vcf_type" value="compressed" format="vcf_bgzip" />
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118 </change_format>
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119 </data>
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120 <data name="out_snvs" format="vcf" label="${tool.name} on ${on_string}, SNVs, vcf">
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121 <change_format>
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122 <when input="oo.vcf_type" value="compressed" format="vcf_bgzip" />
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123 </change_format>
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124 </data>
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125 <data name="out_callable" format="bed" label="${tool.name} on ${on_string}, Callable regions, bed">
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126 <filter>bool(oo['outputCallableRegions'])</filter>
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127 </data>
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128 </outputs>
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129 <tests>
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130 <!-- #1; input bam, decompressed -->
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131 <test expect_num_outputs="2">
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132 <param name="normalBam" value="sample1.bam" ftype="bam"/>
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133 <param name="tumorBam" value="sample2.bam" ftype="bam"/>
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134 <conditional name="ref_cond">
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135 <param name="ref_sel" value="history"/>
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136 <param name="ref" value="hg98.fa" ftype="fasta"/>
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137 </conditional>
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138 <section name="oo">
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139 <param name="vcf_type" value="decompressed"/>
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140 </section>
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141 <output name="out_indels" ftype="vcf">
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142 <assert_contents>
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143 <has_n_lines n="41"/>
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144 <has_line_matching expression="#CHROM&#009;POS&#009;.+"/>
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145 <has_line_matching expression="demo20&#009;3664&#009;.+"/>
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146 </assert_contents>
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147 </output>
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148 <output name="out_snvs" ftype="vcf">
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149 <assert_contents>
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150 <has_n_lines n="52"/>
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151 <has_line_matching expression="#CHROM&#009;POS&#009;.+"/>
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152 <has_line_matching expression="demo20&#009;3537&#009;.+"/>
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153 </assert_contents>
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154 </output>
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155 </test>
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156 <!-- #2; input cram, compressed -->
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157 <test expect_num_outputs="2">
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158 <param name="normalBam" value="sample1.cram" ftype="cram"/>
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159 <param name="tumorBam" value="sample2.cram" ftype="cram"/>
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160 <conditional name="ref_cond">
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161 <param name="ref_sel" value="history"/>
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162 <param name="ref" value="hg98.fa" ftype="fasta"/>
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diff changeset
163 </conditional>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
164 <section name="oo">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
165 <param name="vcf_type" value="compressed"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
166 </section>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
167 <output name="out_indels" file="indels_test2.vcf.gz" ftype="vcf_bgzip" compare="sim_size"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
168 <output name="out_snvs" file="snvs_test2.vcf.gz" ftype="vcf_bgzip" compare="sim_size"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
169 </test>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
170 <!-- #3; input bam, decompressed, no defaults -->
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
171 <test expect_num_outputs="3">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
172 <param name="normalBam" value="sample1.bam" ftype="bam"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
173 <param name="tumorBam" value="sample2.bam" ftype="bam"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
174 <conditional name="ref_cond">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
175 <param name="ref_sel" value="history"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
176 <param name="ref" value="hg98.fa" ftype="fasta"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
177 </conditional>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
178 <param name="optimization" value="--exome" />
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
179 <section name="oo">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
180 <param name="vcf_type" value="decompressed"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
181 <param name="outputCallableRegions" value="true"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
182 </section>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
183 <section name="strelka">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
184 <param name="depthFilterMultiple" value="2.8"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
185 <param name="snvMaxFilteredBasecallFrac" value="0.5"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
186 <param name="snvMaxSpanningDeletionFrac" value="0.76"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
187 <param name="indelMaxWindowFilteredBasecallFrac" value="0.4"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
188 <param name="ssnvPrior" value="0.0002"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
189 <param name="sindelPrior" value="0.000002"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
190 <param name="ssnvNoise" value="0.0000000004"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
191 <param name="sindelNoiseFactor" value="2.1"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
192 <param name="ssnvNoiseStrandBiasFrac" value="0.1"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
193 <param name="minTier1Mapq" value="21"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
194 <param name="minTier2Mapq" value="1"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
195 <param name="ssnvQuality_LowerBound" value="14"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
196 <param name="sindelQuality_LowerBound" value="41"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
197 <param name="ssnvContamTolerance" value="0.16"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
198 <param name="indelContamTolerance" value="0.16"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
199 <param name="maxIndelSize" value="50"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
200 </section>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
201 <output name="out_indels" ftype="vcf">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
202 <assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
203 <has_n_lines n="39"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
204 <has_line_matching expression="#CHROM&#009;POS&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
205 <has_line_matching expression="demo20&#009;3664&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
206 </assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
207 </output>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
208 <output name="out_snvs" ftype="vcf">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
209 <assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
210 <has_n_lines n="51"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
211 <has_line_matching expression="#CHROM&#009;POS&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
212 <has_line_matching expression="demo20&#009;3537&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
213 </assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
214 </output>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
215 <output name="out_callable" ftype="bed">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
216 <assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
217 <has_n_lines n="136"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
218 <has_line_matching expression="demo20&#009;3971&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
219 </assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
220 </output>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
221 </test>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
222 <!-- #4; bam, reference cached -->
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
223 <test expect_num_outputs="2">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
224 <param name="normalBam" dbkey="hg19" value="sample1.bam" ftype="bam"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
225 <param name="tumorBam" value="sample2.bam" ftype="bam"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
226 <conditional name="ref_cond">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
227 <param name="ref_sel" value="cached"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
228 <param name="ref" value="hg19"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
229 </conditional>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
230 <section name="oo">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
231 <param name="vcf_type" value="decompressed"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
232 </section>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
233 <output name="out_indels" ftype="vcf">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
234 <assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
235 <has_n_lines n="41"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
236 <has_line_matching expression="#CHROM&#009;POS&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
237 <has_line_matching expression="demo20&#009;3664&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
238 </assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
239 </output>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
240 <output name="out_snvs" ftype="vcf">
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
241 <assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
242 <has_n_lines n="52"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
243 <has_line_matching expression="#CHROM&#009;POS&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
244 <has_line_matching expression="demo20&#009;3537&#009;.+"/>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
245 </assert_contents>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
246 </output>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
247 </test>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
248 </tests>
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
249 <help><![CDATA[
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
250 .. class:: infomark
c06e033242df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka commit 2e445e7c519b2b77498cb74c03ca6ed12b22423a"
iuc
parents:
diff changeset
251
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252 **What it does**
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253
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254 @HELP_STRELKA@
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255
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256 The somatic calling model improves on the original Strelka method for liquid and late-stage tumor analysis by accounting for possible tumor cell contamination in the normal sample. A final empirical variant re-scoring step using random forest models trained on various call quality features has been added to both callers to further improve precision.
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257
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258 **Input**
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259
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260 @HELP_INPUT@
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261
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262 **Output**
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263
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264 *INDEL*
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265
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266 All somatic indels inferred in the tumor sample in VCF format.
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267
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268 *SNVS*
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269
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270 All somatic SNVs inferred in the tumor sample in VCF format.
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271
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272 *Callability*
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273
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274 The somatic variant caller can be configured with the option --outputCallableRegions, which will extend the somatic SNV quality model calculation to be applied as a test of somatic SNV callability at all positions in the genome. The outcome of this callability calculation will be summarized in a BED-formatted callability track. This BED track contains regions which are determined to be callable, indicating that there is sufficient evidence to either call a somatic SNV or assert the absence of a somatic SNV with a variant frequency of 10% or greater. Both somatic and non-somatic sites are determined to be 'callable' if the somatic or non-somatic quality threshold is at least 15.
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275
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276 .. class:: infomark
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277
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278 **References**
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279
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280 @HELP_REFERENCES@
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281 ]]></help>
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282 <expand macro="citations"/>
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283 </tool>