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annotate Mutect2.xml @ 2:646e6943bcd2 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
author artbio
date Sun, 15 Oct 2023 12:06:24 +0000
parents c51c08cc9fcc
children
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rev   line source
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
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1 <tool id="mutect2" name="gatk4 Mutect2" version="@WRAPPER_VERSION@" profile="21.01">
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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2 <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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3 <macros>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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4 <import>macros.xml</import>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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5 </macros>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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6 <expand macro="requirements"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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7 <expand macro="version_cmd"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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8 <command detect_errors="exit_code">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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9 <![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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10 #include source=$set_sections#
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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11 #include source=$pre_gatk_excl_ints_chth#
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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12 #include source=$pre_gatk_ints_chth#
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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13
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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14 #set ref_flag='--reference="reference.fa"'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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15
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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16 #if str($reference_source.reference_source_selector) == 'history'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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17 ln -s '$reference_source.reference_sequence' reference.fa &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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18 samtools faidx reference.fa &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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19 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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20 #else if str($reference_source.reference_source_selector) == 'cached'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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21 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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22 samtools faidx reference.fa &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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23 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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24 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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25 #set ref_flag=''
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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26 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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27
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
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28 ln -s $tumor tumor.bam &&
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
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29 ln -s $tumor.metadata.bam_index tumor.bam.bai &&
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
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30
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
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31 #if str($mode.mode_parameters) == 'somatic'
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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32 ln -s $mode.normal normal.bam &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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33 ln -s $mode.normal.metadata.bam_index normal.bam.bai &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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34 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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35
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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36 #if str($outputs.output_parameters) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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37 #if str($outputs.debug_assembly) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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38 ln -s '$assembly_region_out' assembly-region.tab &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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39 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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40 #if str($outputs.debug_bam) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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41 ln -s '$bam_output' debug.bam &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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42 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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43 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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44
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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45 gatk GetSampleName --input="tumor.bam" --output="samplename.txt" &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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46 sample=`cat samplename.txt | sed 's/"//g'` &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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47
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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48 #if str($optional.optional_parameters) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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49 #if $optional.panel_of_normals
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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50 #set datatype = $optional.panel_of_normals.datatype
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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51 #if $optional.panel_of_normals.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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52 ln -s '$optional.panel_of_normals' panel_of_normals.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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53 tabix panel_of_normals.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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54 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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55 ln -s '$optional.panel_of_normals' panel_of_normals.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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56 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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57 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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58
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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59 #if $optional.germline_resource
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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60 #set datatype = $optional.germline_resource.datatype
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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61 #if $optional.germline_resource.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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62 ln -s '$optional.germline_resource' germline_resource.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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63 tabix germline_resource.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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64 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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65 ln -s '$optional.germline_resource' germline_resource.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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66 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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67 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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68
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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69 #if $optional.alleles
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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70 #set datatype = $optional.alleles.datatype
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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71 #if $optional.alleles.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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72 ln -s '$optional.alleles' alleles.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
73 tabix alleles.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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74 @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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75 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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76 ln -s '$optional.alleles' alleles.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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77 @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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78 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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79 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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80
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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81 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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82
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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83 gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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84
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
85 #if str($mode.mode_parameters) == 'tumor_only'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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86 --input tumor.bam
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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87 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
88 --input tumor.bam
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
89 --input normal.bam
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
90 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
91
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
92 ## OPTIONAL PARAMETERS ##
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
93
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
94 #if str($optional.optional_parameters) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
95
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
96 #if $optional.panel_of_normals
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
97 #if $optional.panel_of_normals.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
98 --panel-of-normals panel_of_normals.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
99 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
100 --panel-of-normals panel_of_normals.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
101 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
102 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
103
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
104 #if $optional.pedigree
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
105 --pedigree="$optional.pedigree"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
106 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
107
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
108 #if $optional.germline_resource
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
109 #if $optional.germline_resource.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
110 --germline-resource germline_resource.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
111 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
112 --germline-resource germline_resource.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
113 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
114 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
115
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
116 #if $optional.annotation
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
117 #for $annot in str($optional.annotation).split(',')
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
118 --annotation="$annot"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
119 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
120 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
121
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
122 #if $optional.annotation_group
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
123 #for $annot in str($optional.annotation_group).split(',')
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
124 --annotation-group="$annot"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
125 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
126 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
127
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
128 #if $optional.annotations_to_exclude
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
129 #for $annot in str($optional.annotations_to_exclude).split(',')
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
130 --annotations-to-exclude="$annot"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
131 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
132 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
133
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
134 #if $optional.founder_id
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
135 --founder-id="$optional.founder_id"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
136 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
137
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
138 #if $optional.normal_sample
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
139 --normal-sample="$optional.normal_sample"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
140 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
141
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
142 #if $optional.alleles
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
143 --alleles alleles.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
144 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
145
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
146 #if $optional.f1r2_max_depth:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
147 --f1r2-max-depth="$optional.f1r2_max_depth"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
148 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
149
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
150 #if $optional.f1r2_max_depth:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
151 --f1r2-median-mq="$optional.f1r2_median_mq"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
152 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
153
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
154 #if $optional.f1r2_max_depth:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
155 --f1r2-min-bq="$optional.f1r2_min_bq"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
156 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
157
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
158 #if $optional.interval_merging_rule:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
159 --interval-merging-rule="$optional.interval_merging_rule"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
160 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
161
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
162 #if $optional.interval_set_rule:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
163 --interval-set-rule="$optional.interval_set_rule"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
164 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
165
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
166 #if $optional.pcr_indel_qual:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
167 --pcr-indel-qual="$optional.pcr_indel_qual"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
168 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
169
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
170 #if $optional.pcr_snv_qual:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
171 --pcr-snv-qual="$optional.pcr_snv_qual"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
172 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
173
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
174 #if $optional.read_filter
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
175 #for $filter in str($optional.read_filter).split(',')
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
176 --read-filter="$filter"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
177 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
178 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
179
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
180 #if $optional.disable_read_filter
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
181 #for $filter in str($optional.disable_read_filter).split(',')
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
182 --disable-read-filter="$filter"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
183 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
184 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
185
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
186 --base-quality-score-threshold="$optional.base_quality_score_threshold"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
187 --af-of-alleles-not-in-resource="$optional.af_of_alleles_not_in_resource"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
188 --downsampling-stride="$optional.downsampling_stride"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
189 --gcs-max-retries="$optional.gcs_max_retries"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
190 --initial-tumor-lod="$optional.initial_tumor_lod"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
191 --max-population-af="$optional.max_population_af"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
192 --max-reads-per-alignment-start="$optional.max_reads_per_alignment_start"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
193 --min-base-quality-score="$optional.min_base_quality_score"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
194 --native-pair-hmm-threads="\${GALAXY_SLOTS:-1}"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
195 --normal-lod="$optional.normal_lod"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
196 --read-validation-stringency="$optional.read_validation_stringency"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
197 --tumor-lod-to-emit="$optional.tumor_lod_to_emit"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
198 --verbosity="ERROR"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
199 $optional.lenient
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
200 $optional.annotate_with_num_discovered_alleles
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
201 $optional.add_output_sam_program_record
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
202 $optional.disable_bam_index_caching
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
203 $optional.disable_sequence_dictionary_validation
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
204 $optional.genotype_germline_sites
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
205 $optional.genotype_pon_sites
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
206 $optional.ignore_itr_artifacts
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
207 $optional.mitochondria_mode
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
208 $optional.native_pair_hmm_use_double_precision
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
209 $optional.sites_only_vcf_output
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
210 $optional.add_output_vcf_command_line
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
211 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
212
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
213 ## END OPTIONAL PARAMETERS ##
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
214
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
215 ## ADVANCED PARAMETERS ##
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
216
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
217 #if str($advanced.advanced_parameters) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
218
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
219 #if $advanced.kmer_size
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
220 --kmer-size="$advanced.kmer_size"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
221 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
222
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
223 #if $advanced.gvcf_lod_band
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
224 --gvcf-lod-band="$advanced.gvcf_lod_band"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
225 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
226
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
227 #if $advanced.emit_ref_confidence
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
228 --emit-ref-confidence="$advanced.emit_ref_confidence"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
229 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
230
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
231 #if $advanced.max_unpruned_variants
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
232 --max-unpruned-variants="$advanced.max_unpruned_variants"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
233 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
234 --allele-informative-reads-overlap-margin="$advanced.allele_informative_reads_overlap_margin"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
235 --active-probability-threshold="$advanced.active_probability_threshold"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
236 --assembly-region-padding="$advanced.assembly_region_padding"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
237 --bam-writer-type="$advanced.bam_writer_type"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
238 --max-assembly-region-size="$advanced.max_assembly_region_size"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
239 --max-mnp-distance="$advanced.max_mnp_distance"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
240 --max-num-haplotypes-in-population="$advanced.max_num_haplotypes_in_population"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
241 --max-prob-propagation-distance="$advanced.max_prob_propagation_distance"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
242 --max-suspicious-reads-per-alignment-start="$advanced.max_suspicious_reads_per_alignment_start"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
243 --min-assembly-region-size="$advanced.min_assembly_region_size"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
244 --min-dangling-branch-length="$advanced.min_dangling_branch_length"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
245 --min-pruning="$advanced.min_pruning"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
246 --minimum-allele-fraction="$advanced.minimum_allele_fraction"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
247 --num-pruning-samples="$advanced.num_pruning_samples"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
248 --pair-hmm-gap-continuation-penalty="$advanced.pair_hmm_gap_continuation_penalty"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
249 --pair-hmm-implementation="$advanced.pair_hmm_implementation"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
250 --pcr-indel-model="$advanced.pcr_indel_model"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
251 --phred-scaled-global-read-mismapping-rate="$advanced.phred_scaled_global_read_mismapping_rate"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
252 --pruning-lod-threshold="$advanced.pruning_lod_threshold"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
253 --smith-waterman="$advanced.smith_waterman"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
254 $advanced.allow_non_unique_kmers_in_ref
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
255 $advanced.disable_adaptive_pruning
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
256 $advanced.disable_tool_default_annotations
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
257 $advanced.disable_tool_default_read_filters
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
258 $advanced.dont_increase_kmer_sizes_for_cycles
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
259 $advanced.dont_use_soft_clipped_bases
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
260 $advanced.enable_all_annotations
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
261 $advanced.force_active
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
262 $advanced.force_call_filtered_alleles
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
263 $advanced.independent_mates
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
264 $advanced.recover_all_dangling_branches
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
265 $advanced.use_filtered_reads_for_annotations
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
266
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
267 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
268
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
269 ## END ADVANCED PARAMETERS ##
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
270
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
271 ## ADDITIONAL OUTPUT PARAMETERS ##
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
272
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
273 #if str($outputs.output_parameters) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
274 #if str($outputs.debug_assembly) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
275 --assembly-region-out="assembly-region.tab"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
276 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
277 #if str($outputs.debug_bam) == 'yes'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
278 --bam-output="debug.bam"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
279 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
280 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
281
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
282 #include source=$gatk_excl_ints_chth#
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
283 #include source=$gatk_ints_chth#
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
284 #include source=$vcf_output_opts#
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
285 #include source=$gatk_seqdict#
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
286 ]]>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
287 </command>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
288 <inputs>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
289 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
290 <conditional name="mode">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
291 <param name="mode_parameters" type="select" label="Type of analysis">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
292 <option value="tumor_only">Tumor-only</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
293 <option value="somatic">Somatic</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
294 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
295 <when value="tumor_only">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
296 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
297 <when value="somatic">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
298 <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
299 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
300 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
301 <expand macro="gzip_vcf_params"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
302 <expand macro="ref_sel"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
303 <conditional name="optional">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
304 <param name="optional_parameters" type="select" label="Optional parameters">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
305 <option value="no">Use internal defaults</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
306 <option value="yes">Specify parameters</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
307 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
308 <when value="yes">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
309 <expand macro="gatk_excl_ints"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
310 <expand macro="gatk_ints"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
311 <expand macro="seq_dict_sel"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
312 <param name="add_output_sam_program_record" argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" optional="true" checked="true" label="Add Output Sam Program Record" help="If true, adds a PG tag to created SAM/BAM/CRAM files."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
313 <param name="add_output_vcf_command_line" argument="--add-output-vcf-command-line" type="boolean" truevalue="--add-output-vcf-command-line" falsevalue="" optional="true" checked="true" label="Add Output Vcf Command Line" help="If true, adds a command line header line to created VCF files."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
314 <param name="af_of_alleles_not_in_resource" argument="--af-of-alleles-not-in-resource" type="float" optional="true" value="-1.0" label="Af Of Alleles Not In Resource" help="Population allele fraction assigned to alleles not found in germline resource. Please see docs/mutect/mutect2.pdf fora derivation of the default value."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
315 <param name="annotate_with_num_discovered_alleles" argument="--annotate-with-num-discovered-alleles" type="boolean" truevalue="--annotate-with-num-discovered-alleles" falsevalue="" optional="true" checked="false" label="Annotate With Num Discovered Alleles" help="If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
316 <param argument="--annotation" type="select" multiple="true" label="Annotations" help="One or more specific annotations to add to variant calls">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
317 <option value="AlleleFraction">AlleleFraction</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
318 <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
319 <option value="AS_FisherStrand">AS_FisherStrand</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
320 <option value="AS_InbreedingCoeff">AS_InbreedingCoeff</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
321 <option value="AS_MappingQualityRankSumTest">AS_MappingQualityRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
322 <option value="AS_QualByDepth">AS_QualByDepth</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
323 <option value="AS_ReadPosRankSumTest">AS_ReadPosRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
324 <option value="AS_RMSMappingQuality">AS_RMSMappingQuality</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
325 <option value="AS_StrandOddsRatio">AS_StrandOddsRatio</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
326 <option value="BaseQuality">BaseQuality</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
327 <option value="BaseQualityHistogram">BaseQualityHistogram</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
328 <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
329 <option value="ChromosomeCounts">ChromosomeCounts</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
330 <option value="ClippingRankSumTest">ClippingRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
331 <option value="CountNs">CountNs</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
332 <option value="Coverage">Coverage</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
333 <option value="DepthPerAlleleBySample">DepthPerAlleleBySample</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
334 <option value="DepthPerSampleHC">DepthPerSampleHC</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
335 <option value="ExcessHet">ExcessHet</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
336 <option value="FisherStrand">FisherStrand</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
337 <option value="FragmentLength">FragmentLength</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
338 <option value="GenotypeSummaries">GenotypeSummaries</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
339 <option value="InbreedingCoeff">InbreedingCoeff</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
340 <option value="LikelihoodRankSumTest">LikelihoodRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
341 <option value="MappingQuality">MappingQuality</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
342 <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
343 <option value="MappingQualityZero">MappingQualityZero</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
344 <option value="OrientationBiasReadCounts">OrientationBiasReadCounts</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
345 <option value="OriginalAlignment">OriginalAlignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
346 <option value="PossibleDeNovo">PossibleDeNovo</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
347 <option value="QualByDepth">QualByDepth</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
348 <option value="ReadPosition">ReadPosition</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
349 <option value="ReadPosRankSumTest">ReadPosRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
350 <option value="ReferenceBases">ReferenceBases</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
351 <option value="RMSMappingQuality">RMSMappingQuality</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
352 <option value="SampleList">SampleList</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
353 <option value="StrandBiasBySample">StrandBiasBySample</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
354 <option value="StrandOddsRatio">StrandOddsRatio</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
355 <option value="TandemRepeat">TandemRepeat</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
356 <option value="UniqueAltReadCount">UniqueAltReadCount</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
357 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
358 <param name="annotation_group" argument="--annotation-group" type="select" multiple="true" label="Annotation groups" help="One or more annotation groups to add to variant calls">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
359 <option value="AlleleSpecificAnnotation">AlleleSpecificAnnotation</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
360 <option value="AS_StandardAnnotation">AS_StandardAnnotation</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
361 <option value="ReducibleAnnotation">ReducibleAnnotation</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
362 <option value="StandardAnnotation">StandardAnnotation</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
363 <option value="StandardHCAnnotation">StandardHCAnnotation</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
364 <option value="StandardMutectAnnotation">StandardMutectAnnotation</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
365 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
366 <param name="annotations_to_exclude" argument="--annotations-to-exclude" type="select" multiple="true" label="Annotations to exclude" help="Specific annotations to exclude from variant calls">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
367 <option value="AlleleFraction">AlleleFraction</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
368 <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
369 <option value="AS_FisherStrand">AS_FisherStrand</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
370 <option value="AS_InbreedingCoeff">AS_InbreedingCoeff</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
371 <option value="AS_MappingQualityRankSumTest">AS_MappingQualityRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
372 <option value="AS_QualByDepth">AS_QualByDepth</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
373 <option value="AS_ReadPosRankSumTest">AS_ReadPosRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
374 <option value="AS_RMSMappingQuality">AS_RMSMappingQuality</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
375 <option value="AS_StrandOddsRatio">AS_StrandOddsRatio</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
376 <option value="BaseQuality">BaseQuality</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
377 <option value="BaseQualityHistogram">BaseQualityHistogram</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
378 <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
379 <option value="ChromosomeCounts">ChromosomeCounts</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
380 <option value="ClippingRankSumTest">ClippingRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
381 <option value="CountNs">CountNs</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
382 <option value="Coverage">Coverage</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
383 <option value="DepthPerAlleleBySample">DepthPerAlleleBySample</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
384 <option value="DepthPerSampleHC">DepthPerSampleHC</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
385 <option value="ExcessHet">ExcessHet</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
386 <option value="FisherStrand">FisherStrand</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
387 <option value="FragmentLength">FragmentLength</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
388 <option value="GenotypeSummaries">GenotypeSummaries</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
389 <option value="InbreedingCoeff">InbreedingCoeff</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
390 <option value="LikelihoodRankSumTest">LikelihoodRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
391 <option value="MappingQuality">MappingQuality</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
392 <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
393 <option value="MappingQualityZero">MappingQualityZero</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
394 <option value="OrientationBiasReadCounts">OrientationBiasReadCounts</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
395 <option value="OriginalAlignment">OriginalAlignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
396 <option value="PossibleDeNovo">PossibleDeNovo</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
397 <option value="QualByDepth">QualByDepth</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
398 <option value="ReadPosition">ReadPosition</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
399 <option value="ReadPosRankSumTest">ReadPosRankSumTest</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
400 <option value="ReferenceBases">ReferenceBases</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
401 <option value="RMSMappingQuality">RMSMappingQuality</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
402 <option value="SampleList">SampleList</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
403 <option value="StrandBiasBySample">StrandBiasBySample</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
404 <option value="StrandOddsRatio">StrandOddsRatio</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
405 <option value="TandemRepeat">TandemRepeat</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
406 <option value="UniqueAltReadCount">UniqueAltReadCount</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
407 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
408 <param name="pedigree" argument="--pedigree" type="data" optional="true" format="vcf,vcf_bgzip" label="Pedigree" help="Pedigree file for determining the population &quot;founders&quot;. If a file is provided here, a pedigree-based annotation must be added above."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
409 <param name="base_quality_score_threshold" argument="--base-quality-score-threshold" type="integer" optional="true" value="18" label="Base Quality Score Threshold" help="Base qualities below this threshold will be reduced to the minimum (6)"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
410 <param name="callable_depth" argument="--callable-depth" type="integer" optional="true" value="10" label="Minimum depth to be considered callable" help="Does not affect genotyping"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
411 <param name="contamination_fraction_to_filter" argument="--contamination-fraction-to-filter" type="float" optional="true" value="0.0" label="Contamination Fraction To Filter" help="Fraction of contamination in sequencing data (for all samples) to aggressively remove"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
412 <param name="disable_bam_index_caching" argument="--disable-bam-index-caching" type="boolean" truevalue="--disable-bam-index-caching" falsevalue="" optional="true" checked="false" label="Disable Bam Index Caching" help="If true, don&amp;apos;t cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
413 <param name="disable_read_filter" argument="--disable-read-filter" type="select" multiple="true" value="" label="Disable Read Filter" help="Read filters to be disabled before analysis">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
414 <option value="GoodCigarReadFilter">Good cigar string</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
415 <option value="MappedReadFilter">Mapped read</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
416 <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
417 <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
418 <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
419 <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
420 <option value="NotDuplicateReadFilter">Not a duplicate read</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
421 <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
422 <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
423 <option value="WellformedReadFilter">Well-formed read</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
424 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
425 <param name="read_filter" argument="--read-filter" type="select" multiple="true" value="" label="Read Filter" help="Read filters to be applied before analysis">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
426 <option value="AlignmentAgreesWithHeaderReadFilter">Alignment agrees with header</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
427 <option value="AllowAllReadsReadFilter">Allow all reads</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
428 <option value="AmbiguousBaseReadFilter">Ambiguous base</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
429 <option value="CigarContainsNoNOperator">Cigar contains no NO operator</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
430 <option value="FirstOfPairReadFilter">First of pair</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
431 <option value="GoodCigarReadFilter">Good cigar string</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
432 <option value="HasReadGroupReadFilter">Has read group</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
433 <option value="MappedReadFilter">Mapped read</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
434 <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
435 <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
436 <option value="MatchingBasesAndQualsReadFilter">Matching bases and quals</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
437 <option value="MateDifferentStrandReadFilter">Mate different strand</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
438 <option value="MateOnSameContigOrNoMappedMateReadFilter">Mate on same contig or no mapped mate</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
439 <option value="MateUnmappedAndUnmappedReadFilter">Mate unmapped and mapped</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
440 <option value="MetricsReadFilter">Metrics</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
441 <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
442 <option value="NonZeroFragmentLengthReadFilter">Non-zero fragment length</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
443 <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
444 <option value="NotDuplicateReadFilter">Not duplicate</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
445 <option value="NotOpticalDuplicateReadFilter">Not optical duplicate</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
446 <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
447 <option value="NotSupplementaryAlignmentReadFilter">Not a supplementary alignment</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
448 <option value="OverclippedReadFilter">Overclipped</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
449 <option value="PairedReadFilter">Paired</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
450 <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
451 <option value="PrimaryLineReadFilter">Primary line</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
452 <option value="ProperlyPairedReadFilter">Properly paired</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
453 <option value="ReadLengthEqualsCigarLengthReadFilter">Read length equals cigar length</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
454 <option value="SecondOfPairReadFilter">Second of pair</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
455 <option value="SeqIsStoredReadFilter">Sequence is stored</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
456 <option value="SoftClippedReadFilter">Soft clipped</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
457 <option value="ValidAlignmentStartReadFilter">Valid alignment start</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
458 <option value="ValidAlignmentEndReadFilter">Valid alignment end</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
459 <option value="WellformedReadFilter">Well-formed read</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
460 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
461 <param name="disable_sequence_dictionary_validation" argument="--disable-sequence-dictionary-validation" type="boolean" truevalue="--disable-sequence-dictionary-validation" falsevalue="" optional="true" checked="false" label="Disable Sequence Dictionary Validation" help="If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
462 <param name="downsampling_stride" argument="--downsampling-stride" type="integer" optional="true" value="1" label="Downsampling Stride" help="Downsample a pool of reads starting within a range of one or more bases."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
463 <param name="f1r2_max_depth" argument="--f1r2-max-depth" type="integer" optional="true" value="200" label="Sites with depth higher than this value will be grouped" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
464 <param name="f1r2_median_mq" argument="--f1r2-median-mq" type="integer" optional="true" value="50" label="Skip sites with median mapping quality below this value" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
465 <param name="f1r2_min_bq" argument="--base-quality-score-threshold" type="integer" optional="true" value="20" label="Exclude bases below this quality from pileup" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
466 <param name="founder_id" argument="--founder-id" type="text" optional="true" value="" label="Founder Id" help="Samples representing the population &amp;quot;founders&amp;quot;"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
467 <param name="gcs_max_retries" argument="--gcs-max-retries" type="integer" optional="true" value="20" label="Gcs Max Retries" help="If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
468 <param name="genotype_germline_sites" argument="--genotype-germline-sites" type="boolean" truevalue="--genotype-germline-sites" falsevalue="" optional="true" checked="false" label="Genotype Germline Sites" help="(EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
469 <param name="genotype_pon_sites" argument="--genotype-pon-sites" type="boolean" truevalue="--genotype-pon-sites" falsevalue="" optional="true" checked="false" label="Genotype PoN Sites" help="Call sites in the PoN even though they will ultimately be filtered."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
470 <param name="alleles" argument="--alleles" type="data" optional="true" format="vcf" label="Alleles" help="The set of alleles at which to genotype"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
471 <param name="germline_resource" argument="--germline-resource" type="data" optional="true" format="vcf,vcf_bgzip" label="Germline Resource" help="Population vcf of germline sequencing containing allele fractions."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
472 <param name="heterozygosity" argument="--heterozygosity" type="float" optional="true" value="0.001" label="Heterozygosity" help="The expected heterozygosity value used to compute prior probability that a locus is non-reference. The default priors are for provided for humans: het = 1e-3 which means that the probability of N samples being hom-ref at a site is: 1 - sum_i_2N (het / i) Note that heterozygosity as used here is the population genetics concept: http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms would differ from each other (one being A and the other B) at a rate of 1 in 100 bp. Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the het parameters only increases the chance that a site will be called non-reference across all samples, but doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all. The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy, which determines how many chromosomes each individual in the species carries."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
473 <param name="heterozygosity_stdev" argument="--heterozygosity-stdev" type="float" optional="true" value="0.01" label="Heterozygosity Stdev" help="Standard deviation of heterozygosity for SNP and indel calling."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
474 <param name="ignore_itr_artifacts" argument="--ignore-itr-artifacts" type="boolean" truevalue="--ignore-itr-artifacts" falsevalue="" optional="true" checked="false" label="Turn off read transformer that clips artifacts associated with end repair insertions near inverted tandem repeats" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
475 <param name="indel_heterozygosity" argument="--indel-heterozygosity" type="float" optional="true" value="0.000125" label="Indel Heterozygosity" help="Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
476 <param name="initial_tumor_lod" argument="--initial-tumor-lod" type="float" optional="true" value="2.0" label="Initial Tumor Lod" help="LOD threshold to consider pileup active."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
477 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" value="0" label="Interval exclusion padding" help="Amount of padding (in bp) to add to each interval you are excluding" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
478 <param name="interval_padding" argument="--interval-padding" type="integer" value="0" label="Interval padding" help="Amount of padding (in bp) to add to each interval you are including" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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479 <param name="interval_merging_rule" argument="--interval-merging-rule" type="select" optional="true" label="Interval Merging Rule" help="Interval merging rule for abutting intervals">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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480 <option selected="true" value="ALL">All</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
481 <option value="OVERLAPPING_ONLY">Overlapping only</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
482 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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483 <param name="interval_set_rule" argument="--interval-set-rule" type="select" optional="true" label="Interval Set Rule" help="Set merging approach to use for combining interval inputs">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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484 <option selected="true" value="UNION">Union</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
485 <option value="INTERSECTION">Intersection</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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diff changeset
486 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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487 <param name="lenient" argument="--lenient" type="boolean" truevalue="--lenient" falsevalue="" optional="true" checked="false" label="Lenient" help="Lenient processing of VCF files"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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488 <param name="max_population_af" argument="--max-population-af" type="float" optional="true" value="0.01" label="Max Population Af" help="Maximum population allele frequency in tumor-only mode."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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489 <param name="max_reads_per_alignment_start" argument="--max-reads-per-alignment-start" type="integer" optional="true" value="50" label="Max Reads Per Alignment Start" help="Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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diff changeset
490 <param name="min_base_quality_score" argument="--min-base-quality-score" type="integer" optional="true" value="10" label="Min Base Quality Score" help="Minimum base quality required to consider a base for calling"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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491 <param name="mitochondria_mode" argument="--mitochondria-mode" type="boolean" truevalue="--mitochondria-mode" falsevalue="" label="Mitochondria mode sets emission and initial LODs to 0" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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492 <param name="native_pair_hmm_use_double_precision" argument="--native-pair-hmm-use-double-precision" type="boolean" truevalue="--native-pair-hmm-use-double-precision" falsevalue="" optional="true" checked="false" label="Native Pair Hmm Use Double Precision" help="use double precision in the native pairHmm. This is slower but matches the java implementation better"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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493 <param name="normal_lod" argument="--normal-lod" type="float" optional="true" value="2.2" label="Normal Lod" help="LOD threshold for calling normal variant non-germline."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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494 <param name="normal_sample" argument="--normal-sample" type="text" optional="true" value="" label="Normal Sample" help="BAM sample name of normal. May be URL-encoded as output by GetSampleName with -encode argument."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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495 <param name="panel_of_normals" argument="--panel-of-normals" type="data" optional="true" format="vcf,vcf_bgzip" label="Panel Of Normals" help="VCF file of sites observed in normal."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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496 <param name="pcr_indel_qual" argument="--pcr-indel-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR indel qual for overlapping fragments" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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497 <param name="pcr_snv_qual" argument="--pcr-snv-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR SNV qual for overlapping fragments" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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498 <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&apos;t emit genotype fields when writing vcf file output."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
499 <param name="read_validation_stringency" argument="--read-validation-stringency" type="select" optional="true" label="Read Validation Stringency" help="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
500 <option selected="true" value="SILENT">Silent</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
501 <option value="STRICT">Strict</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
502 <option value="LENIENT">Lenient</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
503 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
504 <param name="tumor_lod_to_emit" argument="--tumor-lod-to-emit" type="float" optional="true" value="3.0" label="Tumor Lod To Emit" help="LOD threshold to emit tumor variant to VCF."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
505 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
506 <when value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
507 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
508 <conditional name="advanced">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
509 <param name="advanced_parameters" type="select" label="Advanced parameters">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
510 <option value="no">Use internal defaults</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
511 <option value="yes">Specify parameters</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
512 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
513 <when value="yes">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
514 <param name="allele_informative_reads_overlap_margin" argument="--allele-informative-reads-overlap-margin" type="integer" optional="true" value="2" label="Likelihood and read-based annotations will only take into consideration reads that overlap the variant or any base no further than this distance expressed in base pairs" help="Number of overlapping bases around the variant."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
515 <param name="active_probability_threshold" argument="--active-probability-threshold" type="float" optional="true" value="0.002" label="Active Probability Threshold" help="Minimum probability for a locus to be considered active."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
516 <param name="allow_non_unique_kmers_in_ref" argument="--allow-non-unique-kmers-in-ref" type="boolean" truevalue="--allow-non-unique-kmers-in-ref" falsevalue="" optional="true" checked="false" label="Allow Non Unique Kmers In Ref" help="Allow graphs that have non-unique kmers in the reference"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
517 <param name="assembly_region_padding" argument="--assembly-region-padding" type="integer" optional="true" value="100" label="Assembly Region Padding" help="Number of additional bases of context to include around each assembly region"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
518 <param name="bam_writer_type" argument="--bam-writer-type" type="select" optional="true" label="Bam Writer Type" help="Which haplotypes should be written to the BAM">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
519 <option selected="true" value="CALLED_HAPLOTYPES">Called haplotypes</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
520 <option value="ALL_POSSIBLE_HAPLOTYPES">All possible haplotypes</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
521 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
522
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
523 <param name="disable_adaptive_pruning" argument="--disable-adaptive-pruning" type="boolean" truevalue="--disable-adaptive-pruning" falsevalue="" optional="true" checked="false" label="Disable adaptive pruning" help="Disable the adaptive algorithm for pruning paths in the graph"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
524 <param name="disable_tool_default_annotations" argument="--disable-tool-default-annotations" type="boolean" truevalue="--disable-tool-default-annotations" falsevalue="" optional="true" checked="false" label="Disable Default Annotations" help="Disable all tool default annotations"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
525 <param name="disable_tool_default_read_filters" argument="--disable-tool-default-read-filters" type="boolean" truevalue="--disable-tool-default-read-filters" falsevalue="" optional="true" checked="false" label="Disable default read filters" help="WARNING: many tools will not function correctly without their default read filters on"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
526 <param name="dont_increase_kmer_sizes_for_cycles" argument="--dont-increase-kmer-sizes-for-cycles" type="boolean" truevalue="--dont-increase-kmer-sizes-for-cycles" falsevalue="" optional="true" checked="false" label="Dont Increase Kmer Sizes For Cycles" help="Disable iterating over kmer sizes when graph cycles are detected"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
527 <param name="dont_use_soft_clipped_bases" argument="--dont-use-soft-clipped-bases" type="boolean" truevalue="--dont-use-soft-clipped-bases" falsevalue="" optional="true" checked="false" label="Dont Use Soft Clipped Bases" help="Do not analyze soft clipped bases in the reads"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
528 <param name="emit_ref_confidence" argument="--emit-ref-confidence" type="select" label="Mode for emitting reference confidence scores" help="NOTE: This is a beta feature in Mutect2">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
529 <option value="NONE">None</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
530 <option value="BP_RESOLUTION">Basepair resolution</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
531 <option value="GVCF">Genomic VCF</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
532 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
533 <param name="enable_all_annotations" argument="--enable-all-annotations" type="boolean" truevalue="--enable-all-annotations" falsevalue="" optional="true" checked="false" label="Enable All Annotations" help="Use all possible annotations (not for the faint of heart)"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
534 <param name="force_active" argument="--force-active" type="boolean" truevalue="--force-active" falsevalue="" optional="true" checked="false" label="Mark all regions active" help="If selected, all regions will be marked as active"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
535 <param name="force_call_filtered_alleles" argument="--force-call-filtered-alleles" type="boolean" truevalue="--force-call-filtered-alleles" falsevalue="" optional="true" checked="false" label="Force-call filtered alleles" help="Force-call filtered alleles included in the resource specified by --alleles"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
536 <param name="gvcf_lod_band" argument="--gvcf-lod-band" type="float" optional="true" label="Upper bounds for reference confidence" help="Exclusive upper bounds for reference confidence LOD bands (must be specified in increasing order)" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
537 <param name="independent_mates" argument="--independent-mates" type="boolean" truevalue="--independent-mates" falsevalue="" label="Independent mates" help="Allow paired reads to independently support different haplotypes. Useful for validations with ill-designed synthetic data" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
538 <param name="kmer_size" argument="--kmer-size" type="integer" optional="true" value="" label="Kmer Size" help="Kmer size to use in the read threading assembler"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
539 <param name="max_assembly_region_size" argument="--max-assembly-region-size" type="integer" optional="true" value="300" label="Max Assembly Region Size" help="Maximum size of an assembly region"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
540 <param name="max_mnp_distance" argument="--max-mnp-distance" type="integer" optional="true" value="1" label="Max Mnp Distance" help="Two or more phased substitutions separated by this distance or less are merged into MNPs."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
541 <param name="max_num_haplotypes_in_population" argument="--max-num-haplotypes-in-population" type="integer" optional="true" value="128" label="Max Num Haplotypes In Population" help="Maximum number of haplotypes to consider for your population"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
542 <param name="max_prob_propagation_distance" argument="--max-prob-propagation-distance" type="integer" optional="true" value="50" label="Max Prob Propagation Distance" help="Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
543 <param name="max_suspicious_reads_per_alignment_start" argument="--max-suspicious-reads-per-alignment-start" type="integer" optional="true" value="0" label="Max Suspicious Reads Per Alignment Start" help="Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride. Set to 0 to disable."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
544 <param name="max_unpruned_variants" argument="--max-unpruned-variants" type="integer" optional="true" value="100" label="Maximum number of variants" help="Maximum number of variants in graph the adaptive pruner will allow"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
545 <param name="min_assembly_region_size" argument="--min-assembly-region-size" type="integer" optional="true" value="50" label="Min Assembly Region Size" help="Minimum size of an assembly region"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
546 <param name="min_dangling_branch_length" argument="--min-dangling-branch-length" type="integer" optional="true" value="4" label="Min Dangling Branch Length" help="Minimum length of a dangling branch to attempt recovery"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
547 <param name="min_pruning" argument="--min-pruning" type="integer" optional="true" value="2" label="Min Pruning" help="Minimum support to not prune paths in the graph"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
548 <param name="minimum_allele_fraction" argument="--minimum-allele-fraction" type="float" optional="true" value="0.0" label="Fractions to consider" help="Lower bound of variant allele fractions to consider when calculating variant LOD"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
549 <param name="num_pruning_samples" argument="--num-pruning-samples" type="integer" optional="true" value="1" label="Num Pruning Samples" help="Number of samples that must pass the minPruning threshold"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
550 <param name="pair_hmm_gap_continuation_penalty" argument="--pair-hmm-gap-continuation-penalty" type="integer" optional="true" value="10" label="Pair Hmm Gap Continuation Penalty" help="Flat gap continuation penalty for use in the Pair HMM"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
551 <param name="pair_hmm_implementation" argument="--pair-hmm-implementation" type="select" optional="true" label="Pair Hmm Implementation" help="The PairHMM implementation to use for genotype likelihood calculations">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
552 <option selected="true" value="FASTEST_AVAILABLE">Fastest Available</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
553 <option value="EXACT">Exact</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
554 <option value="ORIGINAL">Original</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
555 <option value="LOGLESS_CACHING">Logless Caching</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
556 <option value="AVX_LOGLESS_CACHING">Logless Caching (AVX)</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
557 <option value="AVX_LOGLESS_CACHING_OMP">Logless Caching (AVX+OMP)</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
558 <option value="EXPERIMENTAL_FPGA_LOGLESS_CACHING">Logless Caching (FPGA, Experimental)</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
559 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
560 <param name="pcr_indel_model" argument="--pcr-indel-model" type="select" optional="true" label="Pcr Indel Model" help="The PCR indel model to use">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
561 <option selected="true" value="CONSERVATIVE">Conservative</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
562 <option value="NONE">None</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
563 <option value="HOSTILE">Hostile</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
564 <option value="AGGRESSIVE">Aggressive</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
565 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
566 <param name="phred_scaled_global_read_mismapping_rate" argument="--phred-scaled-global-read-mismapping-rate" type="integer" optional="true" value="45" label="Phred Scaled Global Read Mismapping Rate" help="The global assumed mismapping rate for reads"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
567 <param name="pruning_lod_threshold" argument="--pruning-lod-threshold" type="float" optional="true" value="2.302585092994046" label="Pruning LOD threshold" help="Likelihood ratio threshold for adaptive pruning algorithm" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
568 <param name="recover_all_dangling_branches" argument="--recover-all-dangling-branches" type="boolean" truevalue="--recover-all-dangling-branches" falsevalue="" label="Recover all dangling branches" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
569 <param name="smith_waterman" argument="--smith-waterman" type="select" optional="true" label="Smith Waterman" help="Which Smith-Waterman implementation to use, generally 'Fastest available' is the right choice">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
570 <option selected="true" value="FASTEST_AVAILABLE">Fastest available</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
571 <option value="AVX_ENABLED">AVX-Enabled</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
572 <option value="JAVA">JAVA</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
573 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
574 <param name="use_filtered_reads_for_annotations" argument="--use-filtered-reads-for-annotations" type="boolean" truevalue="--use-filtered-reads-for-annotations" falsevalue="" optional="true" checked="false" label="Use Filtered Reads For Annotations" help="Use the contamination-filtered read maps for the purposes of annotating variants"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
575 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
576 <when value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
577 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
578 <conditional name="outputs">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
579 <param name="output_parameters" type="select" label="Output parameters" help="Additional outputs for debugging purposes">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
580 <option value="no">Output only variants</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
581 <option value="yes">Generate debugging information</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
582 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
583 <when value="yes">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
584 <param name="debug_activity" argument="--activity-profile-out" type="boolean" checked="false" truevalue="yes" falsevalue="" label="Activity Profile Out" help="Output the raw activity profile results in IGV format"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
585 <param name="debug_assembly" argument="--assembly-region-out" type="boolean" checked="false" truevalue="yes" falsevalue="" label="Assembly Region Out" help="Output the assembly region to this IGV formatted file"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
586 <param name="debug_bam" argument="--bam-output" type="boolean" checked="false" truevalue="yes" falsevalue="" label="Bam Output" help="The assembled haplotypes and locally realigned reads will be written as BAM to this file if requested. This is intended to be used only for troubleshooting purposes, in specific areas where you want to better understand why the caller is making specific calls"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
587 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
588 <when value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
589 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
590 </inputs>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
591 <outputs>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
592 <expand macro="gzip_vcf_output_params"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
593 <data format="tabular" name="assembly_region_out" label="${tool.name} on ${on_string}: Assembly region">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
594 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_assembly']</filter>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
595 </data>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
596 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: Debug BAM output">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
597 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_bam']</filter>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
598 </data>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
599 </outputs>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
600 <tests>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
601 <test expect_num_outputs="2">
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
602 <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
603 <conditional name="mode">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
604 <param name="mode_parameters" value="tumor_only"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
605 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
606 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
607 <param name="gzipped_output" value="false" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
608 <param name="reference_source_selector" value="history" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
609 <param name="optional_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
610 <param name="advanced_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
611 <param name="output_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
612 <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
613 <output name="output_vcf_stats" file="Mutect2-out1.vcf.stats" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
614 </test>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
615 <test expect_num_outputs="2">
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
616 <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
617 <conditional name="mode">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
618 <param name="mode_parameters" value="tumor_only"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
619 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
620 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
621 <param name="gzipped_output" value="false" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
622 <param name="reference_source_selector" value="history" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
623 <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
624 <param name="seqdict_sequence" value="Mutect2-in2.dict" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
625 <param name="optional_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
626 <param name="advanced_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
627 <param name="output_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
628 <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
629 </test>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
630 <test expect_num_outputs="2">
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
631 <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
632 <conditional name="mode">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
633 <param name="mode_parameters" value="tumor_only"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
634 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
635 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
636 <param name="gzipped_output" value="false" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
637 <param name="reference_source_selector" value="history" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
638 <param name="optional_parameters" value="yes" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
639 <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
640 <param name="annotation_group" value="StandardMutectAnnotation" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
641 <param name="advanced_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
642 <param name="output_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
643 <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="4" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
644 </test>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
645 <test expect_num_outputs="2">
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
646 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
647 <conditional name="mode">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
648 <param name="mode_parameters" value="tumor_only"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
649 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
650 <param name="reference_sequence" value="hg38"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
651 <param name="gzipped_output" value="false" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
652 <param name="reference_source_selector" value="cached" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
653 <param name="reference_sequence" value="hg38"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
654 <param name="optional_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
655 <param name="advanced_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
656 <param name="output_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
657 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
658 </test>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
659 <test expect_num_outputs="4">
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
660 <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
661 <conditional name="mode">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
662 <param name="mode_parameters" value="tumor_only"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
663 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
664 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
665 <param name="gzipped_output" value="false" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
666 <param name="reference_source_selector" value="history" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
667 <param name="optional_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
668 <param name="advanced_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
669 <param name="output_parameters" value="yes" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
670 <param name="debug_activity" value="true" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
671 <param name="debug_assembly" value="true" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
672 <param name="debug_bam" value="true" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
673 <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
674 <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
675 <output name="bam_output" file="Mutect2-out5.bam" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
676 </test>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
677 <test expect_num_outputs="2">
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
678 <param name="tumor" ftype="bam" value="tumor.bam" />
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
679 <conditional name="mode">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
680 <param name="mode_parameters" value="somatic"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
681 <param name="normal" ftype="bam" value="normal.bam" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
682 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
683 <param name="reference_sequence" ftype="fasta" value="chr20.fa" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
684 <param name="gzipped_output" value="false" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
685 <param name="reference_source_selector" value="history" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
686 <param name="optional_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
687 <param name="advanced_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
688 <param name="output_parameters" value="no" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
689 <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="2" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
690 </test>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
691 </tests>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
692 <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
693 variants include single nucleotide (SNV) and insertion and deletion
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
694 (indel) variants. The caller combines the DREAM challenge-winning
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
695 somatic genotyping engine of the original MuTect_ (Cibulskis et al. 2013)
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
696 with the assembly-based machinery of HaplotypeCaller (see
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
697 gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell).
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
698
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
699 .. _MuTect: http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
700
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
701 This tool is featured in the *Somatic Short Mutation calling Best
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
702 Practice Workflow*. See gatk.broadinstitute.org/hc/en-us/articles/360035531132
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
703 for an overview of what traditional somatic calling entails, with usage examples. For the
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
704 latest pipeline scripts, see the Mutect2 WDL scripts directory (see
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 0
diff changeset
705 github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl).
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
706 Although we present the tool for somatic calling, it may apply to other
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
707 contexts, such as mitochondrial variant calling.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
708
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
709 Usage examples
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
710 ~~~~~~~~~~~~~~
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
711
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
712 Example commands show how to run Mutect2 for typical scenarios. The two
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
713 modes are (i) *somatic mode* where a tumor sample is matched with a
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
714 normal sample in analysis and (ii) *tumor-only mode* where a single
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
715 sample's alignment data undergoes analysis.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
716
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
717 (i) Tumor with matched normal
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
718 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
719
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
720 Given a matched normal, Mutect2 is designed to call somatic variants
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
721 only. The tool includes logic to skip emitting variants that are clearly
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
722 present in the germline based on provided evidence, e.g. in the matched
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
723 normal. This is done at an early stage to avoid spending computational
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
724 resources on germline events. If the variant's germline status is
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
725 borderline, then Mutect2 will emit the variant to the callset for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
726 subsequent filtering and review.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
727
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
728 ::
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
729
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
730 gatk Mutect2 \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
731 -R reference.fa \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
732 -I tumor.bam \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
733 -tumor tumor_sample_name \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
734 -I normal.bam \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
735 -normal normal_sample_name \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
736 --germline-resource af-only-gnomad.vcf.gz \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
737 --af-of-alleles-not-in-resource 0.00003125 \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
738 --panel-of-normals pon.vcf.gz \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
739 -O somatic.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
740
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
741
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
742 The --af-of-alleles-not-in-resource argument value should match
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
743 expectations for alleles not found in the provided germline resource.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
744 Note the tool does not require a germline resource nor a panel of
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
745 normals (PoN) to run. The tool prefilters sites for the matched normal
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
746 and the PoN. For the germline resource, the tool prefilters on the
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
747 allele. Below is an excerpt of a known variants resource with population
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
748 allele frequencies
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
749
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
750 ::
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
751
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
752 #CHROM POS ID REF ALT QUAL FILTER INFO
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
753 1 10067 . T TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 30.35 PASS AC=3;AF=7.384E-5
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
754 1 10108 . CAACCCT C 46514.32 PASS AC=6;AF=1.525E-4
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
755 1 10109 . AACCCTAACCCT AAACCCT,* 89837.27 PASS AC=48,5;AF=0.001223,1.273E-4
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
756 1 10114 . TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA *,CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T 36728.97 PASS AC=55,9,1;AF=0.001373,2.246E-4,2.496E-5
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
757 1 10119 . CT C,* 251.23 PASS AC=5,1;AF=1.249E-4,2.498E-5
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
758 1 10120 . TA CA,* 14928.74 PASS AC=10,6;AF=2.5E-4,1.5E-4
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
759 1 10128 . ACCCTAACCCTAACCCTAAC A,* 285.71 PASS AC=3,1;AF=7.58E-5,2.527E-5
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
760 1 10131 . CT C,* 378.93 PASS AC=7,5;AF=1.765E-4,1.261E-4
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
761 1 10132 . TAACCC *,T 18025.11 PASS AC=12,2;AF=3.03E-4,5.049E-5
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
762
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
763
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
764 (ii) Tumor-only mode
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
765 ^^^^^^^^^^^^^^^^^^^^
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
766
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
767 This mode runs on a single sample, e.g. single tumor or single normal
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
768 sample. To create a PoN, call on each normal sample in this mode, then
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
769 use CreateSomaticPanelOfNormals to generate the PoN.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
770
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
771 ::
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
772
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
773 gatk Mutect2 \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
774 -R reference.fa \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
775 -I sample.bam \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
776 -tumor sample_name \
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
777 -O single_sample.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
778
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
779
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
780 Further points of interest
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
781 ~~~~~~~~~~~~~~~~~~~~~~~~~~
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
782
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
783 Additional parameters that factor towards filtering, including
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
784 normal-artifact-lod (default threshold 0.0) and tumor-lod (default
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
785 threshold 5.3), are available in FilterMutectCalls. While the tool
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
786 calculates normal-lod assuming a diploid genotype, it calculates
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
787 normal-artifact-lod with the same approach it uses for tumor-lod, i.e.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
788 with a variable ploidy assumption.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
789
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
790 - If the normal artifact log odds becomes large, then FilterMutectCalls applies the artifact-in-normal filter. For matched normal samples with tumor contamination, consider increasing the normal-artifact-lod threshold.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
791
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
792 - The tumor log odds, which is calculated independently of any matched normal, determines whether to filter a tumor variant. Variants with tumor LODs exceeding the threshold pass filtering.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
793
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
794
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
795 If a variant is absent from a given germline resource, then the value
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
796 for --af-of-alleles-not-in-resource applies. For example, gnomAD's
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
797 16,000 samples (~32,000 homologs per locus) becomes a probability of one
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
798 in 32,000 or less. Thus, an allele's absence from the germline resource
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
799 becomes evidence that it is not a germline variant.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
800
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
801 Caveats
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
802 ~~~~~~~
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
803
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
804 Although GATK4 Mutect2 accomodates varying coverage depths, further
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
805 optimization of parameters may improve calling for extreme high depths,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
806 e.g. 1000X.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
807 ]]></help>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
808 <citations>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
809 <expand macro="citations"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
810 </citations>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
811 </tool>