Mercurial > repos > iuc > gatk4_mutect2

annotate gatk4_Mutect2.xml @ 8:55e8a08e39e1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
author iuc
date Tue, 03 Feb 2026 18:50:29 +0000
parents 91d37702c47b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
1 <tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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2 <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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3 <macros>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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4 <import>macros.xml</import>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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5 </macros>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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6 <expand macro="requirements"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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7 <expand macro="version_cmd"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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8 <command detect_errors="exit_code">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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9 <![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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10 #include source=$set_sections#
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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11 #include source=$pre_gatk_excl_ints_chth#
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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12 #include source=$pre_gatk_ints_chth#
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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13
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
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14 #set ref_flag='-R reference.fa'
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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15
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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16 #if str($reference_source.reference_source_selector) == 'history'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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17 ln -s '$reference_source.reference_sequence' reference.fa &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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18 samtools faidx reference.fa &&
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55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
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19 gatk CreateSequenceDictionary -R reference.fa -O reference.dict &&
4
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
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20 #else if str($reference_source.reference_source_selector) == 'cached'
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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21 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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22 samtools faidx reference.fa &&
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
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23 gatk CreateSequenceDictionary -R reference.fa -O reference.dict &&
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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24 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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25 #set ref_flag=''
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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26 #end if
4
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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27
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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28 #if str($mode.mode_parameters) == 'tumor_only'
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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29 ln -s $mode.tumor tumor.bam &&
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
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30 ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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31 #else
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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32 ln -s $mode.tumor tumor.bam &&
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
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33 ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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34 ln -s $mode.normal normal.bam &&
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
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35 ln -s $mode.normal.metadata.bam_index normal.bam.bai &&
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
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36 #end if
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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37
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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38 #if str($outputs.output_parameters) == 'yes'
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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39 #if str($outputs.debug_assembly) == 'yes'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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40 ln -s '$assembly_region_out' assembly-region.tab &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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41 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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42 #if str($outputs.debug_bam) == 'yes'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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43 ln -s '$bam_output' debug.bam &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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44 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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45 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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46
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
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47 gatk GetSampleName -I tumor.bam -O samplename.txt &&
2
5f71f3690b95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
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48 sample=`cat samplename.txt | sed 's/"//g'` &&
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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49
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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50 #if str($optional.optional_parameters) == 'yes'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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51 #if $optional.panel_of_normals
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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52 #set datatype = $optional.panel_of_normals.datatype
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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53 #if $optional.panel_of_normals.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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54 ln -s '$optional.panel_of_normals' panel_of_normals.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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55 tabix panel_of_normals.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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56 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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57 ln -s '$optional.panel_of_normals' panel_of_normals.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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58 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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59 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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60
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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61 #if $optional.germline_resource
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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62 #set datatype = $optional.germline_resource.datatype
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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63 #if $optional.germline_resource.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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64 ln -s '$optional.germline_resource' germline_resource.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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65 tabix germline_resource.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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66 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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67 ln -s '$optional.germline_resource' germline_resource.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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68 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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69 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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70
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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71 #if $optional.alleles
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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72 #set datatype = $optional.alleles.datatype
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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73 #if $optional.alleles.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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74 ln -s '$optional.alleles' alleles.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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75 tabix alleles.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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76 @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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77 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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78 ln -s '$optional.alleles' alleles.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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79 @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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80 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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81 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
82
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
83 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
84
2
5f71f3690b95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
iuc
parents: 1
diff changeset
85 gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
86
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
87 #if str($mode.mode_parameters) == 'tumor_only'
4
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
parents: 3
diff changeset
88 --input tumor.bam
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
89 #else
4
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
parents: 3
diff changeset
90 --input tumor.bam
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
parents: 3
diff changeset
91 --input normal.bam
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
92 #end if
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
93
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
94 ## OPTIONAL PARAMETERS ##
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
95
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
96 #if str($optional.optional_parameters) == 'yes'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
97
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
98 #if $optional.panel_of_normals
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
99 #if $optional.panel_of_normals.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
100 --panel-of-normals panel_of_normals.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
101 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
102 --panel-of-normals panel_of_normals.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
103 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
104 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
105
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
106 #if $optional.pedigree
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
107 --pedigree "$optional.pedigree"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
108 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
109
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
110 #if $optional.germline_resource
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
111 #if $optional.germline_resource.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
112 --germline-resource germline_resource.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
113 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
114 --germline-resource germline_resource.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
115 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
116 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
117
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
118 #if $optional.annotation
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
119 #for $annot in str($optional.annotation).split(',')
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
120 --annotation "$annot"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
121 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
122 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
123
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
124 #if $optional.annotation_group
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
125 #for $annot in str($optional.annotation_group).split(',')
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
126 --annotation-group "$annot"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
127 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
128 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
129
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
130 #if $optional.annotations_to_exclude
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
131 #for $annot in str($optional.annotations_to_exclude).split(',')
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
132 --annotations-to-exclude "$annot"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
133 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
134 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
135
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
136 #if $optional.founder_id
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
137 --founder-id "$optional.founder_id"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
138 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
139
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
140 #if $optional.normal_sample
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
141 --normal-sample "$optional.normal_sample"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
142 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
143
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
144 #if $optional.alleles
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
145 --alleles alleles.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
146 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
147
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
148 #if $optional.f1r2_max_depth:
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
149 --f1r2-max-depth "$optional.f1r2_max_depth"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
150 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
151
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
152 #if $optional.f1r2_median_mq:
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
153 --f1r2-median-mq "$optional.f1r2_median_mq"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
154 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
155
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
156 #if $optional.f1r2_min_bq:
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
157 --f1r2-min-bq "$optional.f1r2_min_bq"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
158 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
159
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
160 #if $optional.interval_merging_rule:
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
161 --interval-merging-rule "$optional.interval_merging_rule"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
162 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
163
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
164 #if $optional.interval_set_rule:
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
165 --interval-set-rule "$optional.interval_set_rule"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
166 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
167
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
168 #if $optional.pcr_indel_qual:
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
169 --pcr-indel-qual "$optional.pcr_indel_qual"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
170 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
171
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
172 #if $optional.pcr_snv_qual:
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
173 --pcr-snv-qual "$optional.pcr_snv_qual"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
174 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
175
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
176 #if $optional.read_filter
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
177 #for $filter in str($optional.read_filter).split(',')
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
178 --read-filter "$filter"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
179 #end for
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
180 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
181
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
182 #if $optional.disable_read_filter
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
183 #for $filter in str($optional.disable_read_filter).split(',')
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
184 --disable-read-filter "$filter"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
185 #end for
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
186 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
187
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
188 --base-quality-score-threshold "$optional.base_quality_score_threshold"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
189 --af-of-alleles-not-in-resource "$optional.af_of_alleles_not_in_resource"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
190 --downsampling-stride "$optional.downsampling_stride"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
191 --gcs-max-retries "$optional.gcs_max_retries"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
192 --initial-tumor-lod "$optional.initial_tumor_lod"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
193 --max-population-af "$optional.max_population_af"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
194 --max-reads-per-alignment-start "$optional.max_reads_per_alignment_start"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
195 --min-base-quality-score "$optional.min_base_quality_score"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
196 --native-pair-hmm-threads "\${GALAXY_SLOTS:-1}"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
197 --normal-lod "$optional.normal_lod"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
198 --read-validation-stringency "$optional.read_validation_stringency"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
199 --tumor-lod-to-emit "$optional.tumor_lod_to_emit"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
200 --verbosity "ERROR"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
201 $optional.lenient
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
202 $optional.annotate_with_num_discovered_alleles
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
203 $optional.add_output_sam_program_record
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
204 $optional.disable_bam_index_caching
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
205 $optional.disable_sequence_dictionary_validation
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
206 $optional.genotype_germline_sites
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
207 $optional.genotype_pon_sites
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
208 $optional.ignore_itr_artifacts
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
209 $optional.mitochondria_mode
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
210 $optional.native_pair_hmm_use_double_precision
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
211 $optional.sites_only_vcf_output
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
212 $optional.add_output_vcf_command_line
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
213 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
214
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
215 ## END OPTIONAL PARAMETERS ##
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
216
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
217 ## ADVANCED PARAMETERS ##
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
218
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
219 #if str($advanced.advanced_parameters) == 'yes'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
220
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
221 #if $advanced.kmer_size
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
222 --kmer-size "$advanced.kmer_size"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
223 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
224
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
225 #if $advanced.gvcf_lod_band
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
226 --gvcf-lod-band "$advanced.gvcf_lod_band"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
227 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
228
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
229 #if $advanced.emit_ref_confidence
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
230 --emit-ref-confidence "$advanced.emit_ref_confidence"
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
231 #end if
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
232
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
233 #if $advanced.max_unpruned_variants
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
234 --max-unpruned-variants "$advanced.max_unpruned_variants"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
235 #end if
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
236 --allele-informative-reads-overlap-margin "$advanced.allele_informative_reads_overlap_margin"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
237 --active-probability-threshold "$advanced.active_probability_threshold"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
238 --assembly-region-padding "$advanced.assembly_region_padding"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
239 --bam-writer-type "$advanced.bam_writer_type"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
240 --max-assembly-region-size "$advanced.max_assembly_region_size"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
241 --max-mnp-distance "$advanced.max_mnp_distance"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
242 --max-num-haplotypes-in-population "$advanced.max_num_haplotypes_in_population"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
243 --max-prob-propagation-distance "$advanced.max_prob_propagation_distance"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
244 --max-suspicious-reads-per-alignment-start "$advanced.max_suspicious_reads_per_alignment_start"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
245 --min-assembly-region-size "$advanced.min_assembly_region_size"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
246 --min-dangling-branch-length "$advanced.min_dangling_branch_length"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
247 --min-pruning "$advanced.min_pruning"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
248 --minimum-allele-fraction "$advanced.minimum_allele_fraction"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
249 --num-pruning-samples "$advanced.num_pruning_samples"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
250 --pair-hmm-gap-continuation-penalty "$advanced.pair_hmm_gap_continuation_penalty"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
251 --callable-depth "$advanced.callable_depth"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
252 --pair-hmm-implementation "$advanced.pair_hmm_implementation"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
253 --pcr-indel-model "$advanced.pcr_indel_model"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
254 --phred-scaled-global-read-mismapping-rate "$advanced.phred_scaled_global_read_mismapping_rate"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
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255 --pruning-lod-threshold "$advanced.pruning_lod_threshold"
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
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256 --smith-waterman "$advanced.smith_waterman"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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257 $advanced.allow_non_unique_kmers_in_ref
1
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258 $advanced.disable_adaptive_pruning
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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259 $advanced.disable_tool_default_annotations
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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260 $advanced.disable_tool_default_read_filters
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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261 $advanced.dont_increase_kmer_sizes_for_cycles
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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262 $advanced.dont_use_soft_clipped_bases
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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263 $advanced.enable_all_annotations
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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264 $advanced.force_active
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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265 $advanced.force_call_filtered_alleles
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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266 $advanced.independent_mates
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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267 $advanced.recover_all_dangling_branches
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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268 $advanced.use_filtered_reads_for_annotations
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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269
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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270 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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271
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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272 ## END ADVANCED PARAMETERS ##
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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273
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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274 ## ADDITIONAL OUTPUT PARAMETERS ##
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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275
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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276 #if str($outputs.output_parameters) == 'yes'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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277 #if str($outputs.debug_assembly) == 'yes'
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
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278 --assembly-region-out "assembly-region.tab"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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279 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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280 #if str($outputs.debug_bam) == 'yes'
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
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281 --bam-output "debug.bam"
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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282 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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283 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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284
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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285 #include source=$gatk_excl_ints_chth#
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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286 #include source=$gatk_ints_chth#
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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287 #include source=$vcf_output_opts#
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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288 #include source=$gatk_seqdict#
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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289 ]]>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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290 </command>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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291 <inputs>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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292 <conditional name="mode">
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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293 <param name="mode_parameters" type="select" label="Type of analysis">
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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294 <option value="tumor_only">Tumor-only</option>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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295 <option value="somatic">Somatic</option>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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296 </param>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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297 <when value="tumor_only">
4
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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298 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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299 </when>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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300 <when value="somatic">
4
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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301 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
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302 <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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303 </when>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
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304 </conditional>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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305 <expand macro="gzip_vcf_params"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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306 <expand macro="ref_sel"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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307 <conditional name="optional">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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308 <param name="optional_parameters" type="select" label="Optional parameters">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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309 <option value="no">Use internal defaults</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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310 <option value="yes">Specify parameters</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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311 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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312 <when value="yes">
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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313 <expand macro="gatk_excl_ints"/>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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314 <expand macro="gatk_ints"/>
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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315 <expand macro="seq_dict_sel"/>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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316 <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."/>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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317 <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."/>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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318 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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319 <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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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320 <param argument="--annotation" type="select" multiple="true" label="Annotations" help="One or more specific annotations to add to variant calls">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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321 <option value="AlleleFraction">AlleleFraction</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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322 <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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323 <option value="AS_FisherStrand">AS_FisherStrand</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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324 <option value="AS_InbreedingCoeff">AS_InbreedingCoeff</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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325 <option value="AS_MappingQualityRankSumTest">AS_MappingQualityRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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326 <option value="AS_QualByDepth">AS_QualByDepth</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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327 <option value="AS_ReadPosRankSumTest">AS_ReadPosRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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328 <option value="AS_RMSMappingQuality">AS_RMSMappingQuality</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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329 <option value="AS_StrandOddsRatio">AS_StrandOddsRatio</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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330 <option value="BaseQuality">BaseQuality</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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331 <option value="BaseQualityHistogram">BaseQualityHistogram</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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332 <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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333 <option value="ChromosomeCounts">ChromosomeCounts</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
334 <option value="ClippingRankSumTest">ClippingRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
335 <option value="CountNs">CountNs</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
336 <option value="Coverage">Coverage</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
337 <option value="DepthPerAlleleBySample">DepthPerAlleleBySample</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
338 <option value="DepthPerSampleHC">DepthPerSampleHC</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
339 <option value="ExcessHet">ExcessHet</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
340 <option value="FisherStrand">FisherStrand</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
341 <option value="FragmentLength">FragmentLength</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
342 <option value="GenotypeSummaries">GenotypeSummaries</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
343 <option value="InbreedingCoeff">InbreedingCoeff</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
344 <option value="LikelihoodRankSumTest">LikelihoodRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
345 <option value="MappingQuality">MappingQuality</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
346 <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
347 <option value="MappingQualityZero">MappingQualityZero</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
348 <option value="OrientationBiasReadCounts">OrientationBiasReadCounts</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
349 <option value="OriginalAlignment">OriginalAlignment</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
350 <option value="PossibleDeNovo">PossibleDeNovo</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
351 <option value="QualByDepth">QualByDepth</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
352 <option value="ReadPosition">ReadPosition</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
353 <option value="ReadPosRankSumTest">ReadPosRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
354 <option value="ReferenceBases">ReferenceBases</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
355 <option value="RMSMappingQuality">RMSMappingQuality</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
356 <option value="SampleList">SampleList</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
357 <option value="StrandBiasBySample">StrandBiasBySample</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
358 <option value="StrandOddsRatio">StrandOddsRatio</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
359 <option value="TandemRepeat">TandemRepeat</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
360 <option value="UniqueAltReadCount">UniqueAltReadCount</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
361 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
362 <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">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
363 <option value="AlleleSpecificAnnotation">AlleleSpecificAnnotation</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
364 <option value="AS_StandardAnnotation">AS_StandardAnnotation</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
365 <option value="ReducibleAnnotation">ReducibleAnnotation</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
366 <option value="StandardAnnotation">StandardAnnotation</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
367 <option value="StandardHCAnnotation">StandardHCAnnotation</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
368 <option value="StandardMutectAnnotation">StandardMutectAnnotation</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
369 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
370 <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">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
371 <option value="AlleleFraction">AlleleFraction</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
372 <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
373 <option value="AS_FisherStrand">AS_FisherStrand</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
374 <option value="AS_InbreedingCoeff">AS_InbreedingCoeff</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
375 <option value="AS_MappingQualityRankSumTest">AS_MappingQualityRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
376 <option value="AS_QualByDepth">AS_QualByDepth</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
377 <option value="AS_ReadPosRankSumTest">AS_ReadPosRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
378 <option value="AS_RMSMappingQuality">AS_RMSMappingQuality</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
379 <option value="AS_StrandOddsRatio">AS_StrandOddsRatio</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
380 <option value="BaseQuality">BaseQuality</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
381 <option value="BaseQualityHistogram">BaseQualityHistogram</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
382 <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
383 <option value="ChromosomeCounts">ChromosomeCounts</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
384 <option value="ClippingRankSumTest">ClippingRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
385 <option value="CountNs">CountNs</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
386 <option value="Coverage">Coverage</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
387 <option value="DepthPerAlleleBySample">DepthPerAlleleBySample</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
388 <option value="DepthPerSampleHC">DepthPerSampleHC</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
389 <option value="ExcessHet">ExcessHet</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
390 <option value="FisherStrand">FisherStrand</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
391 <option value="FragmentLength">FragmentLength</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
392 <option value="GenotypeSummaries">GenotypeSummaries</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
393 <option value="InbreedingCoeff">InbreedingCoeff</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
394 <option value="LikelihoodRankSumTest">LikelihoodRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
395 <option value="MappingQuality">MappingQuality</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
396 <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
397 <option value="MappingQualityZero">MappingQualityZero</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
398 <option value="OrientationBiasReadCounts">OrientationBiasReadCounts</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
399 <option value="OriginalAlignment">OriginalAlignment</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
400 <option value="PossibleDeNovo">PossibleDeNovo</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
401 <option value="QualByDepth">QualByDepth</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
402 <option value="ReadPosition">ReadPosition</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
403 <option value="ReadPosRankSumTest">ReadPosRankSumTest</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
404 <option value="ReferenceBases">ReferenceBases</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
405 <option value="RMSMappingQuality">RMSMappingQuality</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
406 <option value="SampleList">SampleList</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
407 <option value="StrandBiasBySample">StrandBiasBySample</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
408 <option value="StrandOddsRatio">StrandOddsRatio</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
409 <option value="TandemRepeat">TandemRepeat</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
410 <option value="UniqueAltReadCount">UniqueAltReadCount</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
411 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
412 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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413 <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)"/>
1
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414 <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"/>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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415 <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."/>
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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416 <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">
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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417 <option value="GoodCigarReadFilter">Good cigar string</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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418 <option value="MappedReadFilter">Mapped read</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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419 <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
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parents: 0
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420 <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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parents: 0
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421 <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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422 <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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parents: 0
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423 <option value="NotDuplicateReadFilter">Not a duplicate read</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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424 <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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parents: 0
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425 <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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426 <option value="WellformedReadFilter">Well-formed read</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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427 </param>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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428 <param name="read_filter" argument="--read-filter" type="select" multiple="true" value="" label="Read Filter" help="Read filters to be applied before analysis">
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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429 <option value="AlignmentAgreesWithHeaderReadFilter">Alignment agrees with header</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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430 <option value="AllowAllReadsReadFilter">Allow all reads</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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431 <option value="AmbiguousBaseReadFilter">Ambiguous base</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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432 <option value="CigarContainsNoNOperator">Cigar contains no NO operator</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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433 <option value="FirstOfPairReadFilter">First of pair</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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434 <option value="GoodCigarReadFilter">Good cigar string</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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435 <option value="HasReadGroupReadFilter">Has read group</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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436 <option value="MappedReadFilter">Mapped read</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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437 <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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438 <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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439 <option value="MatchingBasesAndQualsReadFilter">Matching bases and quals</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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440 <option value="MateDifferentStrandReadFilter">Mate different strand</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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441 <option value="MateOnSameContigOrNoMappedMateReadFilter">Mate on same contig or no mapped mate</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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442 <option value="MateUnmappedAndUnmappedReadFilter">Mate unmapped and mapped</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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443 <option value="MetricsReadFilter">Metrics</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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444 <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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445 <option value="NonZeroFragmentLengthReadFilter">Non-zero fragment length</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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446 <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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447 <option value="NotDuplicateReadFilter">Not duplicate</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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448 <option value="NotOpticalDuplicateReadFilter">Not optical duplicate</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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449 <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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450 <option value="NotSupplementaryAlignmentReadFilter">Not a supplementary alignment</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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451 <option value="OverclippedReadFilter">Overclipped</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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452 <option value="PairedReadFilter">Paired</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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453 <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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454 <option value="PrimaryLineReadFilter">Primary line</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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455 <option value="ProperlyPairedReadFilter">Properly paired</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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456 <option value="ReadLengthEqualsCigarLengthReadFilter">Read length equals cigar length</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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457 <option value="SecondOfPairReadFilter">Second of pair</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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458 <option value="SeqIsStoredReadFilter">Sequence is stored</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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459 <option value="SoftClippedReadFilter">Soft clipped</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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460 <option value="ValidAlignmentStartReadFilter">Valid alignment start</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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461 <option value="ValidAlignmentEndReadFilter">Valid alignment end</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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462 <option value="WellformedReadFilter">Well-formed read</option>
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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463 </param>
0
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464 <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!"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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465 <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."/>
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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466 <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" />
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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467 <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" />
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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468 <param name="f1r2_min_bq" argument="--base-quality-score-threshold" type="integer" optional="true" value="20" label="Exclude bases below this quality from pileup" />
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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469 <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;"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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470 <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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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471 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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472 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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473 <param name="alleles" argument="--alleles" type="data" optional="true" format="vcf" label="Alleles" help="The set of alleles at which to genotype"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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474 <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."/>
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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475 <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" />
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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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."/>
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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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" />
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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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" />
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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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">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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480 <option selected="true" value="ALL">All</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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481 <option value="OVERLAPPING_ONLY">Overlapping only</option>
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482 </param>
1
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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">
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484 <option selected="true" value="UNION">Union</option>
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485 <option value="INTERSECTION">Intersection</option>
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486 </param>
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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"/>
0
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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."/>
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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."/>
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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"/>
1
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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" />
0
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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"/>
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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."/>
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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."/>
1
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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."/>
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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" />
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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" />
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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."/>
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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.">
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500 <option selected="true" value="SILENT">Silent</option>
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501 <option value="STRICT">Strict</option>
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502 <option value="LENIENT">Lenient</option>
0
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503 </param>
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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."/>
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505 </when>
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506 <when value="no" />
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507 </conditional>
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508 <conditional name="advanced">
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509 <param name="advanced_parameters" type="select" label="Advanced parameters">
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510 <option value="no">Use internal defaults</option>
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511 <option value="yes">Specify parameters</option>
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512 </param>
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513 <when value="yes">
3
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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."/>
0
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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."/>
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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"/>
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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"/>
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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">
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519 <option selected="true" value="CALLED_HAPLOTYPES">Called haplotypes</option>
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520 <option value="ALL_POSSIBLE_HAPLOTYPES">All possible haplotypes</option>
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521 </param>
1
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522
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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"/>
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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"/>
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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"/>
0
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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"/>
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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"/>
1
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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">
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529 <option value="NONE">None</option>
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530 <option value="BP_RESOLUTION">Basepair resolution</option>
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531 <option value="GVCF">Genomic VCF</option>
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532 </param>
0
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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)"/>
1
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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"/>
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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"/>
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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)" />
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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" />
0
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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"/>
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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"/>
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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."/>
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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"/>
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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"/>
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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."/>
1
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parents: 0
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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"/>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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"/>
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
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"/>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
552 <option selected="true" value="FASTEST_AVAILABLE">Fastest Available</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
553 <option value="EXACT">Exact</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
554 <option value="ORIGINAL">Original</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
555 <option value="LOGLESS_CACHING">Logless Caching</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
556 <option value="AVX_LOGLESS_CACHING">Logless Caching (AVX)</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
557 <option value="AVX_LOGLESS_CACHING_OMP">Logless Caching (AVX+OMP)</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
558 <option value="EXPERIMENTAL_FPGA_LOGLESS_CACHING">Logless Caching (FPGA, Experimental)</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
559 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
561 <option selected="true" value="CONSERVATIVE">Conservative</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
562 <option value="NONE">None</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
563 <option value="HOSTILE">Hostile</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
564 <option value="AGGRESSIVE">Aggressive</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
565 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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"/>
1
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
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" />
09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
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" />
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
570 <option selected="true" value="FASTEST_AVAILABLE">Fastest available</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
571 <option value="AVX_ENABLED">AVX-Enabled</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
572 <option value="JAVA">JAVA</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
573 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
575 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
576 <when value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
577 </conditional>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
578 <conditional name="outputs">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
579 <param name="output_parameters" type="select" label="Output parameters" help="Additional outputs for debugging purposes">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
580 <option value="no">Output only variants</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
581 <option value="yes">Generate debugging information</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
582 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
583 <when value="yes">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
584 <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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
585 <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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
586 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
587 <when value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
588 </conditional>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
589 </inputs>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
590 <outputs>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
591 <expand macro="gzip_vcf_output_params"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
592 <data format="tabular" name="assembly_region_out" label="${tool.name} on ${on_string}: Assembly region">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
593 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_assembly']</filter>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
594 </data>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
595 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: Debug BAM output">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
596 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_bam']</filter>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
597 </data>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
598 </outputs>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
599 <tests>
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
600 <test expect_num_outputs='1'>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
601 <conditional name="mode">
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
602 <param name="mode_parameters" value="tumor_only"/>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
603 <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
604 </conditional>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
605 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
606 <param name="gzipped_output" value="false" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
607 <param name="reference_source_selector" value="history" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
608 <param name="optional_parameters" value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
609 <param name="advanced_parameters" value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
610 <param name="output_parameters" value="no" />
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
611 <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="48">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
612 <assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
613 <has_n_lines n="90"/>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
614 </assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
615 </output>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
616 </test>
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
617 <test expect_num_outputs='1'>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
618 <conditional name="mode">
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
619 <param name="mode_parameters" value="tumor_only"/>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
620 <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
621 </conditional>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
622 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
623 <param name="gzipped_output" value="false" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
624 <param name="reference_source_selector" value="history" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
625 <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" />
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
626 <param name="seqdict_source_selector" value="history" />
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
627 <param name="seqdict_sequence" value="Mutect2-in2.dict" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
628 <param name="optional_parameters" value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
629 <param name="advanced_parameters" value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
630 <param name="output_parameters" value="no" />
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
631 <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="48">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
632 <assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
633 <has_n_lines n="128"/>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
634 </assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
635 </output>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
636 </test>
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
637 <test expect_num_outputs='1'>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
638 <conditional name="mode">
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
639 <param name="mode_parameters" value="tumor_only"/>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
640 <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
641 </conditional>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
642 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
643 <param name="gzipped_output" value="false" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
644 <param name="reference_source_selector" value="history" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
645 <param name="optional_parameters" value="yes" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
646 <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
647 <param name="annotation_group" value="StandardMutectAnnotation" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
648 <param name="advanced_parameters" value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
649 <param name="output_parameters" value="no" />
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
650 <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="48">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
651 <assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
652 <has_n_lines n="67"/>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
653 </assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
654 </output>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
655 </test>
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
656 <test expect_num_outputs='1'>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
657 <conditional name="mode">
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
658 <param name="mode_parameters" value="tumor_only"/>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
659 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
660 </conditional>
4
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
parents: 3
diff changeset
661 <param name="reference_sequence" value="hg38"/>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
662 <param name="gzipped_output" value="false" />
4
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
parents: 3
diff changeset
663 <param name="reference_source_selector" value="cached" />
33da9009065f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit c9ff247c1f6923be538cae9565ce99975426e94f"
iuc
parents: 3
diff changeset
664 <param name="reference_sequence" value="hg38"/>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
665 <param name="optional_parameters" value="no" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
666 <param name="advanced_parameters" value="no" />
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
667 <param name="output_parameters" value="no" />
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
668 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="48">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
669 <assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
670 <has_n_lines n="85"/>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
671 </assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
672 </output>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
673 </test>
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
674 <test expect_num_outputs='3'>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
675 <conditional name="mode">
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
676 <param name="mode_parameters" value="tumor_only"/>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
677 <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
678 </conditional>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
679 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
680 <param name="gzipped_output" value="false" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
681 <param name="reference_source_selector" value="history" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
682 <param name="optional_parameters" value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
683 <param name="advanced_parameters" value="no" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
684 <param name="output_parameters" value="yes" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
685 <param name="debug_assembly" value="true" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
686 <param name="debug_bam" value="true" />
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
687 <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="48">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
688 <assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
689 <has_n_lines n="97"/>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
690 </assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
691 </output>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
692 <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
693 <output name="bam_output" file="Mutect2-out5.bam" ftype="bam" />
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
694 </test>
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
695 <test expect_num_outputs='1'>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
696 <conditional name="mode">
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
697 <param name="mode_parameters" value="somatic"/>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
698 <param name="tumor" ftype="bam" value="tumor.bam" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
699 <param name="normal" ftype="bam" value="normal.bam" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
700 </conditional>
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
701 <param name="reference_sequence" ftype="fasta" value="chr20.fa" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
702 <param name="gzipped_output" value="false" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
703 <param name="reference_source_selector" value="history" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
704 <param name="optional_parameters" value="no" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
705 <param name="advanced_parameters" value="no" />
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
706 <param name="output_parameters" value="no" />
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
707 <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="48">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
708 <assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
709 <has_n_lines n="66"/>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
710 </assert_contents>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
711 </output>
3
d2c0c2698f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
712 </test>
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
713 </tests>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
714 <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
715 variants include single nucleotide (SNV) and insertion and deletion
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
716 (indel) variants. The caller combines the DREAM challenge-winning
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
717 somatic genotyping engine of the original MuTect (`Cibulskis et al.,
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
718 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
719 with the assembly-based machinery of
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
720 `HaplotypeCaller <https://web.archive.org/web/20230530034638/https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__.
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
721
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
722 This tool is featured in the *Somatic Short Mutation calling Best
8
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
iuc
parents: 7
diff changeset
723 Practice Workflow*. See `this article <https://web.archive.org/web/20230228153229/https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__
6
04253ade1697 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 commit a786695a05177842dcc89ef6bb21b38d7e7ce2db"
iuc
parents: 5
diff changeset
724 for an overview of what traditional somatic calling entails, with usage examples. For the
0
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
725 latest pipeline scripts, see the `Mutect2 WDL scripts
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
726 directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
727 Although we present the tool for somatic calling, it may apply to other
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
728 contexts, such as mitochondrial variant calling.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
729
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
730 Usage examples
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
731 ~~~~~~~~~~~~~~
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
732
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
733 Example commands show how to run Mutect2 for typical scenarios. The two
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
734 modes are (i) *somatic mode* where a tumor sample is matched with a
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
735 normal sample in analysis and (ii) *tumor-only mode* where a single
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
736 sample's alignment data undergoes analysis.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
737
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
738 (i) Tumor with matched normal
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
739 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
740
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
741 Given a matched normal, Mutect2 is designed to call somatic variants
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
742 only. The tool includes logic to skip emitting variants that are clearly
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
743 present in the germline based on provided evidence, e.g. in the matched
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
744 normal. This is done at an early stage to avoid spending computational
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
745 resources on germline events. If the variant's germline status is
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
746 borderline, then Mutect2 will emit the variant to the callset for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
747 subsequent filtering and review.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
748
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
749 ::
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
750
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
751 gatk Mutect2 \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
752 -R reference.fa \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
753 -I tumor.bam \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
754 -tumor tumor_sample_name \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
755 -I normal.bam \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
756 -normal normal_sample_name \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
757 --germline-resource af-only-gnomad.vcf.gz \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
758 --af-of-alleles-not-in-resource 0.00003125 \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
759 --panel-of-normals pon.vcf.gz \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
760 -O somatic.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
761
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
762
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
763 The --af-of-alleles-not-in-resource argument value should match
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
764 expectations for alleles not found in the provided germline resource.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
765 Note the tool does not require a germline resource nor a panel of
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
766 normals (PoN) to run. The tool prefilters sites for the matched normal
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
767 and the PoN. For the germline resource, the tool prefilters on the
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
768 allele. Below is an excerpt of a known variants resource with population
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
769 allele frequencies
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
770
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
771 ::
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
772
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
773 #CHROM POS ID REF ALT QUAL FILTER INFO
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
774 1 10067 . T TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 30.35 PASS AC=3;AF=7.384E-5
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
775 1 10108 . CAACCCT C 46514.32 PASS AC=6;AF=1.525E-4
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
776 1 10109 . AACCCTAACCCT AAACCCT,* 89837.27 PASS AC=48,5;AF=0.001223,1.273E-4
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
777 1 10114 . TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA *,CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T 36728.97 PASS AC=55,9,1;AF=0.001373,2.246E-4,2.496E-5
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
778 1 10119 . CT C,* 251.23 PASS AC=5,1;AF=1.249E-4,2.498E-5
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
779 1 10120 . TA CA,* 14928.74 PASS AC=10,6;AF=2.5E-4,1.5E-4
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
780 1 10128 . ACCCTAACCCTAACCCTAAC A,* 285.71 PASS AC=3,1;AF=7.58E-5,2.527E-5
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
781 1 10131 . CT C,* 378.93 PASS AC=7,5;AF=1.765E-4,1.261E-4
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
782 1 10132 . TAACCC *,T 18025.11 PASS AC=12,2;AF=3.03E-4,5.049E-5
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
783
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
784
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
785 (ii) Tumor-only mode
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
786 ^^^^^^^^^^^^^^^^^^^^
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
787
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
788 This mode runs on a single sample, e.g. single tumor or single normal
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
789 sample. To create a PoN, call on each normal sample in this mode, then
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
790 use CreateSomaticPanelOfNormals to generate the PoN.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
791
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
792 ::
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
793
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
794 gatk Mutect2 \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
795 -R reference.fa \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
796 -I sample.bam \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
797 -tumor sample_name \
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
798 -O single_sample.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
799
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
800
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
801 Further points of interest
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
802 ~~~~~~~~~~~~~~~~~~~~~~~~~~
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
803
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
804 Additional parameters that factor towards filtering, including
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
805 normal-artifact-lod (default threshold 0.0) and tumor-lod (default
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
806 threshold 5.3), are available in FilterMutectCalls. While the tool
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
807 calculates normal-lod assuming a diploid genotype, it calculates
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
808 normal-artifact-lod with the same approach it uses for tumor-lod, i.e.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
809 with a variable ploidy assumption.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
810
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
811 - 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.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
812
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
813 - 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.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
814
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
815
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
816 If a variant is absent from a given germline resource, then the value
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
817 for --af-of-alleles-not-in-resource applies. For example, gnomAD's
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
818 16,000 samples (~32,000 homologs per locus) becomes a probability of one
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
819 in 32,000 or less. Thus, an allele's absence from the germline resource
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
820 becomes evidence that it is not a germline variant.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
821
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
822 Caveats
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
823 ~~~~~~~
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
824
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
825 Although GATK4 Mutect2 accomodates varying coverage depths, further
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
826 optimization of parameters may improve calling for extreme high depths,
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
827 e.g. 1000X.
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
828 ]]></help>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
829 <citations>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
830 <expand macro="citations"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
831 </citations>
2
5f71f3690b95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
iuc
parents: 1
diff changeset
832 </tool>