Mercurial > repos > iuc > gatk4_mutect2

annotate gatk4_Mutect2.xml @ 4:1cea23583655 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
author iuc
date Fri, 14 Aug 2020 04:55:49 -0400
parents 287c4af133e6
children 53ce8be43212
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
1 <tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@" profile="18.05">
0
f41a1e03538b "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>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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3 <macros>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
4 <import>macros.xml</import>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
5 </macros>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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6 <expand macro="requirements"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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7 <expand macro="version_cmd"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
8 <command detect_errors="exit_code">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
9 <![CDATA[
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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10 #include source=$set_sections#
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
11 #include source=$pre_gatk_excl_ints_chth#
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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12 #include source=$pre_gatk_ints_chth#
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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13
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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14 #set ref_flag='--reference="reference.fa"'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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15
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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16 #if str($reference_source.reference_source_selector) == 'history'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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17 ln -s '$reference_source.reference_sequence' reference.fa &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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18 samtools faidx reference.fa &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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19 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
4
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
20 #else if str($reference_source.reference_source_selector) == 'cached'
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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21 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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22 samtools faidx reference.fa &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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23 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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24 #else
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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25 #set ref_flag=''
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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26 #end if
4
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
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27
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
28 #if str($mode.mode_parameters) == 'tumor_only'
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
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29 ln -s $mode.tumor tumor.bam &&
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
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30 ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
31 #else
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
32 ln -s $mode.tumor tumor.bam &&
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
33 ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
34 ln -s $mode.normal normal.bam &&
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
35 ln -s $mode.normal.metadata.bam_index normal.bam.bai &&
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
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36 #end if
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
37
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
38 #if str($outputs.output_parameters) == 'yes'
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
39 #if str($outputs.debug_assembly) == 'yes'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
40 ln -s '$assembly_region_out' assembly-region.tab &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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41 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
42 #if str($outputs.debug_bam) == 'yes'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
43 ln -s '$bam_output' debug.bam &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
44 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
45 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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46
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
47 gatk GetSampleName --input="tumor.bam" --output="samplename.txt" &&
2
3be27a9a7313 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
iuc
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48 sample=`cat samplename.txt | sed 's/"//g'` &&
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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49
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
50 #if str($optional.optional_parameters) == 'yes'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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51 #if $optional.panel_of_normals
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
52 #set datatype = $optional.panel_of_normals.datatype
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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53 #if $optional.panel_of_normals.is_of_type("vcf_bgzip")
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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54 ln -s '$optional.panel_of_normals' panel_of_normals.vcf.gz &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
55 tabix panel_of_normals.vcf.gz &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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56 #else
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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57 ln -s '$optional.panel_of_normals' panel_of_normals.vcf &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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58 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
59 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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60
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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61 #if $optional.germline_resource
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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62 #set datatype = $optional.germline_resource.datatype
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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63 #if $optional.germline_resource.is_of_type("vcf_bgzip")
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
64 ln -s '$optional.germline_resource' germline_resource.vcf.gz &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
65 tabix germline_resource.vcf.gz &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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66 #else
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
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67 ln -s '$optional.germline_resource' germline_resource.vcf &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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68 #end if
f41a1e03538b "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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
70
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
71 #if $optional.alleles
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
72 #set datatype = $optional.alleles.datatype
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
73 #if $optional.alleles.is_of_type("vcf_bgzip")
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
74 ln -s '$optional.alleles' alleles.vcf.gz &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
75 tabix alleles.vcf.gz &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
76 @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf.gz &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
77 #else
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
78 ln -s '$optional.alleles' alleles.vcf &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
79 @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf &&
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
80 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
81 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
82
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
83 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
84
2
3be27a9a7313 "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 $ref_flag --tumor-sample "\$sample"
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
86
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
87 #if str($mode.mode_parameters) == 'tumor_only'
4
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
88 --input tumor.bam
3
287c4af133e6 "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
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
90 --input tumor.bam
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
91 --input normal.bam
3
287c4af133e6 "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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
93
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
94 ## OPTIONAL PARAMETERS ##
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
95
f41a1e03538b "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'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
97
f41a1e03538b "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
f41a1e03538b "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")
f41a1e03538b "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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
101 #else
f41a1e03538b "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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
103 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
104 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
105
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
106 #if $optional.pedigree
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
107 --pedigree="$optional.pedigree"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
108 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
109
f41a1e03538b "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
f41a1e03538b "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")
f41a1e03538b "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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
113 #else
f41a1e03538b "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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
115 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
116 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
117
f41a1e03538b "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
f41a1e03538b "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(',')
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
120 --annotation="$annot"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
121 #end for
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
122 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
123
f41a1e03538b "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
f41a1e03538b "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(',')
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
126 --annotation-group="$annot"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
127 #end for
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
128 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
129
f41a1e03538b "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
f41a1e03538b "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(',')
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
132 --annotations-to-exclude="$annot"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
133 #end for
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
134 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
135
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
136 #if $optional.founder_id
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
137 --founder-id="$optional.founder_id"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
138 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
139
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
140 #if $optional.normal_sample
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
141 --normal-sample="$optional.normal_sample"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
142 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
143
f41a1e03538b "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
f41a1e03538b "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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
146 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
147
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
148 #if $optional.f1r2_max_depth:
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
149 --f1r2-max-depth="$optional.f1r2_max_depth"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
151
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
152 #if $optional.f1r2_max_depth:
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
153 --f1r2-median-mq="$optional.f1r2_median_mq"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
155
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
156 #if $optional.f1r2_max_depth:
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
157 --f1r2-min-bq="$optional.f1r2_min_bq"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
159
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
160 #if $optional.interval_merging_rule:
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
161 --interval-merging-rule="$optional.interval_merging_rule"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
163
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
164 #if $optional.interval_set_rule:
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
165 --interval-set-rule="$optional.interval_set_rule"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
167
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
168 #if $optional.pcr_indel_qual:
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
169 --pcr-indel-qual="$optional.pcr_indel_qual"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
171
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
172 #if $optional.pcr_snv_qual:
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
173 --pcr-snv-qual="$optional.pcr_snv_qual"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
175
fd2d6e035c3f "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
fd2d6e035c3f "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(',')
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
178 --read-filter="$filter"
fd2d6e035c3f "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
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
181
fd2d6e035c3f "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
fd2d6e035c3f "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(',')
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
184 --disable-read-filter="$filter"
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
185 #end for
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
186 #end if
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
187
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
188 --base-quality-score-threshold="$optional.base_quality_score_threshold"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
189 --af-of-alleles-not-in-resource="$optional.af_of_alleles_not_in_resource"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
190 --downsampling-stride="$optional.downsampling_stride"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
191 --gcs-max-retries="$optional.gcs_max_retries"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
192 --initial-tumor-lod="$optional.initial_tumor_lod"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
193 --max-population-af="$optional.max_population_af"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
194 --max-reads-per-alignment-start="$optional.max_reads_per_alignment_start"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
195 --min-base-quality-score="$optional.min_base_quality_score"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
196 --native-pair-hmm-threads="\${GALAXY_SLOTS:-1}"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
197 --normal-lod="$optional.normal_lod"
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
198 --read-validation-stringency="$optional.read_validation_stringency"
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
199 --tumor-lod-to-emit="$optional.tumor_lod_to_emit"
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
200 --verbosity="ERROR"
fd2d6e035c3f "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
f41a1e03538b "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
fd2d6e035c3f "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
f41a1e03538b "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
f41a1e03538b "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
f41a1e03538b "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
f41a1e03538b "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
fd2d6e035c3f "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
fd2d6e035c3f "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
f41a1e03538b "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
f41a1e03538b "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
212 $optional.add_output_vcf_command_line
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
213 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
214
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
215 ## END OPTIONAL PARAMETERS ##
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
216
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
217 ## ADVANCED PARAMETERS ##
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
218
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
219 #if str($advanced.advanced_parameters) == 'yes'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
220
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
221 #if $advanced.kmer_size
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
222 --kmer-size="$advanced.kmer_size"
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
223 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
224
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
225 #if $advanced.gvcf_lod_band
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
226 --gvcf-lod-band="$advanced.gvcf_lod_band"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
228
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
229 #if $advanced.emit_ref_confidence
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
230 --emit-ref-confidence="$advanced.emit_ref_confidence"
fd2d6e035c3f "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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
232
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
233 #if $advanced.max_unpruned_variants
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
234 --max-unpruned-variants="$advanced.max_unpruned_variants"
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
235 #end if
4
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
236 --allele-informative-reads-overlap-margin="$advanced.allele_informative_reads_overlap_margin"
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
237 --active-probability-threshold="$advanced.active_probability_threshold"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
238 --assembly-region-padding="$advanced.assembly_region_padding"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
239 --bam-writer-type="$advanced.bam_writer_type"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
240 --max-assembly-region-size="$advanced.max_assembly_region_size"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
241 --max-mnp-distance="$advanced.max_mnp_distance"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
242 --max-num-haplotypes-in-population="$advanced.max_num_haplotypes_in_population"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
243 --max-prob-propagation-distance="$advanced.max_prob_propagation_distance"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
244 --max-suspicious-reads-per-alignment-start="$advanced.max_suspicious_reads_per_alignment_start"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
245 --min-assembly-region-size="$advanced.min_assembly_region_size"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
246 --min-dangling-branch-length="$advanced.min_dangling_branch_length"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
247 --min-pruning="$advanced.min_pruning"
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
248 --minimum-allele-fraction="$advanced.minimum_allele_fraction"
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
249 --num-pruning-samples="$advanced.num_pruning_samples"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
250 --pair-hmm-gap-continuation-penalty="$advanced.pair_hmm_gap_continuation_penalty"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
251 --pair-hmm-implementation="$advanced.pair_hmm_implementation"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
252 --pcr-indel-model="$advanced.pcr_indel_model"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
253 --phred-scaled-global-read-mismapping-rate="$advanced.phred_scaled_global_read_mismapping_rate"
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
254 --pruning-lod-threshold="$advanced.pruning_lod_threshold"
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
255 --smith-waterman="$advanced.smith_waterman"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
256 $advanced.allow_non_unique_kmers_in_ref
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
257 $advanced.disable_adaptive_pruning
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
258 $advanced.disable_tool_default_annotations
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
259 $advanced.disable_tool_default_read_filters
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
260 $advanced.dont_increase_kmer_sizes_for_cycles
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
261 $advanced.dont_use_soft_clipped_bases
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
262 $advanced.enable_all_annotations
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
263 $advanced.force_active
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
264 $advanced.force_call_filtered_alleles
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
265 $advanced.independent_mates
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
266 $advanced.recover_all_dangling_branches
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
267 $advanced.use_filtered_reads_for_annotations
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
268
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
269 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
270
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
271 ## END ADVANCED PARAMETERS ##
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
272
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
273 ## ADDITIONAL OUTPUT PARAMETERS ##
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
274
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
275 #if str($outputs.output_parameters) == 'yes'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
276 #if str($outputs.debug_assembly) == 'yes'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
277 --assembly-region-out="assembly-region.tab"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
278 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
279 #if str($outputs.debug_bam) == 'yes'
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
280 --bam-output="debug.bam"
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
281 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
282 #end if
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
283
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
284 #include source=$gatk_excl_ints_chth#
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
285 #include source=$gatk_ints_chth#
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
286 #include source=$vcf_output_opts#
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
287 #include source=$gatk_seqdict#
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
288 ]]>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
289 </command>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
290 <inputs>
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
291 <conditional name="mode">
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
292 <param name="mode_parameters" type="select" label="Type of analysis">
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
293 <option value="tumor_only">Tumor-only</option>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
294 <option value="somatic">Somatic</option>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
295 </param>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
296 <when value="tumor_only">
4
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
297 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
298 </when>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
299 <when value="somatic">
4
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
300 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
301 <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
302 </when>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
303 </conditional>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
304 <expand macro="gzip_vcf_params"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
305 <expand macro="ref_sel"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
306 <conditional name="optional">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
307 <param name="optional_parameters" type="select" label="Optional parameters">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
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308 <option value="no">Use internal defaults</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
309 <option value="yes">Specify parameters</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
310 </param>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
311 <when value="yes">
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
312 <expand macro="gatk_excl_ints"/>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
313 <expand macro="gatk_ints"/>
1
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
314 <expand macro="seq_dict_sel"/>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
315 <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."/>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
diff changeset
316 <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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
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diff changeset
317 <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."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
318 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
319 <param argument="--annotation" type="select" multiple="true" label="Annotations" help="One or more specific annotations to add to variant calls">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
320 <option value="AlleleFraction">AlleleFraction</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
321 <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
322 <option value="AS_FisherStrand">AS_FisherStrand</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
323 <option value="AS_InbreedingCoeff">AS_InbreedingCoeff</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
324 <option value="AS_MappingQualityRankSumTest">AS_MappingQualityRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
325 <option value="AS_QualByDepth">AS_QualByDepth</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
326 <option value="AS_ReadPosRankSumTest">AS_ReadPosRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
327 <option value="AS_RMSMappingQuality">AS_RMSMappingQuality</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
328 <option value="AS_StrandOddsRatio">AS_StrandOddsRatio</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
329 <option value="BaseQuality">BaseQuality</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
330 <option value="BaseQualityHistogram">BaseQualityHistogram</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
331 <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
332 <option value="ChromosomeCounts">ChromosomeCounts</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
333 <option value="ClippingRankSumTest">ClippingRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
334 <option value="CountNs">CountNs</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
335 <option value="Coverage">Coverage</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
336 <option value="DepthPerAlleleBySample">DepthPerAlleleBySample</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
337 <option value="DepthPerSampleHC">DepthPerSampleHC</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
338 <option value="ExcessHet">ExcessHet</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
339 <option value="FisherStrand">FisherStrand</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
340 <option value="FragmentLength">FragmentLength</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
341 <option value="GenotypeSummaries">GenotypeSummaries</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
342 <option value="InbreedingCoeff">InbreedingCoeff</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
343 <option value="LikelihoodRankSumTest">LikelihoodRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
344 <option value="MappingQuality">MappingQuality</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
345 <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
346 <option value="MappingQualityZero">MappingQualityZero</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
347 <option value="OrientationBiasReadCounts">OrientationBiasReadCounts</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
348 <option value="OriginalAlignment">OriginalAlignment</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
349 <option value="PossibleDeNovo">PossibleDeNovo</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
350 <option value="QualByDepth">QualByDepth</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
351 <option value="ReadPosition">ReadPosition</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
352 <option value="ReadPosRankSumTest">ReadPosRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
353 <option value="ReferenceBases">ReferenceBases</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
354 <option value="RMSMappingQuality">RMSMappingQuality</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
355 <option value="SampleList">SampleList</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
356 <option value="StrandBiasBySample">StrandBiasBySample</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
357 <option value="StrandOddsRatio">StrandOddsRatio</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
358 <option value="TandemRepeat">TandemRepeat</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
359 <option value="UniqueAltReadCount">UniqueAltReadCount</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
360 </param>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
361 <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">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
362 <option value="AlleleSpecificAnnotation">AlleleSpecificAnnotation</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
363 <option value="AS_StandardAnnotation">AS_StandardAnnotation</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
364 <option value="ReducibleAnnotation">ReducibleAnnotation</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
365 <option value="StandardAnnotation">StandardAnnotation</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
366 <option value="StandardHCAnnotation">StandardHCAnnotation</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
367 <option value="StandardMutectAnnotation">StandardMutectAnnotation</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
368 </param>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
369 <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">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
370 <option value="AlleleFraction">AlleleFraction</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
371 <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option>
f41a1e03538b "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_FisherStrand">AS_FisherStrand</option>
f41a1e03538b "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_InbreedingCoeff">AS_InbreedingCoeff</option>
f41a1e03538b "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_MappingQualityRankSumTest">AS_MappingQualityRankSumTest</option>
f41a1e03538b "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_QualByDepth">AS_QualByDepth</option>
f41a1e03538b "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_ReadPosRankSumTest">AS_ReadPosRankSumTest</option>
f41a1e03538b "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_RMSMappingQuality">AS_RMSMappingQuality</option>
f41a1e03538b "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_StrandOddsRatio">AS_StrandOddsRatio</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
379 <option value="BaseQuality">BaseQuality</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
380 <option value="BaseQualityHistogram">BaseQualityHistogram</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
381 <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
382 <option value="ChromosomeCounts">ChromosomeCounts</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
383 <option value="ClippingRankSumTest">ClippingRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
384 <option value="CountNs">CountNs</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
385 <option value="Coverage">Coverage</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
386 <option value="DepthPerAlleleBySample">DepthPerAlleleBySample</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
387 <option value="DepthPerSampleHC">DepthPerSampleHC</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
388 <option value="ExcessHet">ExcessHet</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
389 <option value="FisherStrand">FisherStrand</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
390 <option value="FragmentLength">FragmentLength</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
391 <option value="GenotypeSummaries">GenotypeSummaries</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
392 <option value="InbreedingCoeff">InbreedingCoeff</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
393 <option value="LikelihoodRankSumTest">LikelihoodRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
394 <option value="MappingQuality">MappingQuality</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
395 <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
396 <option value="MappingQualityZero">MappingQualityZero</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
397 <option value="OrientationBiasReadCounts">OrientationBiasReadCounts</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
398 <option value="OriginalAlignment">OriginalAlignment</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
399 <option value="PossibleDeNovo">PossibleDeNovo</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
400 <option value="QualByDepth">QualByDepth</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
401 <option value="ReadPosition">ReadPosition</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
402 <option value="ReadPosRankSumTest">ReadPosRankSumTest</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
403 <option value="ReferenceBases">ReferenceBases</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
404 <option value="RMSMappingQuality">RMSMappingQuality</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
405 <option value="SampleList">SampleList</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
406 <option value="StrandBiasBySample">StrandBiasBySample</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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parents:
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407 <option value="StrandOddsRatio">StrandOddsRatio</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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408 <option value="TandemRepeat">TandemRepeat</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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409 <option value="UniqueAltReadCount">UniqueAltReadCount</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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410 </param>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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411 <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."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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412 <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
fd2d6e035c3f "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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413 <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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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414 <param name="contamination_fraction_to_filter" argument="--contamination-fraction-to-filter" type="float" optional="true" value="0.0" label="Contamination Fraction To Filter" help="Fraction of contamination in sequencing data (for all samples) to aggressively remove"/>
f41a1e03538b "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
fd2d6e035c3f "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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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">
fd2d6e035c3f "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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417 <option value="GoodCigarReadFilter">Good cigar string</option>
fd2d6e035c3f "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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418 <option value="MappedReadFilter">Mapped read</option>
fd2d6e035c3f "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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419 <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
fd2d6e035c3f "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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420 <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
fd2d6e035c3f "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>
fd2d6e035c3f "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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422 <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
fd2d6e035c3f "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>
fd2d6e035c3f "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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424 <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
fd2d6e035c3f "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>
fd2d6e035c3f "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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426 <option value="WellformedReadFilter">Well-formed read</option>
fd2d6e035c3f "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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427 </param>
fd2d6e035c3f "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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428 <param name="read_filter" argument="--read-filter" type="select" multiple="true" value="" label="Read Filter" help="Read filters to be applied before analysis">
fd2d6e035c3f "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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429 <option value="AlignmentAgreesWithHeaderReadFilter">Alignment agrees with header</option>
fd2d6e035c3f "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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430 <option value="AllowAllReadsReadFilter">Allow all reads</option>
fd2d6e035c3f "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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431 <option value="AmbiguousBaseReadFilter">Ambiguous base</option>
fd2d6e035c3f "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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432 <option value="CigarContainsNoNOperator">Cigar contains no NO operator</option>
fd2d6e035c3f "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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433 <option value="FirstOfPairReadFilter">First of pair</option>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
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434 <option value="GoodCigarReadFilter">Good cigar string</option>
fd2d6e035c3f "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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435 <option value="HasReadGroupReadFilter">Has read group</option>
fd2d6e035c3f "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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436 <option value="MappedReadFilter">Mapped read</option>
fd2d6e035c3f "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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437 <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
fd2d6e035c3f "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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438 <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
fd2d6e035c3f "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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439 <option value="MatchingBasesAndQualsReadFilter">Matching bases and quals</option>
fd2d6e035c3f "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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440 <option value="MateDifferentStrandReadFilter">Mate different strand</option>
fd2d6e035c3f "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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441 <option value="MateOnSameContigOrNoMappedMateReadFilter">Mate on same contig or no mapped mate</option>
fd2d6e035c3f "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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442 <option value="MateUnmappedAndUnmappedReadFilter">Mate unmapped and mapped</option>
fd2d6e035c3f "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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443 <option value="MetricsReadFilter">Metrics</option>
fd2d6e035c3f "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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444 <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
fd2d6e035c3f "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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445 <option value="NonZeroFragmentLengthReadFilter">Non-zero fragment length</option>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
iuc
parents: 0
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446 <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
fd2d6e035c3f "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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447 <option value="NotDuplicateReadFilter">Not duplicate</option>
fd2d6e035c3f "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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448 <option value="NotOpticalDuplicateReadFilter">Not optical duplicate</option>
fd2d6e035c3f "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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449 <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
fd2d6e035c3f "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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450 <option value="NotSupplementaryAlignmentReadFilter">Not a supplementary alignment</option>
fd2d6e035c3f "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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451 <option value="OverclippedReadFilter">Overclipped</option>
fd2d6e035c3f "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>
fd2d6e035c3f "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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453 <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
fd2d6e035c3f "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>
fd2d6e035c3f "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>
fd2d6e035c3f "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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456 <option value="ReadLengthEqualsCigarLengthReadFilter">Read length equals cigar length</option>
fd2d6e035c3f "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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457 <option value="SecondOfPairReadFilter">Second of pair</option>
fd2d6e035c3f "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>
fd2d6e035c3f "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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459 <option value="SoftClippedReadFilter">Soft clipped</option>
fd2d6e035c3f "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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460 <option value="ValidAlignmentStartReadFilter">Valid alignment start</option>
fd2d6e035c3f "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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461 <option value="ValidAlignmentEndReadFilter">Valid alignment end</option>
fd2d6e035c3f "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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462 <option value="WellformedReadFilter">Well-formed read</option>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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463 </param>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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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!"/>
f41a1e03538b "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
fd2d6e035c3f "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" />
fd2d6e035c3f "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" />
fd2d6e035c3f "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
f41a1e03538b "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;"/>
f41a1e03538b "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"/>
f41a1e03538b "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."/>
f41a1e03538b "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."/>
f41a1e03538b "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"/>
f41a1e03538b "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."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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475 <param name="heterozygosity" argument="--heterozygosity" type="float" optional="true" value="0.001" label="Heterozygosity" help="The expected heterozygosity value used to compute prior probability that a locus is non-reference. The default priors are for provided for humans: het = 1e-3 which means that the probability of N samples being hom-ref at a site is: 1 - sum_i_2N (het / i) Note that heterozygosity as used here is the population genetics concept: http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms would differ from each other (one being A and the other B) at a rate of 1 in 100 bp. Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the het parameters only increases the chance that a site will be called non-reference across all samples, but doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all. The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy, which determines how many chromosomes each individual in the species carries."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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476 <param name="heterozygosity_stdev" argument="--heterozygosity-stdev" type="float" optional="true" value="0.01" label="Heterozygosity Stdev" help="Standard deviation of heterozygosity for SNP and indel calling."/>
1
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477 <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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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478 <param name="indel_heterozygosity" argument="--indel-heterozygosity" type="float" optional="true" value="0.000125" label="Indel Heterozygosity" help="Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept"/>
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479 <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
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480 <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" />
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481 <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
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482 <param name="interval_merging_rule" argument="--interval-merging-rule" type="select" optional="true" label="Interval Merging Rule" help="Interval merging rule for abutting intervals">
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483 <option selected="true" value="ALL">All</option>
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484 <option value="OVERLAPPING_ONLY">Overlapping only</option>
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485 </param>
1
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486 <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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487 <option selected="true" value="UNION">Union</option>
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488 <option value="INTERSECTION">Intersection</option>
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489 </param>
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490 <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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491 <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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492 <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."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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493 <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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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494 <param name="mitochondria_mode" argument="--mitochondria-mode" type="boolean" truevalue="--mitochondria-mode" falsevalue="" label="Mitochondria mode sets emission and initial LODs to 0" />
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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495 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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496 <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."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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497 <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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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498 <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."/>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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499 <param name="pcr_indel_qual" argument="--pcr-indel-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR indel qual for overlapping fragments" />
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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500 <param name="pcr_snv_qual" argument="--pcr-snv-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR SNV qual for overlapping fragments" />
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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501 <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."/>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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502 <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.">
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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503 <option selected="true" value="SILENT">Silent</option>
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504 <option value="STRICT">Strict</option>
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505 <option value="LENIENT">Lenient</option>
0
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506 </param>
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507 <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&amp;apos;t emit genotype fields when writing vcf file output."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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508 <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."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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509 </when>
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510 <when value="no" />
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511 </conditional>
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512 <conditional name="advanced">
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513 <param name="advanced_parameters" type="select" label="Advanced parameters">
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514 <option value="no">Use internal defaults</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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515 <option value="yes">Specify parameters</option>
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516 </param>
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517 <when value="yes">
3
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518 <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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519 <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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520 <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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521 <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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522 <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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523 <option selected="true" value="CALLED_HAPLOTYPES">Called haplotypes</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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524 <option value="ALL_POSSIBLE_HAPLOTYPES">All possible haplotypes</option>
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525 </param>
1
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526
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527 <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"/>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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528 <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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529 <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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530 <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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531 <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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532 <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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533 <option value="NONE">None</option>
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534 <option value="BP_RESOLUTION">Basepair resolution</option>
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535 <option value="GVCF">Genomic VCF</option>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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parents: 0
diff changeset
536 </param>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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537 <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
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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parents: 0
diff changeset
538 <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"/>
fd2d6e035c3f "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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539 <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"/>
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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parents: 0
diff changeset
540 <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)" />
fd2d6e035c3f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
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parents: 0
diff changeset
541 <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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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542 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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543 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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544 <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."/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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545 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
546 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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547 <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
fd2d6e035c3f "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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548 <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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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549 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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550 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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551 <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
fd2d6e035c3f "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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552 <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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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553 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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554 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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555 <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">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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556 <option selected="true" value="FASTEST_AVAILABLE">Fastest Available</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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557 <option value="EXACT">Exact</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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558 <option value="ORIGINAL">Original</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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559 <option value="LOGLESS_CACHING">Logless Caching</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
560 <option value="AVX_LOGLESS_CACHING">Logless Caching (AVX)</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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561 <option value="AVX_LOGLESS_CACHING_OMP">Logless Caching (AVX+OMP)</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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562 <option value="EXPERIMENTAL_FPGA_LOGLESS_CACHING">Logless Caching (FPGA, Experimental)</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
563 </param>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
564 <param name="pcr_indel_model" argument="--pcr-indel-model" type="select" optional="true" label="Pcr Indel Model" help="The PCR indel model to use">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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565 <option selected="true" value="CONSERVATIVE">Conservative</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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parents:
diff changeset
566 <option value="NONE">None</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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parents:
diff changeset
567 <option value="HOSTILE">Hostile</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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568 <option value="AGGRESSIVE">Aggressive</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
569 </param>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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570 <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
fd2d6e035c3f "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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571 <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" />
fd2d6e035c3f "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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572 <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
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
573 <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">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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574 <option selected="true" value="FASTEST_AVAILABLE">Fastest available</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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parents:
diff changeset
575 <option value="AVX_ENABLED">AVX-Enabled</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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576 <option value="JAVA">JAVA</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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577 </param>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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578 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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579 </when>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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580 <when value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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581 </conditional>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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582 <conditional name="outputs">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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583 <param name="output_parameters" type="select" label="Output parameters" help="Additional outputs for debugging purposes">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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584 <option value="no">Output only variants</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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585 <option value="yes">Generate debugging information</option>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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586 </param>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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587 <when value="yes">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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588 <param name="debug_activity" argument="--activity-profile-out" type="boolean" checked="false" truevalue="yes" falsevalue="" label="Activity Profile Out" help="Output the raw activity profile results in IGV format"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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589 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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590 <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"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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591 </when>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
592 <when value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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593 </conditional>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
594 </inputs>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
595 <outputs>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
596 <expand macro="gzip_vcf_output_params"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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597 <data format="tabular" name="assembly_region_out" label="${tool.name} on ${on_string}: Assembly region">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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598 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_assembly']</filter>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
599 </data>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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600 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: Debug BAM output">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
601 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_bam']</filter>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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diff changeset
602 </data>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
603 </outputs>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
604 <tests>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
605 <test>
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
606 <conditional name="mode">
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
607 <param name="mode_parameters" value="tumor_only"/>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
608 <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
609 </conditional>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
610 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
611 <param name="gzipped_output" value="false" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
612 <param name="reference_source_selector" value="history" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
613 <param name="optional_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
614 <param name="advanced_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
615 <param name="output_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
616 <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
617 </test>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
618 <test>
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
619 <conditional name="mode">
287c4af133e6 "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="mode_parameters" value="tumor_only"/>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
621 <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
622 </conditional>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
623 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
624 <param name="gzipped_output" value="false" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
625 <param name="reference_source_selector" value="history" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
626 <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" />
f41a1e03538b "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_source" value="history" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
628 <param name="seqdict_sequence" value="Mutect2-in2.dict" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
629 <param name="optional_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
630 <param name="advanced_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
631 <param name="output_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
632 <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
633 </test>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
634 <test>
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
635 <conditional name="mode">
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
636 <param name="mode_parameters" value="tumor_only"/>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
637 <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
638 </conditional>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
639 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
640 <param name="gzipped_output" value="false" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
641 <param name="reference_source_selector" value="history" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
642 <param name="optional_parameters" value="yes" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
643 <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
644 <param name="annotation_group" value="StandardMutectAnnotation" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
645 <param name="advanced_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
646 <param name="output_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
647 <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
648 </test>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
649 <test>
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
650 <conditional name="mode">
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
651 <param name="mode_parameters" value="tumor_only"/>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
652 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
653 </conditional>
4
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
654 <param name="reference_sequence" value="hg38"/>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
655 <param name="gzipped_output" value="false" />
4
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
656 <param name="reference_source_selector" value="cached" />
1cea23583655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit ff4bacd218035b7052ceadfadaec81dfd5d07b0e"
iuc
parents: 3
diff changeset
657 <param name="reference_sequence" value="hg38"/>
3
287c4af133e6 "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="optional_parameters" value="no" />
287c4af133e6 "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="advanced_parameters" value="no" />
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
660 <param name="output_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
661 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
662 </test>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
663 <test>
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
664 <conditional name="mode">
287c4af133e6 "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="mode_parameters" value="tumor_only"/>
287c4af133e6 "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="tumor" ftype="bam" value="Mutect2-in5.bam" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
667 </conditional>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
668 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
669 <param name="gzipped_output" value="false" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
670 <param name="reference_source_selector" value="history" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
671 <param name="optional_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
672 <param name="advanced_parameters" value="no" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
673 <param name="output_parameters" value="yes" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
674 <param name="debug_activity" value="true" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
675 <param name="debug_assembly" value="true" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
676 <param name="debug_bam" value="true" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
677 <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" />
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
678 <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
679 <output name="bam_output" file="Mutect2-out5.bam" />
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
680 </test>
3
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
681 <test>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
682 <conditional name="mode">
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
683 <param name="mode_parameters" value="somatic"/>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
684 <param name="tumor" ftype="bam" value="tumor.bam" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
685 <param name="normal" ftype="bam" value="normal.bam" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
686 </conditional>
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
687 <param name="reference_sequence" ftype="fasta" value="chr20.fa" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
688 <param name="gzipped_output" value="false" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
689 <param name="reference_source_selector" value="history" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
690 <param name="optional_parameters" value="no" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
691 <param name="advanced_parameters" value="no" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
692 <param name="output_parameters" value="no" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
693 <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="2" />
287c4af133e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
iuc
parents: 2
diff changeset
694 </test>
0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
695 </tests>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
696 <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
697 variants include single nucleotide (SNV) and insertion and deletion
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
698 (indel) variants. The caller combines the DREAM challenge-winning
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
699 somatic genotyping engine of the original MuTect (`Cibulskis et al.,
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
700 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
701 with the assembly-based machinery of
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
702 `HaplotypeCaller <https://www.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php>`__.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
703
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
704 This tool is featured in the *Somatic Short Mutation calling Best
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
705 Practice Workflow*. See
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
706 `Tutorial#11136 <https://software.broadinstitute.org/gatk/documentation/article?id=11136>`__
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
707 for a step-by-step description of the workflow and
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
708 `Article#11127 <https://software.broadinstitute.org/gatk/documentation/article?id=11127>`__
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
709 for an overview of what traditional somatic calling entails. For the
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
710 latest pipeline scripts, see the `Mutect2 WDL scripts
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
711 directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
712 Although we present the tool for somatic calling, it may apply to other
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
713 contexts, such as mitochondrial variant calling.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
714
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
715 Usage examples
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
716 ~~~~~~~~~~~~~~
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
717
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
718 Example commands show how to run Mutect2 for typical scenarios. The two
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
719 modes are (i) *somatic mode* where a tumor sample is matched with a
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
720 normal sample in analysis and (ii) *tumor-only mode* where a single
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
721 sample's alignment data undergoes analysis.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
722
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
723 (i) Tumor with matched normal
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
724 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
725
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
726 Given a matched normal, Mutect2 is designed to call somatic variants
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
727 only. The tool includes logic to skip emitting variants that are clearly
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
728 present in the germline based on provided evidence, e.g. in the matched
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
729 normal. This is done at an early stage to avoid spending computational
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
730 resources on germline events. If the variant's germline status is
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
731 borderline, then Mutect2 will emit the variant to the callset for
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
732 subsequent filtering and review.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
733
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
734 ::
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
735
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
736 gatk Mutect2 \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
737 -R reference.fa \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
738 -I tumor.bam \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
739 -tumor tumor_sample_name \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
740 -I normal.bam \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
741 -normal normal_sample_name \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
742 --germline-resource af-only-gnomad.vcf.gz \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
743 --af-of-alleles-not-in-resource 0.00003125 \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
744 --panel-of-normals pon.vcf.gz \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
745 -O somatic.vcf.gz
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
746
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
747
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
748 The --af-of-alleles-not-in-resource argument value should match
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
749 expectations for alleles not found in the provided germline resource.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
750 Note the tool does not require a germline resource nor a panel of
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
751 normals (PoN) to run. The tool prefilters sites for the matched normal
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
752 and the PoN. For the germline resource, the tool prefilters on the
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
753 allele. Below is an excerpt of a known variants resource with population
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
754 allele frequencies
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
755
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
756 ::
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
757
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
758 #CHROM POS ID REF ALT QUAL FILTER INFO
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
759 1 10067 . T TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 30.35 PASS AC=3;AF=7.384E-5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
760 1 10108 . CAACCCT C 46514.32 PASS AC=6;AF=1.525E-4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
761 1 10109 . AACCCTAACCCT AAACCCT,* 89837.27 PASS AC=48,5;AF=0.001223,1.273E-4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
762 1 10114 . TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA *,CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T 36728.97 PASS AC=55,9,1;AF=0.001373,2.246E-4,2.496E-5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
763 1 10119 . CT C,* 251.23 PASS AC=5,1;AF=1.249E-4,2.498E-5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
764 1 10120 . TA CA,* 14928.74 PASS AC=10,6;AF=2.5E-4,1.5E-4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
765 1 10128 . ACCCTAACCCTAACCCTAAC A,* 285.71 PASS AC=3,1;AF=7.58E-5,2.527E-5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
766 1 10131 . CT C,* 378.93 PASS AC=7,5;AF=1.765E-4,1.261E-4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
767 1 10132 . TAACCC *,T 18025.11 PASS AC=12,2;AF=3.03E-4,5.049E-5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
768
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
769
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
770 (ii) Tumor-only mode
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
771 ^^^^^^^^^^^^^^^^^^^^
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
772
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
773 This mode runs on a single sample, e.g. single tumor or single normal
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
774 sample. To create a PoN, call on each normal sample in this mode, then
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
775 use CreateSomaticPanelOfNormals to generate the PoN.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
776
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
777 ::
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
778
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
779 gatk Mutect2 \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
780 -R reference.fa \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
781 -I sample.bam \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
782 -tumor sample_name \
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
783 -O single_sample.vcf.gz
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
784
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
785
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
786 Further points of interest
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
787 ~~~~~~~~~~~~~~~~~~~~~~~~~~
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
788
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
789 Additional parameters that factor towards filtering, including
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
790 normal-artifact-lod (default threshold 0.0) and tumor-lod (default
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
791 threshold 5.3), are available in FilterMutectCalls. While the tool
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
792 calculates normal-lod assuming a diploid genotype, it calculates
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
793 normal-artifact-lod with the same approach it uses for tumor-lod, i.e.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
794 with a variable ploidy assumption.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
795
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
796 - 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.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
797
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
798 - 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.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
799
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
800
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
801 If a variant is absent from a given germline resource, then the value
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
802 for --af-of-alleles-not-in-resource applies. For example, gnomAD's
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
803 16,000 samples (~32,000 homologs per locus) becomes a probability of one
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
804 in 32,000 or less. Thus, an allele's absence from the germline resource
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
805 becomes evidence that it is not a germline variant.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
806
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
807 Caveats
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
808 ~~~~~~~
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
809
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
810 Although GATK4 Mutect2 accomodates varying coverage depths, further
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
811 optimization of parameters may improve calling for extreme high depths,
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
812 e.g. 1000X.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
813 ]]></help>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
814 <citations>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
815 <expand macro="citations"/>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
816 </citations>
2
3be27a9a7313 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
iuc
parents: 1
diff changeset
817 </tool>