Mercurial > repos > iuc > gatk4_mutect2

comparison gatk4_Mutect2.xml @ 3:287c4af133e6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
author iuc
date Sun, 10 May 2020 17:58:00 -0400
parents 3be27a9a7313
children 1cea23583655
comparison
equal deleted inserted replaced
2:3be27a9a7313 3:287c4af133e6
7 <expand macro="version_cmd"/> 7 <expand macro="version_cmd"/>
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 #include source=$set_sections# 10 #include source=$set_sections#
11 #include source=$pre_gatk_excl_ints_chth# 11 #include source=$pre_gatk_excl_ints_chth#
12 #include source=$bam_index_pre_chth# 12 #include source=$tumor_bam_index_pre_chth#
13 #include source=$normal_bam_index_pre_chth#
13 #include source=$pre_gatk_ints_chth# 14 #include source=$pre_gatk_ints_chth#
14 15
15 #set ref_flag='--reference="reference.fa"' 16 #set ref_flag='--reference="reference.fa"'
16 17
17 #if str($reference_source.reference_source_selector) == 'history' 18 #if str($reference_source.reference_source_selector) == 'history'
25 #else 26 #else
26 #set ref_flag='' 27 #set ref_flag=''
27 #end if 28 #end if
28 29
29 #if str($outputs.output_parameters) == 'yes' 30 #if str($outputs.output_parameters) == 'yes'
30 #if str($outputs.debug_activity) == 'yes'
31 ln -s '$activity_profile_out' activity-profile.tab &&
32 #end if
33 #if str($outputs.debug_assembly) == 'yes' 31 #if str($outputs.debug_assembly) == 'yes'
34 ln -s '$assembly_region_out' assembly-region.tab && 32 ln -s '$assembly_region_out' assembly-region.tab &&
35 #end if 33 #end if
36 #if str($outputs.debug_bam) == 'yes' 34 #if str($outputs.debug_bam) == 'yes'
37 ln -s '$bam_output' debug.bam && 35 ln -s '$bam_output' debug.bam &&
38 #end if 36 #end if
39 #end if 37 #end if
40 38
41 gatk GetSampleName --input="input.bam" --output="samplename.txt" && 39 gatk GetSampleName --input="tumor.bam" --output="samplename.txt" &&
42 sample=`cat samplename.txt | sed 's/"//g'` && 40 sample=`cat samplename.txt | sed 's/"//g'` &&
43 41
44 #if str($optional.optional_parameters) == 'yes' 42 #if str($optional.optional_parameters) == 'yes'
45 #if $optional.panel_of_normals 43 #if $optional.panel_of_normals
46 #set datatype = $optional.panel_of_normals.datatype 44 #set datatype = $optional.panel_of_normals.datatype
76 74
77 #end if 75 #end if
78 76
79 gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample" 77 gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample"
80 78
81 #include source=$gatk_bam_input# 79 #if str($mode.mode_parameters) == 'tumor_only'
80 #include source=$gatk_tumor_bam_input#
81 #else
82 #include source=$gatk_tumor_bam_input#
83 #include source=$gatk_normal_bam_input#
84 #end if
82 85
83 ## OPTIONAL PARAMETERS ## 86 ## OPTIONAL PARAMETERS ##
84 87
85 #if str($optional.optional_parameters) == 'yes' 88 #if str($optional.optional_parameters) == 'yes'
86 89
220 #end if 223 #end if
221 224
222 #if $advanced.max_unpruned_variants 225 #if $advanced.max_unpruned_variants
223 --max-unpruned-variants="$advanced.max_unpruned_variants" 226 --max-unpruned-variants="$advanced.max_unpruned_variants"
224 #end if 227 #end if
225 228 --allele-informative-reads-overlap-margin=="$advanced.allele_informative_reads_overlap_margin"
226 --active-probability-threshold="$advanced.active_probability_threshold" 229 --active-probability-threshold="$advanced.active_probability_threshold"
227 --assembly-region-padding="$advanced.assembly_region_padding" 230 --assembly-region-padding="$advanced.assembly_region_padding"
228 --bam-writer-type="$advanced.bam_writer_type" 231 --bam-writer-type="$advanced.bam_writer_type"
229 --max-assembly-region-size="$advanced.max_assembly_region_size" 232 --max-assembly-region-size="$advanced.max_assembly_region_size"
230 --max-mnp-distance="$advanced.max_mnp_distance" 233 --max-mnp-distance="$advanced.max_mnp_distance"
245 $advanced.allow_non_unique_kmers_in_ref 248 $advanced.allow_non_unique_kmers_in_ref
246 $advanced.disable_adaptive_pruning 249 $advanced.disable_adaptive_pruning
247 $advanced.disable_tool_default_annotations 250 $advanced.disable_tool_default_annotations
248 $advanced.disable_tool_default_read_filters 251 $advanced.disable_tool_default_read_filters
249 $advanced.dont_increase_kmer_sizes_for_cycles 252 $advanced.dont_increase_kmer_sizes_for_cycles
250 $advanced.dont_trim_active_regions
251 $advanced.dont_use_soft_clipped_bases 253 $advanced.dont_use_soft_clipped_bases
252 $advanced.enable_all_annotations 254 $advanced.enable_all_annotations
253 $advanced.force_active 255 $advanced.force_active
254 $advanced.force_call_filtered_alleles 256 $advanced.force_call_filtered_alleles
255 $advanced.independent_mates 257 $advanced.independent_mates
261 ## END ADVANCED PARAMETERS ## 263 ## END ADVANCED PARAMETERS ##
262 264
263 ## ADDITIONAL OUTPUT PARAMETERS ## 265 ## ADDITIONAL OUTPUT PARAMETERS ##
264 266
265 #if str($outputs.output_parameters) == 'yes' 267 #if str($outputs.output_parameters) == 'yes'
266 #if str($outputs.debug_activity) == 'yes'
267 --activity-profile-out="activity-profile.tab"
268 #end if
269 #if str($outputs.debug_assembly) == 'yes' 268 #if str($outputs.debug_assembly) == 'yes'
270 --assembly-region-out="assembly-region.tab" 269 --assembly-region-out="assembly-region.tab"
271 #end if 270 #end if
272 #if str($outputs.debug_bam) == 'yes' 271 #if str($outputs.debug_bam) == 'yes'
273 --bam-output="debug.bam" 272 --bam-output="debug.bam"
279 #include source=$vcf_output_opts# 278 #include source=$vcf_output_opts#
280 #include source=$gatk_seqdict# 279 #include source=$gatk_seqdict#
281 ]]> 280 ]]>
282 </command> 281 </command>
283 <inputs> 282 <inputs>
284 <expand macro="gatk_bam_req_params"/> 283 <conditional name="mode">
284 <param name="mode_parameters" type="select" label="Type of analysis">
285 <option value="tumor_only">Tumor-only</option>
286 <option value="somatic">Somatic</option>
287 </param>
288 <when value="tumor_only">
289 <expand macro="gatk_tumor_bam_req_params"/>
290 </when>
291 <when value="somatic">
292 <expand macro="gatk_tumor_bam_req_params"/>
293 <expand macro="gatk_normal_bam_req_params"/>
294 </when>
295 </conditional>
285 <expand macro="gzip_vcf_params"/> 296 <expand macro="gzip_vcf_params"/>
286 <expand macro="ref_sel"/> 297 <expand macro="ref_sel"/>
287 <conditional name="optional"> 298 <conditional name="optional">
288 <param name="optional_parameters" type="select" label="Optional parameters"> 299 <param name="optional_parameters" type="select" label="Optional parameters">
289 <option value="no">Use internal defaults</option> 300 <option value="no">Use internal defaults</option>
494 <param name="advanced_parameters" type="select" label="Advanced parameters"> 505 <param name="advanced_parameters" type="select" label="Advanced parameters">
495 <option value="no">Use internal defaults</option> 506 <option value="no">Use internal defaults</option>
496 <option value="yes">Specify parameters</option> 507 <option value="yes">Specify parameters</option>
497 </param> 508 </param>
498 <when value="yes"> 509 <when value="yes">
510 <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."/>
499 <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."/> 511 <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."/>
500 <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"/> 512 <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"/>
501 <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"/> 513 <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"/>
502 <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"> 514 <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">
503 <option selected="true" value="CALLED_HAPLOTYPES">Called haplotypes</option> 515 <option selected="true" value="CALLED_HAPLOTYPES">Called haplotypes</option>
506 518
507 <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"/> 519 <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"/>
508 <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"/> 520 <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"/>
509 <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"/> 521 <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"/>
510 <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"/> 522 <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"/>
511 <param name="dont_trim_active_regions" argument="--dont-trim-active-regions" type="boolean" truevalue="--dont-trim-active-regions" falsevalue="" optional="true" checked="false" label="Dont Trim Active Regions" help="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping"/>
512 <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"/> 523 <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"/>
513 <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"> 524 <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">
514 <option value="NONE">None</option> 525 <option value="NONE">None</option>
515 <option value="BP_RESOLUTION">Basepair resolution</option> 526 <option value="BP_RESOLUTION">Basepair resolution</option>
516 <option value="GVCF">Genomic VCF</option> 527 <option value="GVCF">Genomic VCF</option>
573 <when value="no" /> 584 <when value="no" />
574 </conditional> 585 </conditional>
575 </inputs> 586 </inputs>
576 <outputs> 587 <outputs>
577 <expand macro="gzip_vcf_output_params"/> 588 <expand macro="gzip_vcf_output_params"/>
578 <data format="tabular" name="activity_profile_out" label="${tool.name} on ${on_string}: Activity profile">
579 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_activity']</filter>
580 </data>
581 <data format="tabular" name="assembly_region_out" label="${tool.name} on ${on_string}: Assembly region"> 589 <data format="tabular" name="assembly_region_out" label="${tool.name} on ${on_string}: Assembly region">
582 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_assembly']</filter> 590 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_assembly']</filter>
583 </data> 591 </data>
584 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: Debug BAM output"> 592 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: Debug BAM output">
585 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_bam']</filter> 593 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_bam']</filter>
586 </data> 594 </data>
587 </outputs> 595 </outputs>
588 <tests> 596 <tests>
589 <test> 597 <test>
590 <param name="input" ftype="bam" value="Mutect2-in1.bam" /> 598 <conditional name="mode">
599 <param name="mode_parameters" value="tumor_only"/>
600 <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />
601 </conditional>
591 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 602 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
592 <param name="gzipped_output" value="false" /> 603 <param name="gzipped_output" value="false" />
593 <param name="reference_source_selector" value="history" /> 604 <param name="reference_source_selector" value="history" />
594 <param name="optional_parameters" value="no" /> 605 <param name="optional_parameters" value="no" />
595 <param name="advanced_parameters" value="no" /> 606 <param name="advanced_parameters" value="no" />
596 <param name="output_parameters" value="no" /> 607 <param name="output_parameters" value="no" />
597 <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" /> 608 <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" />
598 </test> 609 </test>
599 <test> 610 <test>
600 <param name="input" ftype="bam" value="Mutect2-in2.bam" /> 611 <conditional name="mode">
612 <param name="mode_parameters" value="tumor_only"/>
613 <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />
614 </conditional>
601 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 615 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
602 <param name="gzipped_output" value="false" /> 616 <param name="gzipped_output" value="false" />
603 <param name="reference_source_selector" value="history" /> 617 <param name="reference_source_selector" value="history" />
604 <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" /> 618 <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" />
605 <param name="seqdict_source" value="history" /> 619 <param name="seqdict_source" value="history" />
608 <param name="advanced_parameters" value="no" /> 622 <param name="advanced_parameters" value="no" />
609 <param name="output_parameters" value="no" /> 623 <param name="output_parameters" value="no" />
610 <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" /> 624 <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" />
611 </test> 625 </test>
612 <test> 626 <test>
613 <param name="input" ftype="bam" value="Mutect2-in3.bam" /> 627 <conditional name="mode">
628 <param name="mode_parameters" value="tumor_only"/>
629 <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />
630 </conditional>
614 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 631 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
615 <param name="gzipped_output" value="false" /> 632 <param name="gzipped_output" value="false" />
616 <param name="reference_source_selector" value="history" /> 633 <param name="reference_source_selector" value="history" />
617 <param name="optional_parameters" value="yes" /> 634 <param name="optional_parameters" value="yes" />
618 <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" /> 635 <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" />
620 <param name="advanced_parameters" value="no" /> 637 <param name="advanced_parameters" value="no" />
621 <param name="output_parameters" value="no" /> 638 <param name="output_parameters" value="no" />
622 <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" /> 639 <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" />
623 </test> 640 </test>
624 <test> 641 <test>
625 <param name="input" ftype="bam" value="Mutect2-in4.bam" /> 642 <conditional name="mode">
643 <param name="mode_parameters" value="tumor_only"/>
644 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
645 </conditional>
626 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 646 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
627 <param name="gzipped_output" value="false" /> 647 <param name="gzipped_output" value="false" />
628 <param name="reference_source_selector" value="history" /> 648 <param name="reference_source_selector" value="history" />
629 <param name="optional_parameters" value="yes" /> 649 <param name="optional_parameters" value="no" />
630 <param name="advanced_parameters" value="yes" /> 650 <param name="advanced_parameters" value="no" />
631 <param name="dont_trim_active_regions" value="true" />
632 <param name="output_parameters" value="no" /> 651 <param name="output_parameters" value="no" />
633 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" /> 652 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" />
634 </test> 653 </test>
635 <test> 654 <test>
636 <param name="input" ftype="bam" value="Mutect2-in5.bam" /> 655 <conditional name="mode">
656 <param name="mode_parameters" value="tumor_only"/>
657 <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />
658 </conditional>
637 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 659 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
638 <param name="gzipped_output" value="false" /> 660 <param name="gzipped_output" value="false" />
639 <param name="reference_source_selector" value="history" /> 661 <param name="reference_source_selector" value="history" />
640 <param name="optional_parameters" value="no" /> 662 <param name="optional_parameters" value="no" />
641 <param name="advanced_parameters" value="no" /> 663 <param name="advanced_parameters" value="no" />
642 <param name="output_parameters" value="yes" /> 664 <param name="output_parameters" value="yes" />
643 <param name="debug_activity" value="true" /> 665 <param name="debug_activity" value="true" />
644 <param name="debug_assembly" value="true" /> 666 <param name="debug_assembly" value="true" />
645 <param name="debug_bam" value="true" /> 667 <param name="debug_bam" value="true" />
646 <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" /> 668 <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" />
647 <output name="activity_profile_out" file="Mutect2-out5-1.tabular" /> 669 <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />
648 <output name="assembly_region_out" file="Mutect2-out5-2.tabular" />
649 <output name="bam_output" file="Mutect2-out5.bam" /> 670 <output name="bam_output" file="Mutect2-out5.bam" />
671 </test>
672 <test>
673 <conditional name="mode">
674 <param name="mode_parameters" value="somatic"/>
675 <param name="tumor" ftype="bam" value="tumor.bam" />
676 <param name="normal" ftype="bam" value="normal.bam" />
677 </conditional>
678 <param name="reference_sequence" ftype="fasta" value="chr20.fa" />
679 <param name="gzipped_output" value="false" />
680 <param name="reference_source_selector" value="history" />
681 <param name="optional_parameters" value="no" />
682 <param name="advanced_parameters" value="no" />
683 <param name="output_parameters" value="no" />
684 <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="2" />
650 </test> 685 </test>
651 </tests> 686 </tests>
652 <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short 687 <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short
653 variants include single nucleotide (SNV) and insertion and deletion 688 variants include single nucleotide (SNV) and insertion and deletion
654 (indel) variants. The caller combines the DREAM challenge-winning 689 (indel) variants. The caller combines the DREAM challenge-winning