Mercurial > repos > iuc > gatk4_mutect2

comparison 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
comparison
equal deleted inserted replaced
3:287c4af133e6 4:1cea23583655
1 <tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@2" profile="18.05"> 1 <tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@" profile="18.05">
2 <description>- Call somatic SNVs and indels via local assembly of haplotypes</description> 2 <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
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=$tumor_bam_index_pre_chth#
13 #include source=$normal_bam_index_pre_chth#
14 #include source=$pre_gatk_ints_chth# 12 #include source=$pre_gatk_ints_chth#
15 13
16 #set ref_flag='--reference="reference.fa"' 14 #set ref_flag='--reference="reference.fa"'
17 15
18 #if str($reference_source.reference_source_selector) == 'history' 16 #if str($reference_source.reference_source_selector) == 'history'
19 ln -s '$reference_source.reference_sequence' reference.fa && 17 ln -s '$reference_source.reference_sequence' reference.fa &&
20 samtools faidx reference.fa && 18 samtools faidx reference.fa &&
21 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && 19 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
22 #else if str($reference_source.reference_source_selector) == 'history' 20 #else if str($reference_source.reference_source_selector) == 'cached'
23 ln -s '$reference_source.reference_sequence.fields.path' reference.fa && 21 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
24 samtools faidx reference.fa && 22 samtools faidx reference.fa &&
25 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && 23 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
26 #else 24 #else
27 #set ref_flag='' 25 #set ref_flag=''
28 #end if 26 #end if
29 27
30 #if str($outputs.output_parameters) == 'yes' 28 #if str($mode.mode_parameters) == 'tumor_only'
29 ln -s $mode.tumor tumor.bam &&
30 ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&
31 #else
32 ln -s $mode.tumor tumor.bam &&
33 ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&
34 ln -s $mode.normal normal.bam &&
35 ln -s $mode.normal.metadata.bam_index normal.bam.bai &&
36 #end if
37
38 #if str($outputs.output_parameters) == 'yes'
31 #if str($outputs.debug_assembly) == 'yes' 39 #if str($outputs.debug_assembly) == 'yes'
32 ln -s '$assembly_region_out' assembly-region.tab && 40 ln -s '$assembly_region_out' assembly-region.tab &&
33 #end if 41 #end if
34 #if str($outputs.debug_bam) == 'yes' 42 #if str($outputs.debug_bam) == 'yes'
35 ln -s '$bam_output' debug.bam && 43 ln -s '$bam_output' debug.bam &&
75 #end if 83 #end if
76 84
77 gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample" 85 gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample"
78 86
79 #if str($mode.mode_parameters) == 'tumor_only' 87 #if str($mode.mode_parameters) == 'tumor_only'
80 #include source=$gatk_tumor_bam_input# 88 --input tumor.bam
81 #else 89 #else
82 #include source=$gatk_tumor_bam_input# 90 --input tumor.bam
83 #include source=$gatk_normal_bam_input# 91 --input normal.bam
84 #end if 92 #end if
85 93
86 ## OPTIONAL PARAMETERS ## 94 ## OPTIONAL PARAMETERS ##
87 95
88 #if str($optional.optional_parameters) == 'yes' 96 #if str($optional.optional_parameters) == 'yes'
223 #end if 231 #end if
224 232
225 #if $advanced.max_unpruned_variants 233 #if $advanced.max_unpruned_variants
226 --max-unpruned-variants="$advanced.max_unpruned_variants" 234 --max-unpruned-variants="$advanced.max_unpruned_variants"
227 #end if 235 #end if
228 --allele-informative-reads-overlap-margin=="$advanced.allele_informative_reads_overlap_margin" 236 --allele-informative-reads-overlap-margin="$advanced.allele_informative_reads_overlap_margin"
229 --active-probability-threshold="$advanced.active_probability_threshold" 237 --active-probability-threshold="$advanced.active_probability_threshold"
230 --assembly-region-padding="$advanced.assembly_region_padding" 238 --assembly-region-padding="$advanced.assembly_region_padding"
231 --bam-writer-type="$advanced.bam_writer_type" 239 --bam-writer-type="$advanced.bam_writer_type"
232 --max-assembly-region-size="$advanced.max_assembly_region_size" 240 --max-assembly-region-size="$advanced.max_assembly_region_size"
233 --max-mnp-distance="$advanced.max_mnp_distance" 241 --max-mnp-distance="$advanced.max_mnp_distance"
284 <param name="mode_parameters" type="select" label="Type of analysis"> 292 <param name="mode_parameters" type="select" label="Type of analysis">
285 <option value="tumor_only">Tumor-only</option> 293 <option value="tumor_only">Tumor-only</option>
286 <option value="somatic">Somatic</option> 294 <option value="somatic">Somatic</option>
287 </param> 295 </param>
288 <when value="tumor_only"> 296 <when value="tumor_only">
289 <expand macro="gatk_tumor_bam_req_params"/> 297 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
290 </when> 298 </when>
291 <when value="somatic"> 299 <when value="somatic">
292 <expand macro="gatk_tumor_bam_req_params"/> 300 <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
293 <expand macro="gatk_normal_bam_req_params"/> 301 <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
294 </when> 302 </when>
295 </conditional> 303 </conditional>
296 <expand macro="gzip_vcf_params"/> 304 <expand macro="gzip_vcf_params"/>
297 <expand macro="ref_sel"/> 305 <expand macro="ref_sel"/>
298 <conditional name="optional"> 306 <conditional name="optional">
641 <test> 649 <test>
642 <conditional name="mode"> 650 <conditional name="mode">
643 <param name="mode_parameters" value="tumor_only"/> 651 <param name="mode_parameters" value="tumor_only"/>
644 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" /> 652 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
645 </conditional> 653 </conditional>
646 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 654 <param name="reference_sequence" value="hg38"/>
647 <param name="gzipped_output" value="false" /> 655 <param name="gzipped_output" value="false" />
648 <param name="reference_source_selector" value="history" /> 656 <param name="reference_source_selector" value="cached" />
657 <param name="reference_sequence" value="hg38"/>
649 <param name="optional_parameters" value="no" /> 658 <param name="optional_parameters" value="no" />
650 <param name="advanced_parameters" value="no" /> 659 <param name="advanced_parameters" value="no" />
651 <param name="output_parameters" value="no" /> 660 <param name="output_parameters" value="no" />
652 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" /> 661 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" />
653 </test> 662 </test>