Mercurial > repos > artbio > gatk4
diff Mutect2.xml @ 2:646e6943bcd2 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
| author | artbio |
|---|---|
| date | Sun, 15 Oct 2023 12:06:24 +0000 |
| parents | c51c08cc9fcc |
| children |
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--- a/Mutect2.xml Tue Jan 04 15:10:59 2022 +0000 +++ b/Mutect2.xml Sun Oct 15 12:06:24 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="mutect2" name="gatk4 Mutect2" version="@WRAPPER_VERSION@" profile="18.05"> +<tool id="mutect2" name="gatk4 Mutect2" version="@WRAPPER_VERSION@" profile="21.01"> <description>- Call somatic SNVs and indels via local assembly of haplotypes</description> <macros> <import>macros.xml</import> @@ -25,12 +25,10 @@ #set ref_flag='' #end if - #if str($mode.mode_parameters) == 'tumor_only' - ln -s $mode.tumor tumor.bam && - ln -s $mode.tumor.metadata.bam_index tumor.bam.bai && - #else - ln -s $mode.tumor tumor.bam && - ln -s $mode.tumor.metadata.bam_index tumor.bam.bai && + ln -s $tumor tumor.bam && + ln -s $tumor.metadata.bam_index tumor.bam.bai && + + #if str($mode.mode_parameters) == 'somatic' ln -s $mode.normal normal.bam && ln -s $mode.normal.metadata.bam_index normal.bam.bai && #end if @@ -288,16 +286,15 @@ ]]> </command> <inputs> + <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" /> <conditional name="mode"> <param name="mode_parameters" type="select" label="Type of analysis"> <option value="tumor_only">Tumor-only</option> <option value="somatic">Somatic</option> </param> <when value="tumor_only"> - <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" /> </when> <when value="somatic"> - <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" /> <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" /> </when> </conditional> @@ -504,7 +501,6 @@ <option value="STRICT">Strict</option> <option value="LENIENT">Lenient</option> </param> - <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."/> <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."/> </when> <when value="no" /> @@ -602,10 +598,10 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> + <param name="tumor" ftype="bam" value="Mutect2-in1.bam" /> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> - <param name="tumor" ftype="bam" value="Mutect2-in1.bam" /> </conditional> <param name="reference_sequence" ftype="fasta" value="reference.fa" /> <param name="gzipped_output" value="false" /> @@ -616,26 +612,25 @@ <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" /> <output name="output_vcf_stats" file="Mutect2-out1.vcf.stats" /> </test> - <test> + <test expect_num_outputs="2"> + <param name="tumor" ftype="bam" value="Mutect2-in2.bam" /> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> - <param name="tumor" ftype="bam" value="Mutect2-in2.bam" /> </conditional> <param name="reference_sequence" ftype="fasta" value="reference.fa" /> <param name="gzipped_output" value="false" /> <param name="reference_source_selector" value="history" /> <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" /> - <param name="seqdict_source" value="history" /> <param name="seqdict_sequence" value="Mutect2-in2.dict" /> <param name="optional_parameters" value="no" /> <param name="advanced_parameters" value="no" /> <param name="output_parameters" value="no" /> <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" /> </test> - <test> + <test expect_num_outputs="2"> + <param name="tumor" ftype="bam" value="Mutect2-in3.bam" /> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> - <param name="tumor" ftype="bam" value="Mutect2-in3.bam" /> </conditional> <param name="reference_sequence" ftype="fasta" value="reference.fa" /> <param name="gzipped_output" value="false" /> @@ -647,10 +642,10 @@ <param name="output_parameters" value="no" /> <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="4" /> </test> - <test> + <test expect_num_outputs="2"> + <param name="tumor" ftype="bam" value="Mutect2-in4.bam" /> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> - <param name="tumor" ftype="bam" value="Mutect2-in4.bam" /> </conditional> <param name="reference_sequence" value="hg38"/> <param name="gzipped_output" value="false" /> @@ -661,10 +656,10 @@ <param name="output_parameters" value="no" /> <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" /> </test> - <test> + <test expect_num_outputs="4"> + <param name="tumor" ftype="bam" value="Mutect2-in5.bam" /> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> - <param name="tumor" ftype="bam" value="Mutect2-in5.bam" /> </conditional> <param name="reference_sequence" ftype="fasta" value="reference.fa" /> <param name="gzipped_output" value="false" /> @@ -679,10 +674,10 @@ <output name="assembly_region_out" file="Mutect2-out5-1.tabular" /> <output name="bam_output" file="Mutect2-out5.bam" /> </test> - <test> + <test expect_num_outputs="2"> + <param name="tumor" ftype="bam" value="tumor.bam" /> <conditional name="mode"> <param name="mode_parameters" value="somatic"/> - <param name="tumor" ftype="bam" value="tumor.bam" /> <param name="normal" ftype="bam" value="normal.bam" /> </conditional> <param name="reference_sequence" ftype="fasta" value="chr20.fa" /> @@ -697,16 +692,17 @@ <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short variants include single nucleotide (SNV) and insertion and deletion (indel) variants. The caller combines the DREAM challenge-winning -somatic genotyping engine of the original MuTect (`Cibulskis et al., -2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__) -with the assembly-based machinery of -`HaplotypeCaller <https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__. +somatic genotyping engine of the original MuTect_ (Cibulskis et al. 2013) +with the assembly-based machinery of HaplotypeCaller (see +gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell). + +.. _MuTect: http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html This tool is featured in the *Somatic Short Mutation calling Best -Practice Workflow*. See `this article <https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__ +Practice Workflow*. See gatk.broadinstitute.org/hc/en-us/articles/360035531132 for an overview of what traditional somatic calling entails, with usage examples. For the -latest pipeline scripts, see the `Mutect2 WDL scripts -directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__. +latest pipeline scripts, see the Mutect2 WDL scripts directory (see +github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl). Although we present the tool for somatic calling, it may apply to other contexts, such as mitochondrial variant calling.