Mercurial > repos > elixir-it > mutect2
changeset 0:0cc081cd3992 draft
Uploaded
| author | elixir-it |
|---|---|
| date | Thu, 28 Jun 2018 05:58:45 -0400 |
| parents | |
| children | fbfc333f3eec |
| files | mutect2.xml |
| diffstat | 1 files changed, 312 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutect2.xml Thu Jun 28 05:58:45 2018 -0400 @@ -0,0 +1,312 @@ + <tool id="mutect2" name="MuTect2" version="3.8"> + <description>somatic SNP and indel caller</description> + <macros> + <import>mutect2_macros_add_loc.xml</import> + </macros> + <requirements> + <requirement type="package" version="3.8" >gatk</requirement> + <requirement type="package" version="2.7.1" >picard</requirement> + <requirement type="package" version="1.7" >samtools</requirement> + </requirements> + <command> + <![CDATA[ + ##creation of .bai the -@ option is used to allocate additional threads + samtools index -@ \${GALAXY_SLOTS:-4} $input1 && + samtools index -@ \${GALAXY_SLOTS:-4} $input2 && + + ## TODO creation of symlinks because mutect2 want the extensions of the file + ln -s $input1 tumor.bam && + ln -s $input2 normal.bam && + ln -s $input1".bai" tumor.bam.bai && + ln -s $input2".bai" normal.bam.bai && + #if $reference_source == "history" + ln -s $reference genome.fa && + ln -s $reference".fai" genome.fa.fai + #end if + #if $list + ln -s $list position.bed && + #end if + #if $dbSNP + ln -s $dbSNP dbSNP.vcf && + #end if + #if $cosmic + ln -s $cosmic cosmic.vcf && + #end if + #if $alleles + ln -s $alleles alleles.vcf + #end if + + ##TODO creation of .dict file of the genome required by mutect2 to run + #if $reference_source == "history" + java -jar \$CONDA_DEFAULT_ENV/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log + #end if + + ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it + ##and move the .jar file to \$CONDA_DEFAULT_ENV/opt/gatk-3.8/ then the mutect2 command is runned + gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ; + java -jar \$CONDA_DEFAULT_ENV/opt/gatk-3.8/GenomeAnalysisTK.jar -nct \${GALAXY_SLOTS:-4} -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output + #if $reference_source == "history" + -R genome.fa + #else + -R $reference_source.ref_file.fields.path + #end if + ## TODO advanced inputs section if the optional inputs are present their options are added to the command + #if $dbSNP + --dbsnp dbSNP.vcf + #end if + #if $cosmic + --cosmic cosmic.vcf + #end if + #if $list + -L position.bed + #end if + #if $alleles + --alleles alleles.vcf + #end if + + ##TODO advanced options section if the options inputs are different from the default value the option is added to the command + + #if str($advanced.advanced_parameters) =="show": + #if $advanced.heterozygosity != "0.001" + --heterozygosity $advanced.heterozygosity + #end if + #if $advanced.heterozygosity_stdev != "0.01" + --heterozygosity_stdev $advanced.heterozygosity_stdev + #end if + #if $advanced.indel_heterozygosity != "1.25E-4" + --indel_heterozygosity $advanced.indel_heterozygosity + #end if + #if $advanced.initial_normal_lod != "0.5" + --initial_normal_lod $advanced.initial_normal_lod + #end if + #if $advanced.initial_tumor_lod != "4.0" + --initial_tumor_lod $advanced.initial_tumor_lod + #end if + #if $advanced.max_alt_allele_in_normal_fraction != "0.03" + --max_alt_allele_in_normal_fraction $advanced.max_alt_allele_in_normal_fraction + #end if + #if $advanced.max_alt_alleles_in_normal_count != "1" + --max_alt_alleles_in_normal_count $advanced.max_alt_alleles_in_normal_count + #end if + #if $advanced.max_alt_alleles_in_normal_qscore_sum != "20" + --max_alt_alleles_in_normal_qscore_sum $advanced.max_alt_alleles_in_normal_qscore_sum + #end if + #if $advanced.maxReadsInRegionPerSample != "1000" + --maxReadsInRegionPerSample $advanced.maxReadsInRegionPerSample + #end if + #if $advanced.min_base_quality_score != "10" + --min_base_quality_score $advanced.min_base_quality_score + #end if + #if $advanced.minReadsPerAlignmentStart != "5" + --minReadsPerAlignmentStart $advanced.minReadsPerAlignmentStart + #end if + #if $advanced.normal_lod != "2.2" + --normal_lod $advanced.normal_lod + #end if + #if $advanced.pir_mad_threshold != "3.0" + --pir_mad_threshold $advanced.pir_mad_threshold + #end if + #if $advanced.pir_median_threshold != "10.0" + --pir_median_threshold $advanced.pir_median_threshold + #end if + #if $advanced.power_constant_qscore != "30" + --power_constant_qscore $advanced.power_constant_qscore + #end if + #if $advanced.sample_ploidy != "2" + --sample_ploidy $advanced.sample_ploidy + #end if + #if $advanced.standard_min_confidence_threshold_for_calling != "10.0" + --standard_min_confidence_threshold_for_calling $advanced.standard_min_confidence_threshold_for_calling + #end if + #if $advanced.tumor_lod != "6.3" + --tumor_lod $advanced.tumor_lod + #end if + #if $advanced.contamination_fraction_to_filter != "0.0" + --contamination_fraction_to_filter $contamination_fraction_to_filter + #end if + #if $advanced.dbsnp_normal_lod != "5.5" + --dbsnp_normal_lod $dbsnp_normal_lod + #end if + #if $advanced.debug_read_name != "" + --debug_read_name $debug_read_name + #end if + #if $advanced.genotyping_mode != "DISCOVERY" + --genotyping_mode $genotyping_mode + #end if + #if $advanced.group + --group $advanced.group + #end if + #end if + + ##TODO output section --> if the option string == "yes" the optional output is added + #if str($optional_out1.outFile1) =="yes" + --activeRegionOut $activeRegionOut_output + #end if + #if str($optional_out2.outFile2) =="yes" + --activityProfileOut $activityProfileOut_output + #end if + #if str($optional_out3.outFile3) =="yes" + --graphOutput $graphOutput_output + #end if + #if str($optional_out4.outFile4) =="yes" + --bamOutput $bamOutput_output + #end if + ##TODO the standard error is redirected to the log file + 2> $log + ]]></command> + <inputs> + <expand macro="reference_loc"/> + <param format="bam" name="input1" type="data" label="tumor bam" help="bamfile"/> + <param format="bam" name="input2" type="data" label="normal bam" help="bamfile"/> + <param format="vcf" name="dbSNP" type="data" optional="true" label="dbsnp file.vcf" help="vcf file"/> + <param format="vcf" name="cosmic" type="data" optional="true" label="cosmic file.vcf" help="vcf file"/> + <param format="bed" name="list" type="data" optional="true" label="position list" help="bed file"/> + <param format="vcf" name="alleles" type="data" optional="true" label="set of alleles use in genotyping" help="vcf file"/> + <conditional name="advanced"> + <param name="advanced_parameters" type="select" label="advanced_parameters"> + <option value="hide" selected="true">Hide</option> + <option value="show">Show</option> + </param> + <when value="hide"/> + <when value="show"> + <param name="heterozygosity" type="float" optional="true" value="0.001" help="Heterozygosity value used to compute prior likelihoods for any locus" /> + <param name="heterozygosity_stdev" type="float" optional="true" value="0.01" help="Standard deviation of eterozygosity for SNP and indel calling"/> + <param name="indel_heterozygosity" type="text" value="1.25E-4" optional="true" help="Heterozygosity for indel calling" /> + <param name="initial_normal_lod" type="float" optional="true" value="0.5" help="Initial LOD threshold for calling normal variant" /> + <param name="initial_tumor_lod" type="float" optional="true" value="4.0" help="Initial LOD threshold for calling tumor variant" /> + <param name="max_alt_allele_in_normal_fraction" type="float" optional="true" value="0.03" help="Threshold for maximum alternate allele fraction in normal" /> + <param name="max_alt_alleles_in_normal_count" type="text" optional="true" value="1" help="Threshold for maximum alternate allele counts in normal" /> + <param name="max_alt_alleles_in_normal_qscore_sum" type="text" optional="true" value="20" help="Threshold for maximum alternate allele quality score sum in normal" /> + <param name="maxReadsInRegionPerSample" type="text" optional="true" value="1000" help="Maximum reads in an active region" /> + <param name="min_base_quality_score" type="text" size="2" optional="true" value="10" help="Minimum base quality required to consider a base for calling" /> + <param name="minReadsPerAlignmentStart" type="text" optional="true" value="5" help="Minimum number of reads sharing the same alignment start for each genomic location in an active region" /> + <param name="normal_lod" type="float" optional="true" value="2.2" help="LOD threshold for calling normal non-germline" /> + <param name="pir_mad_threshold" type="float" optional="true" value="3.0" help="threshold for clustered read position artifact MAD" /> + <param name="pir_median_threshold" type="float" optional="true" value="10.0" help="threshold for clustered read position artifact median" /> + <param name="power_constant_qscore" type="text" optional="true" value="30" help="Phred scale quality score constant to use in power calculations" /> + <param name="sample_ploidy" type="text" optional="true" value="2" help="ploidy per sample" /> + <param name="standard_min_confidence_threshold_for_calling" type="float" optional="true" value="10.0" help="The minimum phred-scaled confidence threshold at which variants should be called" /> + <param name="tumor_lod" type="float" optional="true" value="6.3" help="LOD threshold for calling tumor variant" /> + <param name="contamination_fraction_to_filter" type="float" optional="true" value="0.0" help="Fraction of contamination to aggressively remove" /> + <param name="dbsnp_normal_lod" type="float" optional="true" value="5.5" help="LOD threshold for calling normal non-variant at dbsnp sites" /> + <param name="debug_read_name" type="text" optional="true" value="" help="trace this read name through the calling process" /> + <param name="genotyping_mode" type="select" optional="true" help="Specifies how to determine the alternate alleles to use for genotyping" > + <option value="DISCOVERY" selected="true">DISCOVERY</option> + <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> + </param> + <param name="group" type="text" optional="true" help="one or more classes, groups of annotation to apply to variant call" /> + </when> + </conditional> + <conditional name="optional_out1"> + <param name="outFile1" type="select" label="activeRegionOut"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no"/> + <when value="yes"/> + </conditional> + <conditional name="optional_out2"> + <param name="outFile2" type="select" label="activityprofileOut"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no"/> + <when value="yes"/> + </conditional> + <conditional name="optional_out3"> + <param name="outFile3" type="select" label="graphOutput"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no"/> + <when value="yes"/> + </conditional> + <conditional name="optional_out4"> + <param name="outFile4" type="select" label="Bamoutput"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no"/> + <when value="yes"/> + </conditional> + </inputs> + <outputs> + <data format="vcf" name="output" label="${tool.name} on ${on_string}"/> + <data format="txt" name="log" label="${tool.name} on ${on_string} :log"/> + <data format="txt" name="activeRegionOut_output" optional="true" label="${tool.name} on ${on_string} :activeRegionOut"> + <filter>optional_out1['outFile1'] == 'yes'</filter> + </data> + <data format="txt" name="activityProfileOut_output" label="${tool.name} on ${on_string} :activityProfileOut"> + <filter>optional_out2['outFile2'] == 'yes'</filter> + </data> + <data format="txt" name="graphOutput_output" label="${tool.name} on ${on_string} :graphOutput"> + <filter>optional_out3['outFile3'] == 'yes'</filter> + </data> + <data format="txt" name="bamOutput_output" label="${tool.name} on ${on_string} :bamOutput"> + <filter>optional_out4['outFile4'] == 'yes'</filter> + </data> + </outputs> + <tests> + <test> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="test_fasta.fa"/> + </conditional> + <param name="input1" value="mutect2_test_tumoral2.bam" /> + <param name="input2" value="mutect2_test_normal2.bam" /> + </test> + </tests> + <help> + **IMPORTANT** to get the wrapper ready to start the admin user have to download gatk GATK 3.8-0-ge9d806836 from the broadinstitute site https://software.broadinstitute.org/gatk/download/archive and then move it in the conda_prefix folder + the path of the conda_prefix is written in the galaxy.ini(or .yml) file + + MuTect2 is a somatic SNP and indel caller that combines the DREAM challenge-winning somatic genotyping engine of the original MuTect (Cibulskis et al., 2013) with the assembly-based machinery of HaplotypeCaller. + Galaxy wrapper for MuTect2 implements most but not all options available through the command line. Supported options are described below. + + **Optional Inputs** + + + --alleles none Set of alleles to use in genotyping + + --cosmic [] VCF file of COSMIC sites + + --dbsnp none dbSNP file + + --activityProfileOut NA Output the raw activity profile results in IGV format + + --graphOutput NA Write debug assembly graph information to this file + + **Optional Parameters** + + + --contamination_fraction_to_filter 0.0 Fraction of contamination to aggressively remove + + --dbsnp_normal_lod 5.5 LOD threshold for calling normal non-variant at dbsnp sites + + --debug_read_name NA trace this read name through the calling process + + --genotyping_mode DISCOVERY Specifies how to determine the alternate alleles to use for genotyping + + --group [] One or more classes/groups of annotations to apply to variant calls + + --heterozygosity 0.001 Heterozygosity value used to compute prior likelihoods for any locus + + --heterozygosity_stdev 0.01 Standard deviation of eterozygosity for SNP and indel calling + + --indel_heterozygosity 1.25E-4 Heterozygosity for indel calling + + --initial_normal_lod 0.5 Initial LOD threshold for calling normal variant + + --initial_tumor_lod 4.0 Initial LOD threshold for calling tumor variant + + --max_alt_allele_in_normal_fraction 0.03 Threshold for maximum alternate allele fraction in normal + + --max_alt_alleles_in_normal_count 1 Threshold for maximum alternate allele counts in normal + + --max_alt_alleles_in_normal_qscore_sum 20 Threshold for maximum alternate allele quality score sum in normal + + --maxReadsInRegionPerSample 1000 Maximum reads in an active region + + --min_base_quality_score 10 Minimum base quality required to consider a base for calling + + --minReadsPerAlignmentStart 5 Minimum number of reads sharing the same alignment start for each genomic location in an active region + + --normal_lod 2.2 LOD threshold for calling normal non-germline + + --pir_mad_threshold 3.0 threshold for clustered read position artifact MAD + + --pir_median_threshold 10.0 threshold for clustered read position artifact median + + --power_constant_qscore 30 Phred scale quality score constant to use in power calculations + + --sample_ploidy 2 Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). + + --standard_min_confidence_threshold_for_calling 10.0 The minimum phred-scaled confidence threshold at which variants should be called + + --tumor_lod 6.3 LOD threshold for calling tumor variant + + **Advanced Outputs** + + + --bamOutput + + --activeRegionOut + + --activityProfileOut + + --graphOutput + + more information at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php + </help> + <citations> + <citation type="doi">10.1038/nbt.2514</citation> + </citations> +</tool>