Mercurial > repos > devteam > freebayes
diff freebayes.xml @ 25:bf27106652f3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
| author | iuc |
|---|---|
| date | Wed, 08 Feb 2017 12:45:05 -0500 |
| parents | da6e10dee68b |
| children | a028d13cd860 |
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--- a/freebayes.xml Sun Sep 25 09:48:42 2016 -0400 +++ b/freebayes.xml Wed Feb 08 12:45:05 2017 -0500 @@ -1,7 +1,10 @@ -<tool id="freebayes" name="FreeBayes" version="1.0.2.29--1"> - <description> - bayesian genetic variant detector</description> +<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-2"> + <description>bayesian genetic variant detector</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> - <requirement type="package" version="1.0.2.29">freebayes</requirement> + <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement> <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="4.1.3">gawk</requirement> <requirement type="package" version="20160622">parallel</requirement> @@ -9,32 +12,36 @@ <stdio> <exit_code range="1:" /> </stdio> - <command> -<![CDATA[ + <command><![CDATA[ ##set up input files #set $reference_fasta_filename = "localref.fa" #if str( $reference_source.reference_source_selector ) == "history": - ln -s -f "${reference_source.ref_file}" "${reference_fasta_filename}" && - samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 && + ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' && + samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): - ln -s -f "${input_bam}" "b_${bam_count}.bam" && - ln -s -f "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" && + ln -s -f '${input_bam}' 'b_${bam_count}.bam' && + ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' && #end for - ## Tabixize optional input_varinat_vcf file (for --variant-input option) + ## Tabixize optional input_variant_vcf file (for --variant-input option) #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf": - ln -s -f "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" && - ln -s -f "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" && + ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' 'input_variant_vcf.vcf.gz' && + ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' && #end if #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): - samtools view -H b_${bam_count}.bam | grep "^@SQ" | cut -f 2- | awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed && + samtools view -H b_${bam_count}.bam | + grep "^@SQ" | + cut -f 2- | + awk '{ gsub("^SN:","",$1); + gsub("^LN:","",$2); + print $1"\t0\t"$2; }' >> regions_all.bed && #end for sort -u regions_all.bed > regions_uniq.bed && @@ -50,182 +57,188 @@ for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`; do - echo " + echo " + + ## COMMAND LINE STARTS HERE + + freebayes - ## COMMAND LINE STARTS HERE + --region '\$i' - freebayes + #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): + --bam 'b_${bam_count}.bam' + #end for + --fasta-reference '${reference_fasta_filename}' - --region '\$i' + ## Outputs + --vcf './vcf_output/part_\$i.vcf' - #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): - --bam 'b_${bam_count}.bam' - #end for - --fasta-reference '${reference_fasta_filename}' + #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file": + --targets '${target_limit_type.input_target_bed}' + #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region": + --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}' + #end if + + ##advanced options + #if str( $options_type.options_type_selector ) == "simple": + ##do nothing as command like build up to this point is sufficinet for simple diploid calling - ## Outputs - --vcf './vcf_output/part_\$i.vcf' + #elif str( $options_type.options_type_selector ) == "simple_w_filters": + --standard-filters + --min-coverage '${options_type.min_coverage}' + #elif str( $options_type.options_type_selector ) == "naive": + --haplotype-length 0 + --min-alternate-count 1 + --min-alternate-fraction 0 + --pooled-continuous + --report-monomorphic + #elif str( $options_type.options_type_selector ) == "naive_w_filters": + --haplotype-length 0 + --min-alternate-count 1 + --min-alternate-fraction 0 + --pooled-continuous + --report-monomorphic + --standard-filters + --min-coverage '${options_type.min_coverage}' + + ## Command line direct text entry is not allowed at this time for security reasons + #elif str( $options_type.options_type_selector ) == "full": + #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set': + ${options_type.optional_inputs.report_monomorphic} - #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file": - --targets '${target_limit_type.input_target_bed}' - #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region": - --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}' - #end if - - ##advanced options - #if str( $options_type.options_type_selector ) == "simple": - ##do nothing as command like build up to this point is sufficinet for simple diploid calling + #if $options_type.optional_inputs.output_trace_option: + --trace ./trace/part_'\$i'.txt + #end if + #if $options_type.optional_inputs.output_failed_alleles_option: + --failed-alleles ./failed_alleles/part_'\$i'.bed + #end if + #if $options_type.optional_inputs.samples: + --samples '${options_type.optional_inputs.samples}' + #end if + #if $options_type.optional_inputs.populations: + --populations '${options_type.optional_inputs.populations}' + #end if + #if $options_type.optional_inputs.A: + --cnv-map '${options_type.optional_inputs.A}' + #end if + #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf": + --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above + ${options_type.optional_inputs.input_variant_type.only_use_input_alleles} + #end if + #if $options_type.optional_inputs.haplotype_basis_alleles: + --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}' + #end if + #if $options_type.optional_inputs.observation_bias: + --observation-bias '${options_type.optional_inputs.observation_bias}' + #end if + #if $options_type.optional_inputs.contamination_estimates: + --contamination-estimates '${options_type.optional_inputs.contamination_estimates}' + #end if + #end if - #elif str( $options_type.options_type_selector ) == "simple_w_filters": - --standard-filters - --min-coverage '${options_type.min_coverage}' - #elif str( $options_type.options_type_selector ) == "naive": - --haplotype-length 0 - --min-alternate-count 1 - --min-alternate-fraction 0 - --pooled-continuous - --report-monomorphic - #elif str( $options_type.options_type_selector ) == "naive_w_filters": - --haplotype-length 0 - --min-alternate-count 1 - --min-alternate-fraction 0 - --pooled-continuous - --report-monomorphic - --standard-filters - --min-coverage '${options_type.min_coverage}' + ## REPORTING + #if str( $options_type.reporting.reporting_selector ) == "set": + --pvar ${options_type.reporting.pvar} + #end if + ## POPULATION MODEL + #if str( $options_type.population_model.population_model_selector ) == "set": + --theta '${options_type.population_model.T}' + --ploidy '${options_type.population_model.P}' + ${options_type.population_model.J} + ${options_type.population_model.K} + #end if + + ## REFERENCE ALLELE + #if str( $options_type.reference_allele.reference_allele_selector ) == "set": + ${options_type.reference_allele.Z} + --reference-quality '${options_type.reference_allele.reference_quality}' + #end if - ## Command line direct text entry is not allowed at this time for security reasons - #elif str( $options_type.options_type_selector ) == "full": - #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set': - ${options_type.optional_inputs.report_monomorphic} + ## ALLELE SCOPE + #if str( $options_type.allele_scope.allele_scope_selector ) == "set": + ${options_type.allele_scope.I} + ${options_type.allele_scope.i} + ${options_type.allele_scope.X} + ${options_type.allele_scope.u} + ${options_type.allele_scope.no_partial_observations} + + -n '${options_type.allele_scope.n}' + + --haplotype-length '${options_type.allele_scope.haplotype_length}' + --min-repeat-size '${options_type.allele_scope.min_repeat_length}' + --min-repeat-entropy '${options_type.allele_scope.min_repeat_entropy}' + #end if + + ## REALIGNMENT + ${options_type.O} - #if $options_type.optional_inputs.output_trace_option: - --trace ./trace/part_'\$i'.txt - #end if - #if $options_type.optional_inputs.output_failed_alleles_option: - --failed-alleles ./failed_alleles/part_'\$i'.bed - #end if - #if $options_type.optional_inputs.samples: - --samples '${options_type.optional_inputs.samples}' - #end if - #if $options_type.optional_inputs.populations: - --populations '${options_type.optional_inputs.populations}' + ##INPUT FILTERS + #if str( $options_type.input_filters.input_filters_selector ) == "set": + ${options_type.input_filters.use_duplicate_reads} + -m '${options_type.input_filters.m}' + -q '${options_type.input_filters.q}' + -R '${options_type.input_filters.R}' + -Y '${options_type.input_filters.Y}' + -e '${options_type.input_filters.e}' + -F '${options_type.input_filters.F}' + -C '${options_type.input_filters.C}' + -G '${options_type.input_filters.G}' + + #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set": + -Q '${options_type.input_filters.mismatch_filters.Q}' + -U '${options_type.input_filters.mismatch_filters.U}' + -z '${options_type.input_filters.mismatch_filters.z}' + + --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}' + #end if + + --min-coverage '${options_type.input_filters.min_coverage}' + --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}" #end if - #if $options_type.optional_inputs.A: - --cnv-map '${options_type.optional_inputs.A}' + + ## POPULATION AND MAPPABILITY PRIORS + #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set": + ${options_type.population_mappability_priors.k} + ${options_type.population_mappability_priors.w} + ${options_type.population_mappability_priors.V} + ${options_type.population_mappability_priors.a} #end if - #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf": - --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above - ${options_type.optional_inputs.input_variant_type.only_use_input_alleles} + + ## GENOTYPE LIKELIHOODS + #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set": + ${$options_type.genotype_likelihoods.experimental_gls} + + --base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}' + --prob-contamination '${$options_type.genotype_likelihoods.prob_contamination}' #end if - #if $options_type.optional_inputs.haplotype_basis_alleles: - --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}' - #end if - #if $options_type.optional_inputs.observation_bias: - --observation-bias '${options_type.optional_inputs.observation_bias}' - #end if - #if $options_type.optional_inputs.contamination_estimates: - --contamination-estimates '${options_type.optional_inputs.contamination_estimates}' + + ## ALGORITHMIC FEATURES + #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set": + -B '${options_type.algorithmic_features.B}' + -W '${options_type.algorithmic_features.W}' + -D '${options_type.algorithmic_features.D}' + + #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set": + -S '${options_type.algorithmic_features.genotype_variant_threshold.S}' + #end if + + ${options_type.algorithmic_features.N} + ${options_type.algorithmic_features.j} + ${options_type.algorithmic_features.H} + ${options_type.algorithmic_features.genotype_qualities} + ${options_type.algorithmic_features.report_genotype_likelihood_max} + + --genotyping-max-banddepth '${options_type.algorithmic_features.genotyping_max_banddepth}' #end if #end if - ## REPORTING - #if str( $options_type.reporting.reporting_selector ) == "set": - --pvar ${options_type.reporting.pvar} - #end if - ## POPULATION MODEL - #if str( $options_type.population_model.population_model_selector ) == "set": - --theta '${options_type.population_model.T}' - --ploidy '${options_type.population_model.P}' - ${options_type.population_model.J} - ${options_type.population_model.K} - #end if - - ## REFERENCE ALLELE - #if str( $options_type.reference_allele.reference_allele_selector ) == "set": - ${options_type.reference_allele.Z} - --reference-quality '${options_type.reference_allele.reference_quality}' - #end if - - ## ALLELE SCOPE - #if str( $options_type.allele_scope.allele_scope_selector ) == "set": - ${options_type.allele_scope.I} - ${options_type.allele_scope.i} - ${options_type.allele_scope.X} - ${options_type.allele_scope.u} - -n '${options_type.allele_scope.n}' - --haplotype-length '${options_type.allele_scope.haplotype_length}' - --min-repeat-size '${options_type.allele_scope.min_repeat_length}' - --min-repeat-entropy '${options_type.allele_scope.min_repeat_entropy}' - ${options_type.allele_scope.no_partial_observations} - #end if - - ## REALIGNMENT - ${options_type.O} - - ##INPUT FILTERS - #if str( $options_type.input_filters.input_filters_selector ) == "set": - ${options_type.input_filters.use_duplicate_reads} - -m '${options_type.input_filters.m}' - -q '${options_type.input_filters.q}' - -R '${options_type.input_filters.R}' - -Y '${options_type.input_filters.Y}' + "; + done > freebayes_commands.sh && - #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set": - -Q '${options_type.input_filters.mismatch_filters.Q}' - -U '${options_type.input_filters.mismatch_filters.U}' - -z '${options_type.input_filters.mismatch_filters.z}' - --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}' - #end if - - -e '${options_type.input_filters.e}' - -F '${options_type.input_filters.F}' - -C '${options_type.input_filters.C}' - --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}" - -G '${options_type.input_filters.G}' - --min-coverage '${options_type.input_filters.min_coverage}' - #end if - - ## POPULATION AND MAPPABILITY PRIORS - #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set": - ${options_type.population_mappability_priors.k} - ${options_type.population_mappability_priors.w} - ${options_type.population_mappability_priors.V} - ${options_type.population_mappability_priors.a} - #end if - - ## GENOTYPE LIKELIHOODS - #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set": - --base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}' - ${$options_type.genotype_likelihoods.experimental_gls} - --prob-contamination '${$options_type.genotype_likelihoods.prob_contamination}' - #end if - - ## ALGORITHMIC FEATURES - #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set": - ${options_type.algorithmic_features.report_genotype_likelihood_max} - -B '${options_type.algorithmic_features.B}' - --genotyping-max-banddepth '${options_type.algorithmic_features.genotyping_max_banddepth}' - -W '${options_type.algorithmic_features.W}' - ${options_type.algorithmic_features.N} - - #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set": - -S '${options_type.algorithmic_features.genotype_variant_threshold.S}' - #end if - - ${options_type.algorithmic_features.j} - ${options_type.algorithmic_features.H} - -D '${options_type.algorithmic_features.D}' - ${options_type.algorithmic_features.genotype_qualities} - #end if - #end if - - "; - done > freebayes_commands.sh && - cat freebayes_commands.sh | parallel --no-notice -j \${GALAXY_SLOTS:-1} && + cat freebayes_commands.sh | + parallel --no-notice -j \${GALAXY_SLOTS:-1} && ## make VCF header - grep "^#" "./vcf_output/part_\$i.vcf" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`; @@ -233,7 +246,7 @@ ## if this fails then it bails out the script cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true ; - done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > "${output_vcf}" + done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}' #if str( $options_type.options_type_selector ) == "full": #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set': @@ -256,13 +269,12 @@ #end if #end if #end if -]]> - </command> + ]]></command> <inputs> <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Load reference genome from"> - <option value="cached">Local cache</option> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> @@ -278,7 +290,7 @@ <when value="history"> <!-- FIX ME!!!! --> <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" /> <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" - help="You can upload a FASTA sequence to the history and use it as reference" /> + help="You can upload a FASTA sequence to the history and use it as reference" /> </when> </conditional> <conditional name="target_limit_type"> @@ -287,93 +299,91 @@ <option value="limit_by_target_file">Limit by target file</option> <option value="limit_by_region">Limit to region</option> </param> - <when value="do_not_limit"> - <!-- Do nothing here --> - </when> + <when value="do_not_limit" /><!-- Do nothing here --> <when value="limit_by_target_file"> - <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." help="-t --targets"/> + <param name="input_target_bed" type="data" format="bed" label="Limit analysis to regions in a file (BED-format)." argument="--targets"/> </when> <when value="limit_by_region"> - <param name="region_chromosome" type="text" label="Region Chromosome" value="" help="-r --region"/> <!--only once? --> + <param name="region_chromosome" type="text" label="Region Chromosome" value="" argument="--region"/> <!--only once? --> <param name="region_start" type="integer" label="Region Start" value="" /> <param name="region_end" type="integer" label="Region End" value="" /> </when> </conditional> <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Choose parameter selection level" help="Select how much control over the freebayes run you need" > - <option value="simple" selected="True">1:Simple diploid calling</option> - <option value="simple_w_filters">2:Simple diploid calling with filtering and coverage</option> - <option value="naive">3:Frequency-based pooled calling</option> - <option value="naive_w_filters">4:Frequency-based pooled calling with filtering and coverage</option> - <option value="full">5:Complete list of all options</option> - <!-- We will not alloow command line text boxes at this time - <option value="cline">6:Input parameters on the command line</option> - --> + <param name="options_type_selector" type="select" label="Choose parameter selection level" + help="Select how much control over the freebayes run you need" > + <option value="simple" selected="True">1. Simple diploid calling</option> + <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option> + <option value="naive">3. Frequency-based pooled calling</option> + <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option> + <option value="full">5. Full list of options</option> </param> <when value="full"> <conditional name="optional_inputs"> <param name="optional_inputs_selector" type="select" label="Additional inputs" - help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles, - --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates"> + help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles, + --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates"> <option value="do_not_set" selected="true">Do not provide additional inputs</option> <option value="set">Provide additional inputs</option> </param> <when value="set"> <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" - label="Write out failed alleles file" help="--failed-alleles" /> + label="Write out failed alleles file" argument="--failed-alleles" /> <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" - label="Write out algorithm trace file" help="--trace"/> + label="Write out algorithm trace file" argument="--trace"/> <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" - help="-s --samples; default=By default FreeBayes will analyze all samples in its input BAM files"/> + help="default=By default FreeBayes will analyze all samples in its input BAM files" argument="--samples"/> <param name="populations" type="data" format="txt" label="Populations File" optional="True" - help="--populations; default=False. Each line of FILE should list a sample and a population which it is part of. - The population-based bayesian inference model will then be partitioned on the basis of the populations" /> + help="Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will + then be partitioned on the basis of the populations. [default=False]" + argument="--populations" /> <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" - help="-A --cnv-map; default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format: - reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."/> + help="default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format: + reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy." + argument="--cnv-map" /> <conditional name="input_variant_type"> <param name="input_variant_type_selector" type="select" label="Provide variants file"> <option value="do_not_provide" selected="True">Do not provide</option> <option value="provide_vcf">Provide VCF file</option> </param> - <when value="do_not_provide"> - <!-- Do nothing here --> - </when> + <when value="do_not_provide" /><!-- Do nothing here --> <when value="provide_vcf"> - <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm"> + <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm" argument="--variant-input"> <conversion name="Tabixized_input" type="tabix" /> </param> - <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" /> + <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" + label="Only provide variant calls and genotype likelihoods for sites in VCF" argument="--only-use-input-alleles" /> </when> </conditional> <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True" - help="--haplotype-basis-alleles" /> + argument="--haplotype-basis-alleles" /> <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False" - label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes." - help="--report-monomorphic " /> + label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes." + argument="--report-monomorphic" /> <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from" - help="--observation-bias; The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" /> + help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" + argument="--observation-bias" /> <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from" - help="--contamination-estimates; The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates." /> + help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates." + argument="--contamination-estimates" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> + <!-- reporting --> <conditional name="reporting"> - <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option"> + <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option"> <option value="do_not_set" selected="True">Use defaults</option> <option value="set">Set reporting options</option> - </param> - <when value="set"> - <param name="pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than" - help="-P --pvar; default=0.0. Note that post-filtering is generally recommended over the use of this parameter. " /> + </param> + <when value="set"> + <param name="pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than" + help="Note that post-filtering is generally recommended over the use of this parameter. [default=0.0]" + argument="--pvar" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> + <!-- population model --> <conditional name="population_model"> <param name="population_model_selector" type="select" label="Population model options" @@ -383,18 +393,18 @@ </param> <when value="set"> <param name="T" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis" - help="-T --theta; default = 0.001. This serves as the single parameter to the Ewens Sampling Formula prior model." /> - <param name="P" type="integer" value="2" label="Set ploidy for the analysis" help="-p --ploidy; default=2" /> + help="This serves as the single parameter to the Ewens Sampling Formula prior model. [default = 0.001]" argument='--theta'/> + <param name="P" type="integer" value="2" label="Set ploidy for the analysis" + help="default=2" argument='--ploidy' /> <param name="J" type="boolean" truevalue="-J" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing" - help="-J --pooled-discrete; default=False. Model pooled samples using discrete genotypes across pools. - When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy." /> + help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy. [default=False]" + argument="--pooled-discrete"/> <param name="K" type="boolean" truevalue="-K" falsevalue="" checked="False" label="Output all alleles which pass input filters, regardles of genotyping outcome or model" - help="-K, --poled-continuous; default=False." /> + help="default=False." argument="--poled-continuous" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> + <!-- reference allele --> <conditional name="reference_allele"> <param name="reference_allele_selector" type="select" label="Reference allele options" @@ -404,14 +414,13 @@ </param> <when value="set"> <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population" - help="-Z --use-reference-allele; default=False" /> + help="default=False" argument="--use-reference-allele" /> <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" - help="--reference-quality; default=100,60 " /> + help="default=100,60" argument="--reference-quality" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> + <!-- allelic scope --> <conditional name="allele_scope"> <param name="allele_scope_selector" type="select" label="Allelic scope options" @@ -420,94 +429,98 @@ <option value="set">Set alleic scope options</option> </param> <when value="set"> - <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" help="-I --no-snps; default=False" /> - <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" help="-i --no-indels; default=False" /> - <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" help="-X --no-mnps; default=False" /> + <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" + help="default=False" argument="--no-snps" /> + <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" + help="default=False" argument="--no-indels" /> + <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" + help="default=False" argument="--no-mnps" /> <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)." - help="-u --no-complex; default=False" /> + help="default=False" argument="--no-complex" /> <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate" - help="-n --use-best-n-alleles; default=0 (all). Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" /> + help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all. [default=0 (all)]" + argument="--use-best-n-alleles" /> <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" - help="-E --max-complex-gap --haplotype-length; default=3." /> + help="-E --max-complex-gap --haplotype-length; default=3." /> <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp" - help="--min-repeat-size; default=5." /> + help="default=5." argument="--min-repeat-size" /> <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" - help="--min-repeat-entropy; default=0 (off)." /> + help="default=0 (off)." argument="--min-repeat-entropy" /> <param name="no_partial_observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="False" - label="Exclude observations which do not fully span the dynamically-determined detection window" - help="--no-partial-observations; default=use all observations, dividing partial support across matching haplotypes when generating haplotypes." /> + label="Exclude observations which do not fully span the dynamically-determined detection window" + help="default=use all observations, dividing partial support across matching haplotypes when generating haplotypes." + argument="--no-partial-observations" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> + <!-- indel realignment --> - <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels?" - help="-O --dont-left-align-indels; default=False (do left align)." /> + <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels" + help="default=False (do left align)." argument="--dont-left-align-indels" /> + <!-- input filters --> <conditional name="input_filters"> <param name="input_filters_selector" type="select" label="Input filters" - help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -$, -e, -0, -F, -C, -3, -G, and -! options."> + help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -$, -e, -0, -F, -C, -3, -G, and -! options."> <option value="do_not_set" selected="true">No input filters (default)</option> <option value="set">Set input filters</option> </param> - <when value="set"> + <when value="set"> <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" - label="Include duplicate-marked alignments in the analysis." - help="-4 --use-duplicate-reads; default=False (exclude duplicates marked as such in alignments)." /> + label="Include duplicate-marked alignments in the analysis." + help="default=False (exclude duplicates marked as such in alignments)." argument="--use-duplicate-reads" /> <param name="m" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than" - help="-m --min-mapping-quality; default=1" /> + help="default=1" argument="--min-mapping-quality" /> <param name="q" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than" - help="-q --min-base-quality; default=0" /> + help="default=0" argument="--min-base-quality" /> <param name="R" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least" - help="-R --min-supporting-allele-qsum; default=0" /> + help="default=0" argument="--min-supporting-allele-qsum" /> <param name="Y" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" - help="-Y --min-supporting-mapping-qsum; default=0" /> + help="default=0" argument="--min-supporting-mapping-qsum" /> <conditional name="mismatch_filters"> <param name="mismatch_filters_selector" type="select" label="Mismatch filters" - help="Sets -Q, -U, -z, and $ options"> + help="Sets -Q, -U, -z, and $ options"> <option value="do_not_set" selected="true">No mismatch filters (default)</option> <option value="set">Set mismatch filters</option> </param> <when value="set"> - <param name="Q" type="integer" value="10" label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" - help="-Q --mismatch-base-quality-threshold; default=10" /> - <param name="U" type="integer" value="1000" optional="True" label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)" - help="-U --read-mismatch-limit; default=~unbound" /> + <param name="Q" type="integer" value="10" + label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" + help="default=10" argument="--mismatch-base-quality-threshold" /> + <param name="U" type="integer" value="1000" optional="True" + label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)" + help="default=~unbound" argument="--read-mismatch-limit" /> <param name="z" type="float" value="1.0" min="0.0" max="1.0" - label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= Q (second option above)" - help="-z --read-max-mismatch-fraction; default=1.0" /> + label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= Q (second option above)" + help="default=1.0" argument="--read-max-mismatch-fraction" /> <param name="read_snp_limit" type="integer" - value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)" - help="-$amp; --read-snp-limit N " /> + value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)" + argument="--read-snp-limit" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> <param name="e" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps" - help="-e --read-snp-limit; default=~unbounded" /> - <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False" label="Use stringent input base and mapping quality filters" - help="-0 --standard-filters; default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" /> + help="default=~unbounded" argument="--read-snp-limit" /> + <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False" + label="Use stringent input base and mapping quality filters" + help="default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" argument="--standard-filters"/> <param name="F" type="float" value="0.2" - label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" - help="-F --min-alternate-fraction; default=0.2" /> + label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" + help="default=0.2" argument="--min-alternate-fraction" /> <param name="C" type="integer" value="2" - label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" - help="-C --min-alternate-count; default=2" /> + label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" + help="default=2" argument="--min-alternate-count" /> <param name="min_alternate_qsum" type="integer" value="0" - label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" - help="-3 --min-alternate-qsum; default=0" /> + label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" + help="default=0" argument="--min-alternate-qsum" /> <param name="G" type="integer" value="1" - label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" - help="-G --min-alternate-total N; default=1" /> - <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" - help="-! --min-coverage; default=0 " /> + label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" + help="default=1" argument="--min-alternate-total" /> + <expand macro="par_min_cov" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> + <!-- population and mappability priors --> <conditional name="population_mappability_priors"> <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors" @@ -517,105 +530,102 @@ </param> <when value="set"> <param name="k" type="boolean" truevalue="-k" falsevalue="" checked="False" label="No population priors" - help="-k --no-population-priors; default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors." /> + help="default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors." + argument="--no-population-priors" /> <param name="w" type="boolean" truevalue="-w" falsevalue="" checked="False" - label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" - help="-w --hwe-priors-off; default=False" /> + label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" + help="default=False" argument="--hwe-priors-off" /> <param name="V" type="boolean" truevalue="-V" falsevalue="" checked="False" label="Disable incorporation of prior expectations about observations" - help="-V --binomial-obs-priors-off; default=False. Uses read placement probability, strand balance probability, and read position (5''-3'') probability." /> + help="default=False. Uses read placement probability, strand balance probability, and read position (5''-3'') probability." + argument="--binomial-obs-priors-off" /> <param name="a" type="boolean" truevalue="-a" falsevalue="" checked="False" - label="isable use of aggregate probability of observation balance between alleles as a component of the priors" - help="-a --allele-balance-priors-off; default=False " /> + label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" + help="default=False" + argument="--allele-balance-priors-off" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> + <!-- genotype likelihoods --> <conditional name="genotype_likelihoods"> <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options" - help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options."> + help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options."> <option value="do_not_set" selected="true">Use defaults</option> <option value="set">Set genotype likelihood options</option> </param> <when value="set"> - <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at" help="--base-quality-cap" /> + <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at" + argument="--base-quality-cap" /> <param name="experimental_gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="False" - label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual" - help="--experimental-gls; Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples." /> + label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual" + help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples." + argument="--experimental-gls" /> <param name="prob_contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples" - help="--prob-contamination; default=10e-9." /> + help="default=10e-9." argument="--prob-contamination" /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> + <!-- algorithmic features --> <conditional name="algorithmic_features"> <param name="algorithmic_features_selector" type="select" label="Algorithmic features" - help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options"> + help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options"> <option value="do_not_set" selected="true">Use defaults</option> <option value="set">Set algorithmic features</option> </param> <when value="set"> <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False" - label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." - help="--report-genotype-likelihood-max; default=False" /> + label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." + help="default=False" argument="--report-genotype-likelihood-max" /> <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" - help="-B --genotyping-max-iterations; default=1000." /> + help="default=1000." argument="--genotyping-max-iterations" /> <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" - help="--genotyping-max-banddepth; default=6" /> + help="default=6" argument="--genotyping-max-banddepth" /> <param name="W" type="text" value="1,3" - label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" - help="-W --posterior-integration-limits; default=1,3" /> + label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" + help="default=1,3" argument="--posterior-integration-limits" /> <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" - label="Skip sample genotypings for which the sample has no supporting reads" - help="-N --exclude-unobserved-genotypes; default=False" /> + label="Skip sample genotypings for which the sample has no supporting reads" + help="default=False" argument="--exclude-unobserved-genotypes" /> <conditional name="genotype_variant_threshold"> <param name="genotype_variant_threshold_selector" type="select" - label="Limit posterior integration" - help="-S --genotype-variant-threshold"> + label="Limit posterior integration" argument="--genotype-variant-threshold"> <option value="do_not_set" selected="true">Do not limit posterior integration</option> <option value="set">Set posterior integration limit</option> </param> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> <when value="set"> <param name="S" value="" type="integer" - label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample." - help="-S --genotype-variant-threshold; default=~unbounded" /> + label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample." + help="default=~unbounded" argument="--genotype-variant-threshold" /> </when> </conditional> - <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Use mapping quality of alleles when calculating data likelihoods" - help="-j --use-mapping-quality; default=False" /> + <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False" + label="Use mapping quality of alleles when calculating data likelihoods" + help="default=False" argument="--use-mapping-quality" /> <param name="H" type="boolean" truevalue="-H" falsevalue="" checked="False" - label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel" - help="-H --harmonic-indel-quality; default=use a minimum Base Quality in flanking sequence." /> + label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel" + help="default=use a minimum Base Quality in flanking sequence." argument="--harmonic-indel-quality" /> <param name="D" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" - help="-D --read-dependence-factor; default=0.9." /> + help="default=0.9." argument="--read-dependence-factor" /> <param name="genotype_qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="False" - label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" - help="-= --genotype-qualities; default=False " /> + label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" + help="-= --genotype-qualities; default=False " /> </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> + <when value="do_not_set" /><!-- do nothing --> </conditional> </when> - <when value="simple"> - <!-- do nothing --> - </when> + <when value="simple" /><!-- do nothing --> <when value="simple_w_filters"> <!-- add standard-filters to command line --> - <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0 " /> + <expand macro="par_min_cov" /> </when> <when value="naive"> <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic --> </when> <when value="naive_w_filters"> <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters--> - <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0 " /> + <expand macro="par_min_cov" /> </when> </conditional> </inputs> @@ -687,11 +697,11 @@ **Galaxy-specific options** -Galaxy allows six levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are: +Galaxy allows five levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are: 1. *Simple diploid calling*: The simples possible FreeBayes application. Equvalent of using FreeBayes with only a BAM input and no other parameter options. - 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-varinat-threshold 0) and --min-coverage. - 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling varinats in mixtures such as viral, bacterial, or organellar genomes. + 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-varinat-threshold 0) and --min-coverage. + 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling varinats in mixtures such as viral, bacterial, or organellar genomes. 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2. 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets. @@ -945,21 +955,10 @@ ------ -**Citation** - -For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing <http://arxiv.org/abs/1207.3907>`_. +**Acknowledgments** The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko. TNG was developed by Bjoern Gruening - </help> - <citations> - <citation type="bibtex">@misc{1207.3907, -Author = {Erik Garrison}, -Title = {Haplotype-based variant detection from short-read sequencing}, -Year = {2012}, -Eprint = {arXiv:1207.3907}, -url = {http://arxiv.org/abs/1207.3907}, -}</citation> - </citations> + <expand macro="citations" /> </tool>