freebayes: freebayes.xml comparison

comparison freebayes.xml @ 23:52aed7d9ed2b draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd

author	devteam
date	Sun, 25 Sep 2016 09:48:24 -0400
parents	99684adf84de
children	da6e10dee68b

comparison

equal deleted inserted replaced

-:99684adf84de
+:52aed7d9ed2b
-<?xml version="1.0"?>
+<tool id="freebayes" name="FreeBayes" version="1.0.2.29--1">
-<tool id="freebayes" name="FreeBayes" version="0.4.1">
+<description> - bayesian genetic variant detector</description>
 <requirements>
-<requirement type="package" version="0_9_20_b040236">freebayes</requirement>
+<requirement type="package" version="1.0.2.29">freebayes</requirement>
-<requirement type="package" version="0.1.18">samtools</requirement>
+<requirement type="package" version="0.1.19">samtools</requirement>
-</requirements>
+<requirement type="package" version="4.1.3">gawk</requirement>
-<description> - bayesian genetic variant detector</description>
+<requirement type="package" version="20160622">parallel</requirement>
-<command>
+</requirements>
+<stdio>
+<exit_code range="1:" />
+</stdio>
+<command>
+<![CDATA[
 ##set up input files
 #set $reference_fasta_filename = "localref.fa"
 #if str( $reference_source.reference_source_selector ) == "history":
-ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
-samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for FreeBayes" &gt;&amp;2 &amp;&amp;
+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( $reference_source.input_bams ):
-ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
+ln -s "${input_bam}" "b_${bam_count}.bam" &&
-ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
+ln -s "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" &&
 #end for
 ## Tabixize optional input_varinat_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":
-#if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and $options_type.optional_inputs.optional_inputs_selector and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
+ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&
-ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &amp;&amp;
+ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&
-ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &amp;&amp;
 #end if
-##finished setting up inputs
+#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 &&
-##COMMAND LINE STARTS HERE
+#end for
+sort -u regions_all.bed > regions_uniq.bed &&
+## split into even small chunks, this has some disatvantages and will not be used for the moment
+## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
+mkdir vcf_output &&
+mkdir failed_alleles &&
+mkdir trace &&
+## Finished setting up inputs
+for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
+do
+echo "
+## COMMAND LINE STARTS HERE
 freebayes
+--region '\$i'
 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
---bam "localbam_${bam_count}.bam"
+--bam 'b_${bam_count}.bam'
 #end for
---fasta-reference "${reference_fasta_filename}"
+--fasta-reference '${reference_fasta_filename}'
-##outputs
+## Outputs
---vcf "${output_vcf}"
+--vcf './vcf_output/part_\$i.vcf'
 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
---targets "${target_limit_type.input_target_bed}"
+--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}"
+--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
 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
+--standard-filters
---standard-filters
+--min-coverage '${options_type.min_coverage}'
---min-coverage "${options_type.min_coverage}"
 #elif str( $options_type.options_type_selector ) == "naive":
+--haplotype-length 0
---haplotype-length 0
+--min-alternate-count 1
---min-alternate-count 1
+--min-alternate-fraction 0
---min-alternate-fraction 0
+--pooled-continuous
---pooled-continuous
+--report-monomorphic
---report-monomorphic
 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
+--haplotype-length 0
---haplotype-length 0
+--min-alternate-count 1
---min-alternate-count 1
+--min-alternate-fraction 0
---min-alternate-fraction 0
+--pooled-continuous
---pooled-continuous
+--report-monomorphic
---report-monomorphic
+--standard-filters
---standard-filters
+--min-coverage '${options_type.min_coverage}'
---min-coverage "${options_type.min_coverage}"
+## Command line direct text entry is not allowed at this time for security reasons
-##    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':
-#if $options_type.optional_inputs.optional_inputs_selector:
+${options_type.optional_inputs.report_monomorphic}
-	  ${options_type.optional_inputs.report_monomorphic}
+#if $options_type.optional_inputs.output_trace_option:
+--trace ./trace/part_'\$i'.txt
-#if $options_type.optional_inputs.output_trace_option:
+#end if
---trace "${output_trace}"
+#if $options_type.optional_inputs.output_failed_alleles_option:
-#end if
+--failed-alleles ./failed_alleles/part_'\$i'.bed
+#end if
-#if $options_type.optional_inputs.output_failed_alleles_option:
+#if $options_type.optional_inputs.samples:
---failed-alleles "${output_failed_alleles_bed}"
+--samples '${options_type.optional_inputs.samples}'
 #end if
+#if $options_type.optional_inputs.populations:
-#if $options_type.optional_inputs.samples:
+--populations '${options_type.optional_inputs.populations}'
---samples "${options_type.optional_inputs.samples}"
+#end if
-#end if
+#if $options_type.optional_inputs.A:
+--cnv-map '${options_type.optional_inputs.A}'
-#if $options_type.optional_inputs.populations:
+#end if
---populations "${options_type.optional_inputs.populations}"
+#if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
-#end if
+--variant-input 'input_variant_vcf.vcf.gz'  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above
+${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
-#if $options_type.optional_inputs.A:
+#end if
---cnv-map "${options_type.optional_inputs.A}"
+#if $options_type.optional_inputs.haplotype_basis_alleles:
-#end if
+--haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
+#end if
-#if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
+#if $options_type.optional_inputs.observation_bias:
---variant-input "input_variant_vcf.vcf.gz"  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above
+--observation-bias '${options_type.optional_inputs.observation_bias}'
-${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
+#end if
-#end if
+#if $options_type.optional_inputs.contamination_estimates:
+--contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
-#if $options_type.optional_inputs.haplotype_basis_alleles:
+#end if
---haplotype-basis-alleles "${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
 ## REPORTING
+#if str( $options_type.reporting.reporting_selector ) == "set":
-#if str( $options_type.reporting.reporting_selector ) == "True":
 --pvar ${options_type.reporting.pvar}
 #end if
+## POPULATION MODEL
-## POPULATION MODEL
+#if str( $options_type.population_model.population_model_selector ) == "set":
+--theta '${options_type.population_model.T}'
-#if str( $options_type.population_model.population_model_selector ) == "True":
+--ploidy '${options_type.population_model.P}'
---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":
-#if str( $options_type.reference_allele.reference_allele_selector ) == "True":
 ${options_type.reference_allele.Z}
---reference-quality "${options_type.reference_allele.reference_quality}"
+--reference-quality '${options_type.reference_allele.reference_quality}'
 #end if
 ## ALLELE SCOPE
+#if str( $options_type.allele_scope.allele_scope_selector ) == "set":
-#if str( $options_type.allele_scope.allele_scope_selector ) == "True":
 ${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}"
+-n '${options_type.allele_scope.n}'
---haplotype-length "${options_type.allele_scope.haplotype_length}"
+--haplotype-length '${options_type.allele_scope.haplotype_length}'
---min-repeat-size "${options_type.allele_scope.min_repeat_length}"
+--min-repeat-size '${options_type.allele_scope.min_repeat_length}'
---min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}"
+--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":
-#if str( $options_type.input_filters.input_filters_selector ) == "True":
 ${options_type.input_filters.use_duplicate_reads}
--m "${options_type.input_filters.m}"
+-m '${options_type.input_filters.m}'
--q "${options_type.input_filters.q}"
+-q '${options_type.input_filters.q}'
--R "${options_type.input_filters.R}"
+-R '${options_type.input_filters.R}'
--Y "${options_type.input_filters.Y}"
+-Y '${options_type.input_filters.Y}'
-#if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "True":
+#if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
--Q "${options_type.input_filters.mismatch_filters.Q}"
+-Q '${options_type.input_filters.mismatch_filters.Q}'
--U "${options_type.input_filters.mismatch_filters.U}"
+-U '${options_type.input_filters.mismatch_filters.U}'
--z "${options_type.input_filters.mismatch_filters.z}"
+-z '${options_type.input_filters.mismatch_filters.z}'
---read-snp-limit "${options_type.input_filters.mismatch_filters.read_snp_limit}"
+--read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}'
 #end if
--e "${options_type.input_filters.e}"
+-e '${options_type.input_filters.e}'
--F "${options_type.input_filters.F}"
+-F '${options_type.input_filters.F}'
--C "${options_type.input_filters.C}"
+-C '${options_type.input_filters.C}'
 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
--G "${options_type.input_filters.G}"
+-G '${options_type.input_filters.G}'
---min-coverage "${options_type.input_filters.min_coverage}"
+--min-coverage '${options_type.input_filters.min_coverage}'
 #end if
 ## POPULATION AND MAPPABILITY PRIORS
+#if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
-#if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "True":
 ${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":
-#if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True":
+--base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}'
---base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}"
 ${$options_type.genotype_likelihoods.experimental_gls}
---prob-contamination "${$options_type.genotype_likelihoods.prob_contamination}"
+--prob-contamination '${$options_type.genotype_likelihoods.prob_contamination}'
 #end if
 ## ALGORITHMIC FEATURES
+#if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
-#if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True":
 ${options_type.algorithmic_features.report_genotype_likelihood_max}
--B "${options_type.algorithmic_features.B}"
+-B '${options_type.algorithmic_features.B}'
---genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}"
+--genotyping-max-banddepth '${options_type.algorithmic_features.genotyping_max_banddepth}'
--W "${options_type.algorithmic_features.W}"
+-W '${options_type.algorithmic_features.W}'
 ${options_type.algorithmic_features.N}
-#if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "True":
+#if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set":
--S "${options_type.algorithmic_features.genotype_variant_threshold.S}"
+-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}"
+-D '${options_type.algorithmic_features.D}'
 ${options_type.algorithmic_features.genotype_qualities}
 #end if
 #end if
-</command>
+";
+done > freebayes_commands.sh &&
-<inputs>
+cat freebayes_commands.sh | parallel --no-notice -j \${GALAXY_SLOTS:-1} &&
-<conditional name="reference_source">
-<param name="reference_source_selector" type="select" label="Load reference genome from">
+## make VCF header
-<option value="cached">Local cache</option>
-<option value="history">History</option>
+grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
-</param>
-<when value="cached">
+for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
-<repeat name="input_bams" title="Sample BAM file" min="1">
+do
-<param name="input_bam" type="data" format="bam" label="BAM file">
+## if this fails then it bails out the script
-<validator type="unspecified_build" />
+cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
-<validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+;
+done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > "${output_vcf}"
+#if str( $options_type.options_type_selector ) == "full":
+#if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
+#if $options_type.optional_inputs.output_failed_alleles_option:
+&&
+for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
+do
+cat "./failed_alleles/part_\$i.bed"
+;
+done > '${output_failed_alleles_bed}'
+#end if
+#if $options_type.optional_inputs.output_trace_option:
+&&
+for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
+do
+cat './trace/part_\$i.txt'
+;
+done > '${output_trace}'
+#end if
+#end if
+#end if
+]]>
+</command>
+<inputs>
+<conditional name="reference_source">
+<param name="reference_source_selector" type="select" label="Load reference genome from">
+<option value="cached">Local cache</option>
+<option value="history">History</option>
 </param>
-</repeat>
+<when value="cached">
+<param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
-<param name="ref_file" type="select" label="Using reference genome">
+<validator type="unspecified_build" />
-<options from_data_table="fasta_indexes"></options>
+<validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
-<validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+</param>
-</param>
+<param name="ref_file" type="select" label="Using reference genome">
-</when>
+<options from_data_table="fasta_indexes"></options>
-<when value="history"> <!-- FIX ME!!!! -->
+<validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-<repeat name="input_bams" title="Sample BAM file" min="1">
+</param>
-<param name="input_bam" type="data" format="bam" label="BAM file" />
+</when>
-</repeat>
+<when value="history"> <!-- FIX ME!!!! -->
-<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" />
+<param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" />
-</when>
+<param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
-</conditional>
+help="You can upload a FASTA sequence to the history and use it as reference" />
+</when>
-<conditional name="target_limit_type">
+</conditional>
-<param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
+<conditional name="target_limit_type">
-<option value="do_not_limit" selected="True">Do not limit</option>
+<param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
-<option value="limit_by_target_file">Limit by target file</option>
+<option value="do_not_limit" selected="True">Do not limit</option>
-<option value="limit_by_region">Limit to region</option>
+<option value="limit_by_target_file">Limit by target file</option>
-</param>
+<option value="limit_by_region">Limit to region</option>
-<when value="do_not_limit">
+</param>
-<!-- Do nothing here -->
+<when value="do_not_limit">
-</when>
-<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"/>
-</when>
-<when value="limit_by_region">
-<param name="region_chromosome" type="text" label="Region Chromosome" value="" help="-r --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>
-<when value="full">
-<conditional name="optional_inputs">
-<param name="optional_inputs_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to provide 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" />
-<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" />
-<param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" help="--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"/>
-<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" />
-<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."/>
-<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="provide_vcf">
+<when value="limit_by_target_file">
-<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_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." help="-t --targets"/>
-<conversion name="Tabixized_input" type="tabix" />
+</when>
-</param>
+<when value="limit_by_region">
-<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="region_chromosome" type="text" label="Region Chromosome" value="" help="-r --region"/> <!--only once? -->
-</when>
+<param name="region_start" type="integer" label="Region Start" value="" />
-</conditional>
+<param name="region_end" type="integer" label="Region End" value="" />
-<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" />
+</when>
-<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  " />
-<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" />
-<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." />
-</when>
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
 </conditional>
+<conditional name="options_type">
-<!-- reporting -->
+<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>
-<conditional name="reporting">
+<option value="simple_w_filters">2:Simple diploid calling with filtering and coverage</option>
-<param name="reporting_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set reporting option?" help="Sets -P --pvar option" />
+<option value="naive">3:Frequency-based pooled calling</option>
-<when value="set">
+<option value="naive_w_filters">4:Frequency-based pooled calling with filtering and coverage</option>
-<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.  " />
+<option value="full">5:Complete list of all options</option>
-</when>
+<!-- We will not alloow command line text boxes at this time
-<when value="do_not_set">
+<option value="cline">6:Input parameters on the command line</option>
-<!-- do nothing -->
+-->
-</when>
+</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">
+<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" />
+<param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False"
+label="Write out algorithm trace file" help="--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"/>
+<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" />
+<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."/>
+<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="provide_vcf">
+<param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm">
+<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" />
+</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" />
+<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  " />
+<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" />
+<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." />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</conditional>
+<!-- reporting -->
+<conditional name="reporting">
+<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.  " />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</conditional>
+<!-- population model -->
+<conditional name="population_model">
+<param name="population_model_selector" type="select" label="Population model options"
+help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options  " >
+<option value="do_not_set" selected="true">Use defaults</option>
+<option value="set">Set population model options</option>
+</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" />
+<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." />
+<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." />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</conditional>
+<!-- reference allele -->
+<conditional name="reference_allele">
+<param name="reference_allele_selector" type="select" label="Reference allele options"
+help="Sets --use-reference-allele and --reference-quality options.">
+<option value="do_not_set" selected="true">Use defaults</option>
+<option value="set">Set reference allele options</option>
+</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" />
+<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  " />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</conditional>
+<!-- allelic scope -->
+<conditional name="allele_scope">
+<param name="allele_scope_selector" type="select" label="Allelic scope options"
+help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options.">
+<option value="do_not_set" selected="true">Use defaults</option>
+<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="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)."
+help="-u --no-complex; default=False" />
+<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" />
+<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." />
+<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." />
+<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)." />
+<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." />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</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)." />
+<!-- 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, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options.">
+<option value="do_not_set" selected="true">No input filters (default)</option>
+<option value="set">Set input filters</option>
+</param>
+<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)." />
+<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" />
+<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" />
+<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" />
+<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" />
+<conditional name="mismatch_filters">
+<param name="mismatch_filters_selector" type="select" label="Mismatch filters"
+help="Sets -Q, -U, -z, and &#36; 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="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" />
+<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 " />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</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" />
+<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" />
+<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" />
+<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" />
+<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  " />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</conditional>
+<!-- population and mappability priors -->
+<conditional name="population_mappability_priors">
+<param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
+help="Sets -k, -w, -V, and -a options.">
+<option value="do_not_set" selected="true">Use defaults</option>
+<option value="set">Set population and mappability priors</option>
+</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." />
+<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" />
+<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&#39;'-3&#39;') probability." />
+<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  " />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</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.">
+<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="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." />
+<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." />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</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">
+<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" />
+<param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step"
+help="-B --genotyping-max-iterations; default=1000." />
+<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" />
+<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" />
+<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" />
+<conditional name="genotype_variant_threshold">
+<param name="genotype_variant_threshold_selector" type="select"
+label="Limit posterior integration"
+help="-S --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="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" />
+</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="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." />
+<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." />
+<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  " />
+</when>
+<when value="do_not_set">
+<!-- do nothing -->
+</when>
+</conditional>
+</when>
+<when value="simple">
+<!-- do nothing -->
+</when>
+<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  " />
+</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  " />
+</when>
 </conditional>
+</inputs>
-<!-- population model -->
+<outputs>
+<data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
-<conditional name="population_model">
+<data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
-	  <param name="population_model_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set population model?" help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options  " />
+<filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
-	    <when value="set">
+</data>
-	      <param name="T" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis" help="-T --theta; default = 0.001. This serves as the single parameter to the Ewens Sampling Formula prior model." />
+<data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
-	      <param name="P" type="integer" value="2" label="Set ploidy for the analysis" help="-p --ploidy; default=2" />
+<filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>
-	      <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." />
+</data>
-	      <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.  " />
+</outputs>
-	    </when>
+<tests>
-	    <when value="do_not_set">
+<test>
-	      <!-- do nothing -->
+<param name="reference_source_selector" value="history" />
-	      </when>
+<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
-	</conditional>
+<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
+<param name="options_type_selector" value="simple"/>
-<!-- reference allele -->
+<output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
+</test>
-<conditional name="reference_allele">
+<test>
-<param name="reference_allele_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Use reference allele?" help="Sets --use-reference-allele and --reference-quality options  " />
+<param name="reference_source_selector" value="history" />
-<when value="set">
+<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
-<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" />
+<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
-<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  " />
+<param name="options_type_selector" value="naive_w_filters"/>
-</when>
+<param name="min_coverage" value="14"/>
-<when value="do_not_set">
+<output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
-<!-- do nothing -->
+</test>
-</when>
+<test>
-</conditional>
+<param name="reference_source_selector" value="history" />
+<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
-<!-- allelic scope -->
+<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
+<param name="options_type_selector" value="naive_w_filters"/>
-<conditional name="allele_scope">
+<param name="min_coverage" value="14"/>
-<param name="allele_scope_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set allelic scope?" help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options  " />
+<output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>
-<when value="set">
+</test>
-<param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" help="-I --no-snps; default=False" />
+<test>
-<param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" help="-i --no-indels; default=False" />
+<param name="reference_source_selector" value="history" />
-<param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" help="-X --no-mnps; default=False" />
+<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
-<param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)." help="-u --no-complex; default=False" />
+<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
-<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" />
+<param name="options_type_selector" value="full"/>
-<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." />
+<param name="population_model_selector" value="set"/>
-<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." />
+<param name="P" value="1"/>
-<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)." />
+<output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>
-<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.  " />
+</test>
-</when>
+</tests>
-<when value="do_not_set">
+<help>
-<!-- do nothing -->
-</when>
-</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).  " />
-<!-- input filters -->
-<conditional name="input_filters">
-<param name="input_filters_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set input filters?" help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options  " />
-<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)." />
-<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" />
-<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" />
-<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" />
-<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" />
-<conditional name="mismatch_filters">
-<param name="mismatch_filters_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Perform mismatch filtering?" help="Sets -Q, -U, -z, and &#36; options" />
-<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="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" />
-<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 " />
-</when>
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
-</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" />
-<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" />
-<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" />
-<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" />
-<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  " />
-</when>
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
-</conditional>
-<!-- population and mappability priors -->
-<conditional name="population_mappability_priors">
-<param name="population_mappability_priors_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set population and mappability priors?" help="Sets -k, -w, -V, and -a options  " />
-<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." />
-<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" />
-<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&#39;'-3&#39;') probability." />
-<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  " />
-</when>
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
-</conditional>
-<!-- genotype likelihoods -->
-<conditional name="genotype_likelihoods">
-<param name="genotype_likelihoods_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak genotype likelihoods?" help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options. " />
-<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="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." />
-<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." />
-</when>
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
-</conditional>
-<!-- algorithmic features -->
-<conditional name="algorithmic_features">
-<param name="algorithmic_features_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak algorithmic features?" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options  " />
-<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" />
-<param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." />
-<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" />
-<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" />
-<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" />
-<conditional name="genotype_variant_threshold">
-<param name="genotype_variant_threshold_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to to limit posterior integration" help="-S --genotype-variant-threshold" />
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
-<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" />
-</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="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." />
-<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." />
-<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  " />
-</when>
-<when value="do_not_set">
-<!-- do nothing -->
-</when>
-</conditional>
-</when>
-<when value="simple">
-<!-- do nothing -->
-</when>
-<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  " />
-</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  " />
-</when>
-</conditional>
-</inputs>
-<outputs>
-<data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
-<data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
-<filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] is True and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
-</data>
-<data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
-<filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] is True and options_type['optional_inputs']['output_trace_option'] is True</filter>
-</data>
-</outputs>
-<tests>
-<test>
-<param name="reference_source_selector" value="history" />
-<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
-<param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/>
-<param name="options_type_selector" value="simple"/>
-<output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
-</test>
-<test>
-<param name="reference_source_selector" value="history" />
-<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
-<param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/>
-<param name="options_type_selector" value="naive_w_filters"/>
-<param name="min_coverage" value="14"/>
-<output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
-</test>
-</tests>
-<stdio>
-<exit_code range="1:" />
-</stdio>
-<help>
 **What it does**
 FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
 See https://github.com/ekg/freebayes for details on FreeBayes.
-This Galaxy instance of FreeBayes corresponds to release 0.9.20
 ------
 **Description**
 **Citation**
 For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing &lt;http://arxiv.org/abs/1207.3907&gt;`_.
 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
+TNG was developed by Bjoern Gruening
-</help>
+</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>
 </tool>

Mercurial > repos > devteam > freebayes

comparison freebayes.xml @ 23:52aed7d9ed2b draft