freebayes: freebayes.xml comparison

comparison freebayes.xml @ 30:ef2c525bd8cd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"

author	iuc
date	Wed, 06 Nov 2019 17:02:57 -0500
parents	156b60c1530f
children	57def2d7c093

comparison

equal deleted inserted replaced

-:156b60c1530f
+:ef2c525bd8cd
-<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0">
+<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@">
 <description>bayesian genetic variant detector</description>
 <macros>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements">
 --fasta-reference '${reference_fasta_filename}'
 ## Outputs
 --vcf './vcf_output/part_\$i.vcf'
+## Coverage
+#if str($coverage_options.coverage_options_selector) == "set":
+@COVERAGE@
+#end if
 ##advanced options
 #if str( $options_type.options_type_selector ) == "simple":
 #pass
 #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
+--min-alternate-fraction 0.05
 --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
+--min-alternate-fraction 0.05
 --pooled-continuous
 --report-monomorphic
 --standard-filters
---min-coverage ${options_type.min_coverage}
 #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 $options_type.optional_inputs.output_trace_option:
 -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
 ## POPULATION AND MAPPABILITY PRIORS
 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--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="coverage_options">
+<param name="coverage_options_selector" type="select" label="Read coverage"
+help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
+<option value="do_not_set" selected="true">Use defaults</option>
+<option value="set">Specify coverage options</option>
+</param>
+<when value="set">
+<expand macro="par_min_cov" />
+</when>
+<when value="do_not_set" />
+</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. 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, --variant-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>
 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
-<param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="0"
+<param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
 <param name="no_partial_observations" argument="--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="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
 </when>
 label="Exclude reads with more than this number of separate gaps"
 help="default=~unbounded" />
 <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false"
 label="Use stringent input base and mapping quality filters"
 help="Equivalent to -m 30 -q 20 -R 0 -S 0" />
-<param name="F" argument="--min-alternate-fraction" type="float" value="0.2"
+<param name="F" argument="--min-alternate-fraction" type="float" value="0.05"
 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
 <param name="C" argument="--min-alternate-count" 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" />
 <param name="min_alternate_qsum" argument="--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" />
 <param name="G" argument="--min-alternate-total" 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" />
-<expand macro="par_min_cov" />
 </when>
 <when value="do_not_set" />
 </conditional>
 <!-- population and mappability priors -->
 </when>
 <when value="do_not_set" />
 </conditional>
 </when>
 <when value="simple" />
-<when value="simple_w_filters">
+<when value="simple_w_filters" />
-<!-- add standard-filters to command line -->
+<when value="naive" />
-<expand macro="par_min_cov" />
+<when value="naive_w_filters" />
-</when>
-<when value="naive">
-<!-- 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">
-<!-- build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
-<expand macro="par_min_cov" />
-</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)">
 <param name="reference_source_selector" value="history" />
 <param name="processmode" value="individual" />
 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
 <param name="options_type_selector" value="naive_w_filters"/>
+<param name="coverage_options_selector" value="set" />
 <param name="min_coverage" value="14"/>
 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
 </test>
 <test>
 <param name="reference_source_selector" value="history" />
 <param name="processmode" value="individual" />
 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
 <param name="options_type_selector" value="naive_w_filters"/>
+<param name="coverage_options_selector" value="set" />
 <param name="min_coverage" value="14"/>
 <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
 </test>
 <test>
 <param name="reference_source_selector" value="history" />
 <param name="options_type_selector" value="full"/>
 <param name="population_model_selector" value="set"/>
 <param name="P" value="1"/>
 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
 </test>
+<test>
+<param name="reference_source_selector" value="history" />
+<param name="processmode" value="individual" />
+<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
+<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
+<param name="options_type_selector" value="simple"/>
+<param name="coverage_options_selector" value="set" />
+<param name="min_coverage" value="250" />
+<output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />
+</test>
+<test>
+<param name="reference_source_selector" value="history" />
+<param name="processmode" value="individual" />
+<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
+<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
+<param name="options_type_selector" value="simple"/>
+<param name="coverage_options_selector" value="set" />
+<param name="limit_coverage" value="400" />
+<output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
+</test>
+<test>
+<param name="reference_source_selector" value="history" />
+<param name="processmode" value="individual" />
+<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
+<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
+<param name="options_type_selector" value="simple"/>
+<param name="coverage_options_selector" value="set" />
+<param name="skip_coverage" value="100" />
+<output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
+</test>
 </tests>
-<help>
+<help><![CDATA[
 **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.
 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 parameters.
 ------
+**Command-line parameters**
+**Input**::
+--bam FILE                          The file or set of BAM files to be analyzed.
+--bam-list FILE                     A file containing a list of BAM files to be analyzed.
+--stdin                             Read BAM input on stdin.
+--fasta-reference FILE              Use FILE as the reference sequence for analysis.
+An index file (FILE.fai) will be created if none exists.
+If neither --targets nor --region are specified, FreeBayes
+will analyze every position in this reference.
+--targets FILE                      Limit analysis to targets listed in the BED-format FILE.
+--region <chrom>:<start>-<end>      Limit analysis to the specified region, 0-base coordinates,
+end_position not included (same as BED format).
+Either '-' or '..' maybe used as a separator.
+--samples FILE                      Limit analysis to samples listed (one per line) in the FILE.
+By default FreeBayes will analyze all samples in its input
+BAM files.
+--populations FILE                  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.
+--cnv-map FILE                      Read a copy number map from the BED file FILE, which has
+either a sample-level ploidy:
+sample_name copy_number
+or a region-specific format:
+seq_name start end sample_name copy_number
+... for each region in each sample which does not have the
+default copy number as set by --ploidy. These fields can be delimited
+by space or tab.
+**Output**::
+--vcf FILE                          Output VCF-format results to FILE. (default: stdout)
+--gvcf                              Write gVCF output, which indicates coverage in uncalled regions.
+--gvcf-chunk NUM                    When writing gVCF output emit a record for every NUM bases.
+--gvcf-dont-use-chunk               When writing the gVCF output emit a record for all bases if
+set to "true" , will also route an int to --gvcf-chunk
+similar to --output-mode EMIT_ALL_SITES from GATK
+--variant-input VCF                 Use variants reported in VCF file as input to the algorithm.
+Variants in this file will included in the output even if
+there is not enough support in the data to pass input filters.
+--only-use-input-alleles            Only provide variant calls and genotype likelihoods for sites
+and alleles which are provided in the VCF input, and provide
+output in the VCF for all input alleles, not just those which
+have support in the data.
+--haplotype-basis-alleles VCF       When specified, only variant alleles provided in this input
+VCF will be used for the construction of complex or haplotype
+alleles.
+--report-all-haplotype-alleles      At sites where genotypes are made over haplotype alleles,
+provide information about all alleles in output, not only
+those which are called.
+--report-monomorphic                Report even loci which appear to be monomorphic, and report all
+considered alleles, even those which are not in called genotypes.
+Loci which do not have any potential alternates have '.' for ALT.
+--pvar N                            Report sites if the probability that there is a polymorphism
+at the site is greater than N.  default: 0.0.  Note that post-
+filtering is generally recommended over the use of this parameter.
+--strict-vcf                        Generate strict VCF format (FORMAT/GQ will be an int)
+**Population model**::
+--theta N                           The expected mutation rate or pairwise nucleotide diversity
+among the population under analysis.  This serves as the
+single parameter to the Ewens Sampling Formula prior model
+default: 0.001
+--ploidy N                          Sets the default ploidy for the analysis to N.  default: 2
+--pooled-discrete                   Assume that samples result from pooled sequencing.
+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.
+--pooled-continuous                 Output all alleles which pass input filters, regardles of
+genotyping outcome or model.
+**Reference allele**::
+--use-reference-allele              This flag includes the reference allele in the analysis as
+if it is another sample from the same population.
+--reference-quality MQ,BQ           Assign mapping quality of MQ to the reference allele at each
+site and base quality of BQ.  default: 100,60
+**Allele scope**::
+--use-best-n-alleles N              Evaluate only the best N SNP alleles, ranked by sum of
+supporting quality scores.  (Set to 0 to use all; default: all)
+--max-complex-gap
+--haplotype-length N                Allow haplotype calls with contiguous embedded matches of up
+to this length. Set N=-1 to disable clumping. (default: 3)
+--min-repeat-size                   When assembling observations across repeats, require the total repeat
+length at least this many bp.  (default: 5)
+--min-repeat-entropy N              To detect interrupted repeats, build across sequence until it has
+entropy > N bits per bp. Set to 0 to turn off. (default: 1)
+--no-partial-observations           Exclude observations which do not fully span the dynamically-determined
+detection window.  (default, use all observations, dividing partial
+support across matching haplotypes when generating haplotypes.)
+**Indel realignment**::
+--dont-left-align-indels            Turn off left-alignment of indels, which is enabled by default.
+**Input filters**::
+--use-duplicate-reads               Include duplicate-marked alignments in the analysis.
+default: exclude duplicates marked as such in alignments
+--min-mapping-quality Q             Exclude alignments from analysis if they have a mapping
+quality less than Q.  default: 1
+--min-base-quality Q                Exclude alleles from analysis if their supporting base
+quality is less than Q.  default: 0
+--min-supporting-allele-qsum Q      Consider any allele in which the sum of qualities of supporting
+observations is at least Q.  default: 0
+--min-supporting-mapping-qsum Q     Consider any allele in which and the sum of mapping qualities of
+supporting reads is at least Q.  default: 0
+--mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base
+quality of the mismatch is >= Q.  default: 10
+--read-mismatch-limit N             Exclude reads with more than N mismatches where each mismatch
+has base quality >= mismatch-base-quality-threshold.
+default: ~unbounded
+--read-max-mismatch-fraction N      Exclude reads with more than N [0,1] fraction of mismatches where
+each mismatch has base quality >= mismatch-base-quality-threshold
+default: 1.0
+--read-snp-limit N                  Exclude reads with more than N base mismatches, ignoring gaps
+with quality >= mismatch-base-quality-threshold.
+default: ~unbounded
+--read-indel-limit N                Exclude reads with more than N separate gaps.
+default: ~unbounded
+--standard-filters                  Use stringent input base and mapping quality filters
+Equivalent to -m 30 -q 20 -R 0 -S 0
+--min-alternate-fraction N          Require at least this fraction of observations supporting
+an alternate allele within a single individual in the
+in order to evaluate the position.  default: 0.05
+--min-alternate-count N             Require at least this count of observations supporting
+an alternate allele within a single individual in order
+to evaluate the position.  default: 2
+--min-alternate-qsum N              Require at least this sum of quality of observations supporting
+an alternate allele within a single individual in order
+to evaluate the position.  default: 0
+--min-alternate-total N             Require at least this count of observations supporting
+an alternate allele within the total population in order
+to use the allele in analysis.  default: 1
+--min-coverage N                    Require at least this coverage to process a site. default: 0
+--limit-coverage N                  Downsample per-sample coverage to this level if greater than this coverage.
+default: no limit
+--skip-coverage N                   Skip processing of alignments overlapping positions with coverage >N.
+This filters sites above this coverage, but will also reduce data nearby.
+default: no limit
+**Population priors**::
+--no-population-priors              Equivalent to --pooled-discrete --hwe-priors-off and removal of
+Ewens Sampling Formula component of priors.
+**Mappability priors**::
+--hwe-priors-off                    Disable estimation of the probability of the combination
+arising under HWE given the allele frequency as estimated
+by observation frequency.
+--binomial-obs-priors-off           Disable incorporation of prior expectations about observations.
+Uses read placement probability, strand balance probability,
+and read position (5'-3') probability.
+--allele-balance-priors-off         Disable use of aggregate probability of observation balance between alleles
+as a component of the priors.
+**Genotype likelihoods**::
+--observation-bias FILE             Read length-dependent allele observation biases from FILE.
+The format is [length] [alignment efficiency relative to reference]
+where the efficiency is 1 if there is no relative observation bias.
+--base-quality-cap Q                Limit estimated observation quality by capping base quality at Q.
+--prob-contamination F              An estimate of contamination to use for all samples.  default: 10e-9
+--legacy-gls                        Use legacy (polybayes equivalent) genotype likelihood calculations
+--contamination-estimates FILE      A file containing per-sample estimates of contamination, such as
+those generated by VerifyBamID.  The format should be:
+sample p(read=R|genotype=AR) p(read=A|genotype=AA)
+Sample '*' can be used to set default contamination estimates.
+**Algorithmic features**::
+--report-genotype-likelihood-max    Report genotypes using the maximum-likelihood estimate provided
+from genotype likelihoods.
+--genotyping-max-iterations N       Iterate no more than N times during genotyping step. default: 1000.
+--genotyping-max-banddepth N        Integrate no deeper than the Nth best genotype by likelihood when
+genotyping. default: 6.
+--posterior-integration-limits N,M  Integrate all genotype combinations in our posterior space
+which include no more than N samples with their Mth best
+data likelihood. default: 1,3.
+--exclude-unobserved-genotypes      Skip sample genotypings for which the sample has no supporting reads.
+--genotype-variant-threshold N      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.  default: ~unbounded
+--use-mapping-quality               Use mapping quality of alleles when calculating data likelihoods.
+--harmonic-indel-quality            Use a weighted sum of base qualities around an indel, scaled by the
+distance from the indel.  By default use a minimum BQ in flanking sequence.
+--read-dependence-factor N          Incorporate non-independence of reads by scaling successive
+observations by this factor during data likelihood
+calculations.  default: 0.9
+--genotype-qualities                Calculate the marginal probability of genotypes and report as GQ in
+each sample field in the VCF output.
+------
 **Acknowledgments**
 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
 TNG was developed by Bjoern Gruening.
+]]>
 </help>
 <expand macro="citations">
 <citation type="bibtex">
 @article{Tange2011a,
 title = {GNU Parallel - The Command-Line Power Tool},

Mercurial > repos > devteam > freebayes

comparison freebayes.xml @ 30:ef2c525bd8cd draft