freebayes: freebayes.xml comparison

comparison freebayes.xml @ 40:0d8581534009 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d

author	iuc
date	Tue, 05 Aug 2025 13:47:58 +0000
parents	85dc96ebc770
children

comparison

equal deleted inserted replaced

-:85dc96ebc770
+:0d8581534009
-<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
+<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1" profile="23.0">
 <description>bayesian genetic variant detector</description>
+<macros>
+<import>macros.xml</import>
+</macros>
 <xrefs>
 <xref type="bio.tools">freebayes</xref>
 </xrefs>
-<macros>
-<import>macros.xml</import>
-</macros>
 <expand macro="requirements">
+<requirement type="package" version="3.11">grep</requirement>
 <requirement type="package" version="5.3.1">gawk</requirement>
-<requirement type="package" version="20250422">parallel</requirement>
+<requirement type="package" version="20250622">parallel</requirement>
 </expand>
 <expand macro="version_command" />
 <command detect_errors="exit_code"><![CDATA[
 ##set up input files
 ${options_type.algorithmic_features.genotype_qualities}
 ${options_type.algorithmic_features.report_genotype_likelihood_max}
 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
 #end if
+#end if
+#if str($output_options.flavor) == "gvcf":
+--gvcf
+#elif str($output_options.flavor) == "gvcf_custom":
+--gvcf
+#if $output_options.gvcf_block_size == 0:
+## special-casing the 0 case for performance
+--gvcf-dont-use-chunk t
+#else:
+--gvcf-chunk $output_options.gvcf_block_size
+#end if
 #end if
 ";
 done > freebayes_commands.sh &&
 </param>
 <when value="do_not_provide" />
 <when value="provide_vcf">
 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
 label="Use variants reported in this VCF dataset as input to the algorithm"/>
-<param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
+<param argument="--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" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
+<param argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
-<param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
+<param argument="--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" />
-<param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
+<param argument="--observation-bias" type="data" format="tabular" optional="true"
 label="Load read length-dependent allele observation biases from"
 help="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" argument="--contamination-estimates" type="data" format="tabular" optional="true"
+<param argument="--contamination-estimates" type="data" format="tabular" optional="true"
 label="Upload per-sample estimates of contamination from"
 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" />
-<param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
+<param argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
 label="Trim trailing reference matches" />
 </when>
 <when value="do_not_set" />
 </conditional>
 <option value="set">Set reference allele options</option>
 </param>
 <when value="set">
 <param name="Z" argument="--use-reference-allele" 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" />
-<param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
+<param argument="--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)" />
 </when>
 <when value="do_not_set" />
 </conditional>
 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
 label="Ignore complex events (composites of other classes)" />
 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
 label="How many best SNP alleles to evaluate"
 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"
+<param 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="1"
+<param 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"
+<param 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>
 <when value="do_not_set" />
 </conditional>
 <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
 help="default=~unbounded" />
 <param argument="--read-max-mismatch-fraction" 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 >= mismatch-base-quality-threshold (second option above)" />
-<param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
+<param argument="--read-snp-limit" type="integer" value="1000"
 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
 help="default=~unbounded" />
 </when>
 <when value="do_not_set" />
 </conditional>
 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" argument="--base-quality-cap" type="integer" value="0"
+<param argument="--base-quality-cap" type="integer" value="0"
 label="Limit estimated observation quality by capping base quality at" />
-<param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
+<param argument="--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="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
-<param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"
+<param argument="--prob-contamination" type="float" value="10e-9"
 label="An estimate of contamination to use for all samples" />
 </when>
 <when value="do_not_set" />
 </conditional>
 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" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
+<param argument="--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" />
 <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"
 label="Iterate no more than N times during genotyping step" />
-<param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"
+<param argument="--genotyping-max-banddepth" type="integer" value="6"
 label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
 <param name="W" argument="--posterior-integration-limits" 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" />
 <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
 label="Skip sample genotypings for which the sample has no supporting reads" />
-<param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"
+<param argument="--genotype-variant-threshold" type="integer" value="" optional="true"
 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" />
 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
 label="Use mapping quality of alleles when calculating data likelihoods" />
 <param name="H" argument="--harmonic-indel-quality" 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="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
 <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
 label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
-<param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
+<param argument="--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" />
 </when>
 <when value="do_not_set" />
 </conditional>
 </when>
 <when value="simple" />
 <when value="simple_w_filters" />
 <when value="naive" />
 <when value="naive_w_filters" />
+</conditional>
+<conditional name="output_options">
+<param name="flavor" type="select" label="Type of main output to produce" help="The tool will, by default, produce VCF output with information about sites with called variants. If you want also information (such as depth of coverage) about non-called sites, you can use the gVCF or gVCF with custom block size options. The first collapses the stats of entire blocks of consecutive non-called sites into one non-call record. The second gives you control over how many consecutive non-called sites should be combined into a non-call record.">
+<option value="vcf">VCF (default)</option>
+<option value="gvcf">gVCF (--gvcf)</option>
+<option value="gvcf_custom">gVCF with custom block size</option>
+</param>
+<when value="vcf" />
+<when value="gvcf" />
+<when value="gvcf_custom">
+<param name="gvcf_block_size" type="integer" value="0" min="0" max="2147483647" label="Maximal block size for consecutive non-called sites" help="Consolidate data from any non-called site together with the N next non-called sites into one gVCF record, i.e. produce gVCF block records of maximally N+1 sites. Blocks can be shorter if terminated by the end of a chromosome or a site with a called variant. Setting this parameter to 0 produces a separate record for every non-called site, but can result in very large output." />
+</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 ${on_string} (failed alleles)">
 <data format="txt" name="output_trace" label="${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'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>
 </data>
 </outputs>
 <tests>
-<test>
+<test expect_num_outputs="1">
 <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="simple"/>
 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
 </test>
-<test>
+<test expect_num_outputs="1">
+<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="simple" />
+<conditional name="output_options">
+<param name="flavor" value="gvcf" />
+</conditional>
+<output name="output_vcf" file="freebayes-phix174.gvcf" lines_diff="4" />
+</test>
+<test expect_num_outputs="1">
+<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="simple" />
+<conditional name="output_options">
+<param name="flavor" value="gvcf_custom" />
+</conditional>
+<!-- This test produces one record per reference position
+so the test file only contains the first part of the expected output up to the second variant site -->
+<output name="output_vcf" file="freebayes-phix174.full.sample.gvcf" compare="contains" lines_diff="2" />
+</test>
+<test expect_num_outputs="1">
 <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 that user-provided (variant-input option) sites are included in output -->
-<test>
+<test expect_num_outputs="1">
 <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="full"/>
 <assert_contents>
 <has_line_matching expression="phiX174&#009;1134&#009;\.&#009;A&#009;\.&#009;.+"/>
 </assert_contents>
 </output>
 </test>
-<test>
+<test expect_num_outputs="1">
 <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="full"/>
 <param name="population_model_selector" value="set"/>
 <param name="P" value="1"/>
 <param name="trim_complex_tail" value="--trim-complex-tail"/>
 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
 </test>
-<test>
+<test expect_num_outputs="1">
 <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>
+<test expect_num_outputs="1">
 <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>
+<test expect_num_outputs="1">
 <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>
-<test> <!-- Test with CRAM -->
+<test expect_num_outputs="1"> <!-- Test with CRAM -->
 <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="cram" value="freebayes-phix174.cram"/>
 <param name="options_type_selector" value="simple"/>

Mercurial > repos > devteam > freebayes

comparison freebayes.xml @ 40:0d8581534009 draft default tip