/tools/human_genome_variation/freebayes.xml
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1<?xml version="1.0"?> 2<tool id="freebayes_wrapper" name="Call SNPS with Freebayes" version="0.5.0"> 3 <requirements> 4 <requirement type="package">freebayes</requirement> 5 </requirements> 6 <description>Bayesian genetic variant detector</description> 7 <command> 8 ln -s $reference localref.fa; 9 ln -s $bamfile localbam.bam; 10 samtools faidx localref.fa; 11 samtools sort localbam.bam localbam.bam; 12 samtools index localbam.bam; 13 freebayes --fasta-reference localref.fa localbam.bam --vcf $output 14 #if $params.source_select == "full": 15 $params.showRefRepeats 16 -T $params.theta 17 -p $params.ploidy 18 $params.pooled 19 $params.mnps 20 $params.nosnps 21 -n $params.bestAlleles 22 $params.allAlleles 23 $params.duplicateReads 24 -M $params.refMapQuality 25 $params.ignoreRefAllele 26 $params.haploidReference 27 -m $params.minMapQuality 28 -q $params.minBaseQuality 29 $params.noFilters 30 -x $params.indelExclusionWindow 31 <!-- -D $readDependenceFactor --> 32 -V $params.diffusionPriorScalar 33 -W $params.postIntegBandwidth 34 -Y $params.postIntegBanddepth 35 -F $params.minAltFraction 36 -C $params.minAltCount 37 -G $params.minAltTotal 38 --min-coverage $params.minCoverage 39 #end if 40 </command> 41 <inputs> 42 <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/> 43 <param format="bam" name="bamfile" type="data" label="Bam Alignment File"/> 44 <conditional name="params"> 45 <param name="source_select" type="select" label="Freebayes Settings to Use" help="For straight forward mapping needs use Commonly Used settings. If you want full control use Full Parameter List"> 46 <option value="pre_set">Commonly Used</option> 47 <option value="full">Full Parameter List</option> 48 </param> 49 <when value="pre_set"/> 50 <when value="full"> 51 <param name="indels" type="select" label="Include insertion and deletion alleles in the analysis"> 52 <option value="">No</option> 53 <option value="-i -N --report-all-alternates --left-align-indels">Yes</option> 54 </param> 55 <param name="theta" size="5" type="float" value="0.001" label="Theta" help="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"/> 56 <param name="showRefRepeats" type="select" label="Show Reference Repeats" help="Calculate and show information about reference repeats in the VCF output"> 57 <option value="">No</option> 58 <option value="-_">Yes</option> 59 </param> 60 <param name="ploidy" size="5" type="integer" value="2" label="Ploidy" help="Sets the default ploidy for the analysis"/> 61 <param name="pooled" type="select" label="Pooled" help="Assume that samples result from pooled sequencing. When using this flag, set --ploidy to the number of alleles in each sample"> 62 <option value="">No</option> 63 <option value="-J">Yes</option> 64 </param> 65 <param name="mnps" type="select" label="Include multi-nuceotide polymorphisms in the analysis"> 66 <option value="">No</option> 67 <option value="--mnps">Yes</option> 68 </param> 69 <param name="nosnps" type="select" label="Ignore SNP alleles"> 70 <option value="">No</option> 71 <option value="--no-snps">Yes</option> 72 </param> 73 <param name="duplicateReads" type="select" label="Include duplicate-marked alignments in the analysis"> 74 <option value="">No</option> 75 <option value="--use-duplicate-reads">Yes</option> 76 </param> 77 <param name="bestAlleles" size="5" type="integer" value="2" label="Use Best N Alleles" help="Evaluate only the best N alleles, ranked by sum of supporting quality scores"/> 78 <param name="allAlleles" type="select" label="Evaluate all possible alleles"> 79 <option value="">No</option> 80 <option value="--use-all-alleles">Yes</option> 81 </param> 82 <param name="refMapQuality" size="5" type="integer" value="100" label="Assign mapping quality of Q to the reference allele at each site"/> 83 <param name="refBaseQuality" size="5" type="integer" value="60" label="Reference Base Quality" help="Assign a base quality of Q to the reference allele at each site"/> 84 <param name="minMapQuality" size="5" type="integer" value="10" label="Minimum Mapping Quality" help="Exclude alignments from analysis if they have a mapping quality less than Q"/> 85 <param name="minBaseQuality" size="5" type="integer" value="5" label="Minimum Base Quality" help="Exclude alleles from analysis if their supporting base quality is less than Q"/> 86 <param name="indelExclusionWindow" size="5" type="integer" value="0" label="Indel Exclusion Window" help="Ignore portions of alignments N bases from a putative insertion or deletion allele"/> 87 <param name="ignoreRefAllele" type="select" label="Ignore Reference Allele" help="By default, the reference allele is considered as another sample. This flag excludes it from the analysis"> 88 <option value="">No</option> 89 <option value="--ignore-reference-allele">Yes</option> 90 </param> 91 <param name="haploidReference" type="select" label="Haploid Reference" help="If using the reference sequence as a sample, consider it to be haploid"> 92 <option value="">No</option> 93 <option value="--haploid-reference">Yes</option> 94 </param> 95 <param name="noFilters" type="select" label="No Filters" help="Do not use any input base and mapping quality filters. Equivalent to -m 0 -q 0 -R 0 -S 0"> 96 <option value="">No</option> 97 <option value="--no-filters">Yes</option> 98 </param> 99 <!-- <param name="readDependenceFactor" size="5" type="float" value="0.9" label="Read Dependence Factor" help="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations"/> --> 100 <param name="diffusionPriorScalar" size="5" type="float" value="1" label="Diffusion Prior Scalar" help="Downgrade the significance of P(genotype combo | allele frequency) by taking the Nth root of this component of the prior"/> 101 <param name="postIntegBandwidth" size="5" type="integer" value="2" label="Posterior Integratoin Bandwidth" help="Integrate all genotype combinations in our posterior space which lie no more than N steps from the most likely combination in terms of data likelihoods, taking the N steps from the most to least likely genotype for each individual"/> 102 <param name="postIntegBanddepth" size="5" type="integer" value="2" label="Posterior Integratoin Banddepth" help="Generate all genotype combinations for which up to this number of samples have up to their -W'th worst genotype according to data likelihood"/> 103 <param name="minAltFraction" size="5" type="integer" value="0" label="Minimum Alternative Fraction" help="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position"/> 104 <param name="minAltCount" size="5" type="integer" value="1" label="Minimum Alternative Count" help="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"/> 105 <param name="minAltTotal" size="5" type="integer" value="1" label="Minimum Alternative Total" help="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis"/> 106 <param name="minCoverage" size="5" type="integer" value="0" label="Minimum Coverage" help="Require at least this coverage to process a site"/> 107 </when> 108 </conditional> 109 </inputs> 110 <outputs> 111 <data format="vcf" name="output" metadata_source="reference" /> 112 </outputs> 113 <tests> 114 <test> 115 <param name="reference" ftype="fasta" value="mosaik_test_ref.fasta"/> 116 <param name="bamfile" ftype="bam" value="freebayes_in.bam"/> 117 <param name="source_select" value="pre_set"/> 118 <output name="output" file="freebayes_out.vcf" lines_diff="4"/> 119 </test> 120 </tests> 121 <help> 122This tool uses Freebayes to call SNPS given a reference sequence and a BAM alignment file. 123 </help> 124</tool>