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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>