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1 <?xml version="1.0"?>
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2 <tool id="freebayes_wrapper" name="Call SNPS with Freebayes" version="0.5.0">
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3 <requirements>
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4 <requirement type="package">freebayes</requirement>
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5 </requirements>
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6 <description>Bayesian genetic variant detector</description>
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7 <command>
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8 ln -s $reference localref.fa;
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9 ln -s $bamfile localbam.bam;
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10 samtools faidx localref.fa;
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11 samtools sort localbam.bam localbam.bam;
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12 samtools index localbam.bam;
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13 freebayes --fasta-reference localref.fa localbam.bam --vcf $output
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14 #if $params.source_select == "full":
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15 $params.showRefRepeats
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16 -T $params.theta
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17 -p $params.ploidy
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18 $params.pooled
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19 $params.mnps
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20 $params.nosnps
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21 -n $params.bestAlleles
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22 $params.allAlleles
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23 $params.duplicateReads
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24 -M $params.refMapQuality
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25 $params.ignoreRefAllele
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26 $params.haploidReference
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27 -m $params.minMapQuality
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28 -q $params.minBaseQuality
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29 $params.noFilters
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30 -x $params.indelExclusionWindow
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31 <!-- -D $readDependenceFactor -->
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32 -V $params.diffusionPriorScalar
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33 -W $params.postIntegBandwidth
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34 -Y $params.postIntegBanddepth
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35 -F $params.minAltFraction
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36 -C $params.minAltCount
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37 -G $params.minAltTotal
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38 --min-coverage $params.minCoverage
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39 #end if
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40 </command>
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41 <inputs>
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42 <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/>
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43 <param format="bam" name="bamfile" type="data" label="Bam Alignment File"/>
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44 <conditional name="params">
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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">
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46 <option value="pre_set">Commonly Used</option>
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47 <option value="full">Full Parameter List</option>
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48 </param>
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49 <when value="pre_set"/>
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50 <when value="full">
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51 <param name="indels" type="select" label="Include insertion and deletion alleles in the analysis">
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52 <option value="">No</option>
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53 <option value="-i -N --report-all-alternates --left-align-indels">Yes</option>
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54 </param>
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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"/>
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56 <param name="showRefRepeats" type="select" label="Show Reference Repeats" help="Calculate and show information about reference repeats in the VCF output">
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57 <option value="">No</option>
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58 <option value="-_">Yes</option>
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59 </param>
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60 <param name="ploidy" size="5" type="integer" value="2" label="Ploidy" help="Sets the default ploidy for the analysis"/>
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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">
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62 <option value="">No</option>
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63 <option value="-J">Yes</option>
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64 </param>
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65 <param name="mnps" type="select" label="Include multi-nuceotide polymorphisms in the analysis">
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66 <option value="">No</option>
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67 <option value="--mnps">Yes</option>
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68 </param>
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69 <param name="nosnps" type="select" label="Ignore SNP alleles">
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70 <option value="">No</option>
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71 <option value="--no-snps">Yes</option>
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72 </param>
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73 <param name="duplicateReads" type="select" label="Include duplicate-marked alignments in the analysis">
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74 <option value="">No</option>
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75 <option value="--use-duplicate-reads">Yes</option>
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76 </param>
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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"/>
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78 <param name="allAlleles" type="select" label="Evaluate all possible alleles">
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79 <option value="">No</option>
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80 <option value="--use-all-alleles">Yes</option>
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81 </param>
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82 <param name="refMapQuality" size="5" type="integer" value="100" label="Assign mapping quality of Q to the reference allele at each site"/>
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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"/>
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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"/>
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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"/>
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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"/>
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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">
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88 <option value="">No</option>
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89 <option value="--ignore-reference-allele">Yes</option>
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90 </param>
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91 <param name="haploidReference" type="select" label="Haploid Reference" help="If using the reference sequence as a sample, consider it to be haploid">
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92 <option value="">No</option>
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93 <option value="--haploid-reference">Yes</option>
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94 </param>
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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">
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96 <option value="">No</option>
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97 <option value="--no-filters">Yes</option>
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98 </param>
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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"/> -->
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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"/>
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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"/>
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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"/>
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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"/>
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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"/>
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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"/>
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106 <param name="minCoverage" size="5" type="integer" value="0" label="Minimum Coverage" help="Require at least this coverage to process a site"/>
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107 </when>
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108 </conditional>
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109 </inputs>
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110 <outputs>
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111 <data format="vcf" name="output" metadata_source="reference" />
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112 </outputs>
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113 <tests>
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114 <test>
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115 <param name="reference" ftype="fasta" value="mosaik_test_ref.fasta"/>
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116 <param name="bamfile" ftype="bam" value="freebayes_in.bam"/>
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117 <param name="source_select" value="pre_set"/>
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118 <output name="output" file="freebayes_out.vcf" lines_diff="4"/>
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119 </test>
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120 </tests>
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121 <help>
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122 This tool uses Freebayes to call SNPS given a reference sequence and a BAM alignment file.
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123 </help>
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124 </tool>
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