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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:27:37 -0500
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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" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">freebayes</requirement>
5 <requirement type="package" version="0.1.16">samtools</requirement>
6 </requirements>
7 <description>Bayesian genetic variant detector</description>
8 <command>
9 ln -s $reference localref.fa &amp;&amp;
10 ln -s $bamfile localbam.bam &amp;&amp;
11 samtools faidx localref.fa 2&gt;&amp;1 || echo "Error running samtools faidx for FreeBayes" &gt;&amp;2 &amp;&amp;
12 samtools sort localbam.bam localbam.bam 2&gt;&amp;1 || echo "Error running samtools sort for FreeBayes" &gt;&amp;2 &amp;&amp;
13 samtools index localbam.bam 2&gt;&amp;1 || echo "Error running samtools index for FreeBayes" &gt;&amp;2 &amp;&amp;
14 freebayes --fasta-reference localref.fa localbam.bam --vcf $output
15 #if $params.source_select == "full":
16 $params.showRefRepeats
17 -T $params.theta
18 -p $params.ploidy
19 $params.pooled
20 $params.mnps
21 $params.nosnps
22 -n $params.bestAlleles
23 $params.allAlleles
24 $params.duplicateReads
25 -M $params.refMapQuality
26 $params.ignoreRefAllele
27 $params.haploidReference
28 -m $params.minMapQuality
29 -q $params.minBaseQuality
30 $params.noFilters
31 -x $params.indelExclusionWindow
32 <!-- -D $readDependenceFactor -->
33 -V $params.diffusionPriorScalar
34 -W $params.postIntegBandwidth
35 -Y $params.postIntegBanddepth
36 -F $params.minAltFraction
37 -C $params.minAltCount
38 -G $params.minAltTotal
39 --min-coverage $params.minCoverage
40 #end if
41 </command>
42 <inputs>
43 <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/>
44 <param format="bam" name="bamfile" type="data" label="Bam Alignment File"/>
45 <conditional name="params">
46 <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">
47 <option value="pre_set">Commonly Used</option>
48 <option value="full">Full Parameter List</option>
49 </param>
50 <when value="pre_set"/>
51 <when value="full">
52 <param name="indels" type="select" label="Include insertion and deletion alleles in the analysis">
53 <option value="">No</option>
54 <option value="-i -N --report-all-alternates --left-align-indels">Yes</option>
55 </param>
56 <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"/>
57 <param name="showRefRepeats" type="select" label="Show Reference Repeats" help="Calculate and show information about reference repeats in the VCF output">
58 <option value="">No</option>
59 <option value="-_">Yes</option>
60 </param>
61 <param name="ploidy" size="5" type="integer" value="2" label="Ploidy" help="Sets the default ploidy for the analysis"/>
62 <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">
63 <option value="">No</option>
64 <option value="-J">Yes</option>
65 </param>
66 <param name="mnps" type="select" label="Include multi-nuceotide polymorphisms in the analysis">
67 <option value="">No</option>
68 <option value="--mnps">Yes</option>
69 </param>
70 <param name="nosnps" type="select" label="Ignore SNP alleles">
71 <option value="">No</option>
72 <option value="--no-snps">Yes</option>
73 </param>
74 <param name="duplicateReads" type="select" label="Include duplicate-marked alignments in the analysis">
75 <option value="">No</option>
76 <option value="--use-duplicate-reads">Yes</option>
77 </param>
78 <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"/>
79 <param name="allAlleles" type="select" label="Evaluate all possible alleles">
80 <option value="">No</option>
81 <option value="--use-all-alleles">Yes</option>
82 </param>
83 <param name="refMapQuality" size="5" type="integer" value="100" label="Assign mapping quality of Q to the reference allele at each site"/>
84 <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"/>
85 <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"/>
86 <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"/>
87 <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"/>
88 <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">
89 <option value="">No</option>
90 <option value="--ignore-reference-allele">Yes</option>
91 </param>
92 <param name="haploidReference" type="select" label="Haploid Reference" help="If using the reference sequence as a sample, consider it to be haploid">
93 <option value="">No</option>
94 <option value="--haploid-reference">Yes</option>
95 </param>
96 <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">
97 <option value="">No</option>
98 <option value="--no-filters">Yes</option>
99 </param>
100 <!-- <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"/> -->
101 <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"/>
102 <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"/>
103 <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"/>
104 <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"/>
105 <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"/>
106 <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"/>
107 <param name="minCoverage" size="5" type="integer" value="0" label="Minimum Coverage" help="Require at least this coverage to process a site"/>
108 </when>
109 </conditional>
110 </inputs>
111 <outputs>
112 <data format="vcf" name="output" metadata_source="reference" />
113 </outputs>
114 <tests>
115 <test>
116 <param name="reference" ftype="fasta" value="mosaik_test_ref.fasta"/>
117 <param name="bamfile" ftype="bam" value="freebayes_in.bam"/>
118 <param name="source_select" value="pre_set"/>
119 <output name="output" file="freebayes_out.vcf" lines_diff="4"/>
120 </test>
121 </tests>
122 <help>
123 This tool uses Freebayes to call SNPS given a reference sequence and a BAM alignment file.
124 </help>
125 </tool>