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author iuc
date Sun, 11 Aug 2024 21:06:06 +0000
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1 <tool id="basil" name="basil" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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2 <description>Breakpoint detection, including large insertions</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.2.0</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">anise_basil</requirement>
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9 </requirements>
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10 <version_command>basil --version 2&gt;&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command>
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11 <command detect_errors="aggressive"><![CDATA[
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12 #if $reference_source.reference_source_selector == 'history':
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13 ln -f -s '$reference_source.ref' ref.fa &&
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14 #else:
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15 ln -f -s '$reference_source.ref.fields.path' ref.fa &&
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16 #end if
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17 ln -s '$bam' 'in.bam' &&
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18 ln -s '$vcf' 'out.vcf' &&
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19 basil
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20 --input-reference 'ref.fa'
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21 --input-mapping 'in.bam'
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22 --out-vcf 'out.vcf'
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23 --oea-min-support-each-side '$min_oea_each_side'
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24 ]]></command>
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25 <inputs>
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26 <conditional name="reference_source">
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27 <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
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28 <option value="cached">Use a built-in genome index</option>
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29 <option value="history">Use a genome from history and build index</option>
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30 </param>
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31 <when value="cached">
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32 <param name="ref" type="select" label="Using reference genome" help="Select genome from the list">
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33 <options from_data_table="all_fasta">
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34 <filter type="sort_by" column="2"/>
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35 <validator type="no_options" message="No reference genomes are available"/>
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36 </options>
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37 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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38 </param>
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39 </when>
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40 <when value="history">
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41 <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
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42 </when>
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43 </conditional>
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44 <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/>
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45 <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion. In range [1..inf]. This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered."/>
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46 </inputs>
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47 <outputs>
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48 <data name="vcf" format="vcf"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <conditional name="reference_source">
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53 <param name="reference_source_selector" value="history" />
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54 <param name="ref" ftype="fasta" value="ref.fa"/>
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55 </conditional>
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56 <param name="ref" value="ref.fa"/>
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57 <param name="bam" value="simulated.bam"/>
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58 <param name="min_oea_each_side" value="2"/>
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59 <output name="vcf" file="basil.vcf"/>
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60 </test>
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61 <test>
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62 <conditional name="reference_source">
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63 <param name="reference_source_selector" value="cached" />
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64 <param name="ref" value="genome"/>
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65 </conditional>
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66 <param name="bam" value="simulated.bam"/>
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67 <param name="min_oea_each_side" value="2"/>
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68 <output name="vcf" file="basil.vcf"/>
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. Use BASIL to analyze BAM files for tentative insertion sites.
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73
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74 Note that BASIL will in general detect all kinds of breakpoints, e.g. for inversions on real-world data.
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75
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76 BASIL VCF fields
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77
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78 A typical line in BASIL might look as follows.
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79
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80 1 5001 site_0 T <INS> . PASS IMPRECISE;SVTYPE=INS GSCORE:CLEFT:CRIGHT:OEALEFT:OEARIGHT 46.4256:10:12:35:32
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81
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82 The first seven columns are as usually in VCF files (ref name, 1-based position, reference base, abbreviation for long insertion, no assigned quality, passing all filters, imprecise insertion SV).
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83
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84 The eighth column contains the names of the score values given in the ninth column:
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85
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86 GSCORE Geometric mean of the sum of "1 + $score" for all of the following scores.
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87 CLEFT Number of clipping signatures supporting the site from the left side.
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88 CRIGHT Number of clipping signatures supporting the site from the right side.
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89 OEALEFT Number of OEA alignments supporting the site from the left.
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90 OEARIGHT Number of OEA alignmetns supproting the site from the right.
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91
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92 Generally, one should filter for a minimum support of OEA records on each side, e.g. a value of 10 makes sense for a 30x coverage and showed good results on simulated data.
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93
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94 For a ranking, GSCORE is a suitable measure but we did not develop any statistical model for BASIL matches and it is a mean of pseudocounts only. It carries no statistically precise meaning.
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95 ]]></help>
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96 <citations>
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97 <citation type="doi">10.1093/bioinformatics/btv051</citation>
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98 </citations>
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99 </tool>