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1 <tool id="bcftools_query" name="BCFtools query" version="1.0.0">
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2 <description>Output VCF/BCF fields in user-defined format</description>
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3 <requirements>
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4 <requirement type="package" version="1.3">bcftools</requirement>
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5 </requirements>
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6 <command>
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7 #if str( $input_file_index ) != "None":
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8 ln -s -f $input input_file.${input.ext} &&
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9 ln -s -f $input_file_index input_file.${input.ext}.tbi &&
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10 #end if
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11
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12 bcftools query
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13 --output "${output_file}"
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14 --format "${format}"
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15 #if str( $regions_file ) != "None":
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16 --regions-file "${regions_file}"
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17 #end if
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18 #if str( $regions ) != "":
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19 --regions "${regions}"
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20 #end if
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21 #if str( $targets_file ) != "None":
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22 --targets-file "${targets_file}"
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23 #end if
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24 #if str( $targets ) != "":
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25 --targets "${targets}"
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26 #end if
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27 #if str( $samples_file ) != "None":
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28 --samples-file "${samples_file}"
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29 #end if
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30 #if str( $samples ) != "":
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31 --samples "${samples}"
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32 #end if
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33 #if str( $expr_cond.set_expr ) == "True":
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34 #if str( $expr_cond.include_or_exclude ) == "include":
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35 --include "${expr_cond.expr}"
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36 #else
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37 --exclude "${expr_cond.expr}"
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38 #end if
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39 #end if
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40 #if str( $collapse ) != "None":
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41 --collapse "${collapse}"
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42 #end if
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43 ${print_header}
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44 ${list_samples}
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45 ${allow_undef_tags}
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46
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47 #if str( $input_file_index ) != "None":
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48 input_file.${input.ext}
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49 #else
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50 $input
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51 #end if
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52 </command>
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53 <inputs>
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54 <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
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55 <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
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56 <param name="format" type="text" size="80" label="Output format string (required)" help="-f. Example: "%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n". See BCFtools documentation for more info.">
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57 <sanitizer invalid_char="">
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58 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid>
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59 </sanitizer>
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60 </param>
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61 <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
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62 <param name="regions" type="text" size="80" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
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63 <sanitizer invalid_char="">
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64 <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
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65 </sanitizer>
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66 </param>
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67 <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
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68 <param name="targets" type="text" size="80" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
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69 <sanitizer invalid_char="">
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70 <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
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71 </sanitizer>
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72 </param>
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73 <param name="samples_file" type="data" optional="true" label="Samples file" help="-S. File of sample names to include. One sample per line."/>
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74 <param name="samples" type="text" size="80" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" />
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75 <conditional name="expr_cond">
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76 <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, e. Include/ exclude sites for which expression is true. Must use valid expression."/>
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77 <when value="true">
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78 <param name="include_or_exclude" type="select" label="Include or exclude by expression">
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79 <option value="include">Include</option>
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80 <option value="exclude">Exclude</option>
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81 </param>
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82 <param name="expr" type="text" size="80" label="Expression">
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83 <sanitizer invalid_char="">
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84 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid>
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85 </sanitizer>
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86 </param>
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87 </when>
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88 </conditional>
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89 <param name="collapse" optional="True" type="select" label="Collapse records" help="-c. Controls how to treat records with duplicate positions, and defines compatible records across multiple input files.">
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90 <option value="some">Some (only records where some subset of ALT alleles match are compatible)</option>
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91 <option value="all">All (all records are compatible, regardless of whether ALT alleles match)</option>
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92 <option value="snps">SNPs (all SNP records are compatible, regardless of whether ALT alleles match) </option>
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93 <option value="indels">Indels (all indel records are compatible, regardless of whether REF and ALT alleles match) </option>
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94 <option value="both">Both (SNPs are compatible and indels are compatible)</option>
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95 </param>
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96 <param name="print_header" type="boolean" checked="False" truevalue="--print-header" falsevalue="" label="Print header" help="-H" />
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97 <param name="list_samples" type="boolean" checked="False" truevalue="--list-samples" falsevalue="" label="Print sample names to stdout, then exit" help="-l" />
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98 <param name="allow_undef_tags" type="boolean" checked="False" truevalue="--allow-undef-tags" falsevalue="" label="Allow undefined tags" help="-u. If there are undefined tags in the format string, print "." instead of throwing an error." />
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99 </inputs>
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100 <outputs>
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101 <data name="output_file" format="txt" label="${tool.name} on ${on_string}" />
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102 </outputs>
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103 <help>
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104 **About this tool**
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105
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106 **BCFtools query**: Extract fields from VCF or BCF files and output them in user-defined format.
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107
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108 Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
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109 </help>
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110 </tool>
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