annotate macros.xml @ 5:a15210afaf1d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:45:43 -0400
parents c6071203aaa0
children 29ba253e2e05
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1 <macros>
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2 <token name="@VERSION@">1.4.0</token>
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3 <xml name="stdio">
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4 <stdio>
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5 <exit_code range="1:" />
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6 <exit_code range=":-1" />
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7 <regex match="Error:" />
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8 <regex match="Exception:" />
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9 </stdio>
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10 </xml>
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="1.4">bcftools</requirement>
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14 <requirement type="package" version="1.4">htslib</requirement>
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15 <yield />
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16 </requirements>
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17 </xml>
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18 <xml name="samtools_requirement">
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19 <requirement type="package" version="1.3.1">samtools</requirement>
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20 </xml>
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21 <xml name="version_command">
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22 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
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23 </xml>
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24
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25 <xml name="citations">
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26 <citations>
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27 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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28 <yield />
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29 </citations>
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30 </xml>
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31 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
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32 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
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33 <token name="@THREADS@">
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34 --threads \${GALAXY_SLOTS:-4}
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35 </token>
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36 <token name="@PREPARE_ENV@">
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37 <![CDATA[
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38 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
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39 ]]>
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40 </token>
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41 <xml name="macro_input">
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42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
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43 </xml>
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44 <token name="@PREPARE_INPUT_FILE@">
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45 <![CDATA[
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46 ## May need to symlink input if there is an associated
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47 #set $input_vcf = 'input.vcf.gz'
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48 #if $input_file.is_of_type('vcf')
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49 bgzip -c '$input_file' > $input_vcf &&
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50 bcftools index $input_vcf &&
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51 #elif $input_file.is_of_type('vcf_bgzip')
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52 ln -s '$input_file' $input_vcf
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53 #elif $input_file.is_of_type('bcf')
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54 #set $input_vcf = 'input.bcf'
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55 ln -s '$input_file' $input_vcf &&
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56 #if $input_file.metadata.bcf_index:
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57 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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58 #else
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59 bcftools index $input_vcf &&
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60 #end if
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61 #elif $input_file.is_of_type('bcf_bgzip')
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62 ln -s '$input_file' $input_vcf
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63 #end if
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64 ]]>
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65 </token>
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66 <token name="@INPUT_FILE@">
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67 $input_vcf
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68 </token>
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69
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70 <xml name="macro_inputs">
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71 <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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72 </xml>
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73 <token name="@PREPARE_INPUT_FILES@">
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74 <![CDATA[
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75 ## May need to symlink input if there is an associated
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76 #set $input_vcfs = []
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77 #set $vcfs_list_file = 'vcfs_list'
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78 #for (i, input_file) in enumerate($input_files):
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79 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
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80 #if $input_file.is_of_type('vcf')
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81 bgzip -c '$input_file' > $input_vcf &&
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82 bcftools index $input_vcf &&
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83 #elif $input_file.is_of_type('vcf_bgz')
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84 ln -s '$input_file' $input_vcf
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85 #elif $input_file.is_of_type('bcf')
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86 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
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87 ln -s '$input_file' $input_vcf &&
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88 #if $input_file.metadata.bcf_index:
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89 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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90 #else
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91 bcftools index $input_vcf &&
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92 #end if
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93 #elif $input_file.is_of_type('bcfvcf_bgz')
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94 ln -s '$input_file' $input_vcf &&
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95 #end if
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96 echo '$input_vcf' >> $vcfs_list_file &&
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97 $input_vcfs.append($input_vcf)
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98 #end for
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99 ]]>
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100 </token>
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101 <token name="@INPUT_FILES@">
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102 #echo ' '.join($input_vcfs)#
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103 </token>
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104 <token name="@INPUT_LIST_FILE@">
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105 $vcfs_list_file
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106 </token>
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107
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108 <xml name="macro_fasta_ref">
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109 <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />
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110 </xml>
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111 <token name="@PREPARE_FASTA_REF@">
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112 <![CDATA[
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113 #set $input_fa_ref = None
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114 #if 'fasta_ref' in $section and $section.fasta_ref:
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115 #set $input_fa_ref = 'ref.fa'
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116 ln -s '$section.fasta_ref' $input_fa_ref &&
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117 samtools faidx $input_fa_ref &&
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118 #end if
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119 ]]>
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120 </token>
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121 <token name="@FASTA_REF@">
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122 #if $input_fa_ref is not None:
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123 --fasta-ref $input_fa_ref
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124 #elif 'fasta_ref' in $section and $section.fasta_ref:
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125 --fasta-ref '${section.fasta_ref}'
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126 #end if
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127 </token>
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128
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129 <xml name="macro_ref_fasta">
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130 <conditional name="reference_source">
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131 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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132 <option value="cached">Locally cached</option>
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133 <option value="history">History</option>
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134 </param>
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135 <when value="cached">
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136 <param name="ref_file" type="select" label="Select reference genome">
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137 <options from_data_table="fasta_indexes">
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138 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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139 </options>
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140 <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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141 </param>
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142 </when>
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143 <when value="history"> <!-- FIX ME!!!! -->
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144 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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145 </when>
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146 </conditional>
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147 </xml>
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148
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149
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150 <xml name="macro_AF_file">
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151 <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
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152 </xml>
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153 <!-- This may need to bgzip and tabix the file -->
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154 <token name="@PREPARE_AF_FILE@">
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155 <![CDATA[
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156 #if 'AF_file' in $section and $section.AF_file:
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157 #pass
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158 #end if
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159 ]]>
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160 </token>
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161 <token name="@AF_FILE@">
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162 #if 'AF_file' in $section and $section.AF_file:
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163 --AF-file '${section.AF_file}'
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164 #end if
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165 </token>
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166
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167 <xml name="macro_estimate_AF">
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168 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
0
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169 </xml>
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170 <token name="@ESTIMATE_AF@">
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171 #if 'estimate_AF' in $section and $section.estimate_AF:
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172 --estimate-AF "${section.estimate_AF}"
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173 #end if
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174 </token>
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175
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176 <xml name="macro_exons_file">
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177 <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
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178 </xml>
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179 <token name="@PREPARE_EXONS_FILE@">
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180 <![CDATA[
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181 #set $exons_path = None
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182 #if 'exons_file' in $section and $section.exons_file:
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183 #set $exons_path = 'exons_file.tab.gz'
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184 bgzip -c "$section.exons_file" > $exons_path &&
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185 tabix -s 1 -b 2 -e 3 $exons_path &&
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186 #end if
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187 ]]>
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188 </token>
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189 <token name="@EXONS_FILE@">
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190 #if 'exons_file' in $section and $section.exons_file:
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191 --exons $exons_path
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192 #end if
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193 </token>
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194
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195 <xml name="macro_ploidy_file">
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196 <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
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197 </xml>
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198 <token name="@PLOIDY_FILE@">
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199 #if 'ploidy_file' in $section and $section.ploidy_file:
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200 --ploidy "${section.ploidy_file}"
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201 #end if
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202 </token>
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203
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204 <xml name="macro_collapse_opt_none">
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205 <option value="none">none - require the exact same set of alleles in all files</option>
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206 </xml>
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207 <xml name="macro_collapse_opt_id">
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208 <option value="id">id - only records with identical ID column are compatible. </option>
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209 </xml>
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210 <xml name="macro_collapse">
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211 <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
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212 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
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213 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
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214 <option value="both">both - indels and snps </option>
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215 <option value="some">some - at least some of the ALTs must match</option>
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216 <option value="any">any - any combination of alleles</option>
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217 <yield/>
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218 </param>
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219 </xml>
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220 <token name="@COLLAPSE@">
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221 #if $section.collapse:
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222 --collapse ${section.collapse}
0
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223 #end if
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224 </token>
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225
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226 <xml name="macro_apply_filters">
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227 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
0
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228 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
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229 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
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230 </param>
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231 </xml>
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232 <token name="@APPLY_FILTERS@">
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233 #if $section.apply_filters:
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234 --apply-filters '${section.apply_filters}'
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235 #end if
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236 </token>
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237
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238 <xml name="macro_select_output_type">
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239 <param name="output_type" type="select">
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240 <option value="b">compressed BCF</option>
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241 <!-- no galaxy datatypes for these
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242 <option value="u">uncompressed BCF</option>
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243 <option value="z">compressed VCF</option>
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244 -->
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245 <option value="v">uncompressed VCF</option>
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246 </param>
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247 </xml>
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248 <token name="@OUTPUT_TYPE@">
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249 #if str($output_type) != "__none__":
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250 --output-type '${output_type}'
0
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251 #end if
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252 </token>
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253
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254 <xml name="macro_vcf_output">
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255 <data name="output_file" format="vcf">
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256 <change_format>
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257 <when input="output_type" value="b" format="bcf" />
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258 <when input="output_type" value="u" format="bcf" />
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259 <when input="output_type" value="z" format="vcf_bgzip" />
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260 <when input="output_type" value="v" format="vcf" />
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261 </change_format>
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262 </data>
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263 </xml>
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264
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265 <xml name="macro_regions">
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266 <conditional name="regions">
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267 <param name="regions_src" type="select" label="Regions">
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268 <option value="__none__">None</option>
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269 <option value="regions">regions</option>
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270 <option value="regions_file">regions-file</option>
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271 </param>
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272 <when value="__none__"/>
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273 <when value="regions">
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274 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
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275 help="Each region is specifed as: chr or chr:pos or chr:from-to">
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276 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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277 </param>
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278 </when>
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279 <when value="regions_file">
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280 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
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281 </when>
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282 </conditional>
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283 </xml>
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284 <token name="@PREPARE_REGIONS_FILE@">
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285 <![CDATA[
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286 #set $regions_path = None
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287 #if 'regions' in $section
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288 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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289 #if $section.regions.regions_file.ext.startswith('bed'):
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290 #set $regions_path = 'regions_file.bed'
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291 ln -s '$section.regions.regions_file' $regions_path &&
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292 #end if
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293 #end if
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294 #end if
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295 ]]>
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296 </token>
0
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297 <token name="@REGIONS@">
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298 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
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299 --regions '$section.regions.regions'
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300 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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301 #if $regions_path is not None:
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302 --regions-file '$regions_path'
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303 #else:
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304 --regions-file '$section.regions.regions_file'
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305 #end if
0
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306 #end if
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307 </token>
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308 <xml name="macro_targets_file">
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309 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
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310 <yield/>
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311 </param>
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312 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
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313 </xml>
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314 <token name="@PREPARE_TARGETS_FILE@">
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315 <![CDATA[
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316 #set $targets_path = None
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317 #if 'targets' in $section
0
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318 #if $section.targets.targets_src == 'targets_file':
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319 #set $targets_path = 'targets_file.tab.gz'
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320 bgzip -c "$section.targets.targets_file" > $targets_path &&
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321 tabix -s 1 -b 2 -e 2 $targets_path &&
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322 #end if
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323 #elif $tgts_sec.targets_file:
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324 #set $targets_path = 'targets_file.tab.gz'
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325 bgzip -c "$section.targets_file" > $targets_path &&
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326 tabix -s 1 -b 2 -e 2 $targets_path &&
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327 #end if
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328 ]]>
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329 </token>
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330 <token name="@TARGETS_FILE@">
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331 <![CDATA[
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332 #if $targets_path is not None:
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333 --targets-file "${section.invert_targets_file}${targets_path}"
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334 #elif $section.targets_file:
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335 --targets-file "${section.invert_targets_file}${section.targets_file}"
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336 #end if
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337 ]]>
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338 </token>
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339
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340 <xml name="macro_targets">
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341 <conditional name="targets">
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342 <param name="targets_src" type="select" label="Targets">
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343 <option value="__none__">None</option>
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344 <option value="targets">targets</option>
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345 <option value="targets_file">targets-file</option>
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346 </param>
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347 <when value="__none__"/>
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348 <when value="targets">
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349 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
0
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350 help="Each target is specifed as: chr or chr:pos or chr:from-to">
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351 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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352 </param>
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353 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
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354 </when>
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355 <when value="targets_file">
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356 <expand macro="macro_targets_file">
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357 </expand>
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358 </when>
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359 </conditional>
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360 </xml>
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361 <token name="@TARGETS@">
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362 <![CDATA[
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363 #if $targets_path:
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364 --targets-file "${section.targets.invert_targets_file}${targets_path}"
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365 #else:
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366 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
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367 --targets '${section.targets.invert_targets_file}${section.targets.targets}'
0
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368 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
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369 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
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370 #end if
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371 #end if
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372 ]]>
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373 </token>
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374
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375 <xml name="macro_samples">
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376 <param name="samples" type="text" value="" label="Samples" optional="true"
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377 help="(-s) comma separated list of samples to annotate (or exclude)">
0
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378 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
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379 </param>
3
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380 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
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381 help="inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
3
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382 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
0
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383 help="(-S) file of samples to include" />
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384 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
0
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385 help="inverts the query/filtering applied by Samples File" />
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386 </xml>
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387 <token name="@SAMPLES@">
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388 #set $samples_defined = False
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389 #if str($section.samples) != '':
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390 #set $samples_defined = True
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391 --samples '${section.invert_samples}${section.samples}'
0
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392 #end if
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393 #if $section.samples_file:
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394 #set $samples_defined = True
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395 --samples-file "${section.invert_samples_file}${section.samples_file}"
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396 #end if
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397 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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398
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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399 <xml name="macro_sample">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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400 <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
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401 </xml>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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402 <token name="@SAMPLE@">
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403 #if $section.sample:
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404 --sample '${section.sample}'
0
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405 #end if
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406 </token>
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diff changeset
407
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
408
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409 <xml name="macro_include">
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410 <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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411 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
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412 <sanitizer sanitize="False"/>
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413 </param>
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414 </xml>
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415 <token name="@INCLUDE@">
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416 #if $section.include:
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417 --include '${section.include}'
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418 #end if
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419 </token>
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diff changeset
420
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421 <xml name="macro_exclude">
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422 <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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423 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
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424 <sanitizer sanitize="False"/>
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425 </param>
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426 </xml>
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427 <token name="@EXCLUDE@">
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428 #if $section.exclude:
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429 --exclude '${section.exclude}'
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430 #end if
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431 </token>
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432
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433 <xml name="macro_columns">
3
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434 <param name="columns" type="text" value="" label="Columns" optional="true"
0
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435 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
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436 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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437 </param>
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438 </xml>
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439 <token name="@COLUMNS@">
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440 #if $section.columns != '':
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441 --columns '${section.columns}'
0
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442 #end if
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443 </token>
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444
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445 <xml name="macro_haploid2diploid">
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446 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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447 </xml>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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448
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449 <xml name="macro_vcf_ids">
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450 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
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451 </xml>
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452 <token name="@VCF_IDS@">
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453 ${section.vcf_ids}
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diff changeset
454 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
455
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
456 <token name="@OUTPUT_HELP@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
457 <![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
458 Output Type
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
459 -----------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
460
3
35f66846632e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents: 2
diff changeset
461 Output compressed BCF (b), or uncompressed VCF (v).
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
462 Use the BCF option when piping between bcftools subcommands to speed up
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
463 performance by removing unecessary compression/decompression
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
464 and VCF<->BCF conversion.
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
465
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
466 This Galaxy tool recommends using the compressed BCF format
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
467 as piping is not implemented, and uncompressed data would
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
468 use unnecessary amounts of space.
4
c6071203aaa0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
469 ]]></token>
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
470 <token name="@REGIONS_HELP@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
471 <![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
472 Region Selections
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
473 -----------------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
474
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
475 Regions can be specified in a VCF,
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
476 BED, or tab-delimited file (the default). The columns of the
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
477 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
478 where positions are 1-based and inclusive. Uncompressed
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
479 files are stored in memory, while bgzip-compressed and
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
480 tabix-indexed region files are streamed. Note that sequence
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
481 names must match exactly, "chr20" is not the same as "20".
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
482 Also note that chromosome ordering in FILE will be
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
483 respected, the VCF will be processed in the order in which
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
484 chromosomes first appear in FILE. However, within
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
485 chromosomes, the VCF will always be processed in ascending
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
486 genomic coordinate order no matter what order they appear in
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
487 FILE. Note that overlapping regions in FILE can result in
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
488 duplicated out of order positions in the output. This option
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
489 requires indexed VCF/BCF files.
4
c6071203aaa0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
490 ]]></token>
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
491 <token name="@TARGETS_HELP@"><![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
492 Targets
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
493 -------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
494
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
495 Similar to regions, but the next position is accessed by streaming the whole
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
496 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
497 applied simultaneously: regions uses the index to jump to a region and targets discards
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
498 positions which are not in the targets. Unlike regions, targets can be prefixed with
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
499 "^" to request logical complement. For example, "^X,Y,MT" indicates that
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
500 sequences X, Y and MT should be skipped. Yet another difference between the two
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
501 is that regions checks both start and end positions of indels, whereas targets checks
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
502 start positions only.
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
503
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
504 For the bcftools call command, with the option -C alleles, third column of the
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
505 targets file must be comma-separated list of alleles, starting with the
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
506 reference allele. Note that the file must be compressed and index. Such a file
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
507 can be easily created from a VCF using::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
508
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
509 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
510 ]]>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
511 <!-- TODO: galaxy-ify -->
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
512 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
513
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
514
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
515 <token name="@COLLAPSE_HELP@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
516 Collapse
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
517 --------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
518
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
519 Controls how to treat records with duplicate positions and defines compatible
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
520 records across multiple input files. Here by "compatible" we mean records which
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
521 should be considered as identical by the tools. For example, when performing
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
522 line intersections, the desire may be to consider as identical all sites with
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
523 matching positions (bcftools isec -c all), or only sites with matching variant
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
524 type (bcftools isec -c snps -c indels), or only sites with all alleles
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
525 identical (bcftools isec -c none).
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
526
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
527
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
528 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
529 | Flag value | Result |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
530 +============+================================================================+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
531 | none | only records with identical REF and ALT alleles are compatible |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
532 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
533 | some | only records where some subset of ALT alleles match are |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
534 | | compatible |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
535 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
536 | all | all records are compatible, regardless of whether the ALT |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
537 | | alleles match or not. In the case of records with the same |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
538 | | position, only the first wil lbe considered and appear on |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
539 | | output. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
540 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
541 | snps | any SNP records are compatible, regardless of whether the ALT |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
542 | | alleles match or not. For duplicate positions, only the first |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
543 | | SNP record will be considered and appear on output. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
544 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
545 | indels | all indel records are compatible, regardless of whether the |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
546 | | REF and ALT alleles match or not. For duplicate positions, |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
547 | | only the first indel record will be considered and appear on |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
548 | | output. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
549 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
550 | both | abbreviation of "-c indels -c snps" |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
551 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
552 | id | only records with identical ID column are compatible. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
553 | | Supportedby bcftools merge only. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
554 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
555 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
556
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
557 <token name="@EXPRESSIONS_HELP@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
558 <![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
559 Expressions
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
560 -----------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
561
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
562 Valid expressions may contain:
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
563
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
564 - numerical constants, string constants
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
565
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
566 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
567
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
568 1, 1.0, 1e-4
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
569 "String"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
570
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
571 - arithmetic operators
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
572
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
573 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
574
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
575 +,*,-,/
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
576
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
577 - comparison operators
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
578
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
579 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
580
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
581 == (same as =), >, >=, <=, <, !=
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
582
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
583 - regex operators "~" and its negation "!~"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
584
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
585 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
586
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
587 INFO/HAYSTACK ~ "needle"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
588
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
589 - parentheses
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
590
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
591 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
592
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
593 (, )
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
594
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
595 - logical operators
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
596
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
597 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
598
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
599 && (same as &), ||, |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
600
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
601 - INFO tags, FORMAT tags, column names
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
602
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
603 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
604
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
605 INFO/DP or DP
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
606 FORMAT/DV, FMT/DV, or DV
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
607 FILTER, QUAL, ID, REF, ALT[0]
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
608
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
609 - 1 (or 0) to test the presence (or absence) of a flag
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
610
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
611 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
612
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
613 FlagA=1 && FlagB=0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
614
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
615 - "." to test missing values
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
616
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
617 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
618
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
619 DP=".", DP!=".", ALT="."
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
620
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
621 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
622
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
623 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
624
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
625 GT="."
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
626
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
627 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
628
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
629 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
630
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
631 TYPE="indel" | TYPE="snp"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
632
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
633 - array subscripts, "*" for any field
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
634
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
635 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
636
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
637 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
638 DP4[*] == 0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
639 CSQ[*] ~ "missense_variant.*deleterious"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
640
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
641 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
642
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
643 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
644
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
645 MAX, MIN, AVG, SUM, STRLEN, ABS
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
646
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
647 - variables calculated on the fly if not present: number of alternate alleles; number of samples; count of alternate alleles; minor allele count (similar to AC but is always smaller than 0.5); frequency of alternate alleles (AF=AC/AN); frequency of minor alleles (MAF=MAC/AN); number of alleles in called genotypes
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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648
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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649 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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650
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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651 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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652
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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653 **Notes:**
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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654
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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655 - String comparisons and regular expressions are case-insensitive
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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656 - If the subscript "*" is used in regular expression search, the whole field
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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657 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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658 true for the string vector INFO/STR=AB,CD.
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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659 - Variables and function names are case-insensitive, but not tag names. For
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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660 example, "qual" can be used instead of "QUAL", "strlen()" instead of
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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661 "STRLEN()" , but not "dp" instead of "DP".
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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662
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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663 **Examples:**
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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664
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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665 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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666
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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667 MIN(DV)>5
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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668 MIN(DV/DP)>0.3
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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669 MIN(DP)>10 & MIN(DV)>3
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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670 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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671 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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672 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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673 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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674 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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675 MIN(DP)>35 && AVG(GQ)>50
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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676 ID=@file .. selects lines with ID present in the file
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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677 ID!=@~/file .. skip lines with ID present in the ~/file
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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678 MAF[0]<0.05 .. select rare variants at 5% cutoff
4
c6071203aaa0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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679 ]]></token>
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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680 </macros>
Uuc}", Ed%2 y*e&Y$"nBE+QF~ܷ{~=O}}usyw'FcGn;_:'3 WG|08ۚm~ |M'~{$)@fIlŻf,x[^4Cpp* /ju9g+FW]?q@@y*ba740_f|B6Vl[93F18 C:}zFFo>qٟ/L9B?.|Dv/WL'(xCFh^n^OEneщ@%sި*3bq*O{_͊ $vukJ'EW"XH |Dvϟ{Ϣ5W (e xɉ%Mgczw!oȐ3=jqӌ蠃t@JFό|d/***y)2/5^X!zc9\'N}6ĚEgK;ZUyv ^[ŋa=rMJ%femde6dfnBc;O(s2  l[_ÛVW=I5H۠_wQlN0Ъׯ8?}hn`(Z ;y賧T 3?v1ÇcP@;0egN$\ɯ>R+8>< (DAǏQK(nP[^<3=|>pTDBR җ4]ڐEN.Νdޱ"9&/Cdr%J;>Q7od2%vd Abd_'_V*~l)DŅt֖>r􉒕]]( a/P TIJj6Z"Yz7H!P ѓh>'Oh ",|c`?f?3 \z`mq[Qܲ??-3=` =5eTTTs("Hו鉪IEEno䗔\~?77߈]Y ,u<;inauno݄SWm]v:gq k"*۠'FG26S|:m4}YP=e5.J#Gpp03AJCG" "SkjfVX^ӆ_9UJ|A/.;W1|9-[4: tDQϗ/,X~Z>ςb|NW+c벨ȼ n*{)dMmPuǎr!w֚Rӯ)kW ` 0! {ν|"Ǧ6:Z[;jE&yyxu׭ݶm[w#( k]5ۿx,5]e7-ng֫6Ϸ5J%kG;QVV|Ob=XyG޶!v2͘Ը~5da扝_svcj;;!R;\Pg͏mv@ccLO鉮bJSX օ6εf͚<._:Y}] m]]]]znD&CfCfFcؔD[`%'rԤQ}%B XM^R S<~xzFe-+aS~@L]hQWg[QZZzAzO<qQOc`l]C.{^;!x<$քE!uv/nDʞKP_ܹ߮W}K S'7'&%]y37<-uHzb60` I3 F+.ڧg\.TfFz9]nhwf!gr U21Pb%F˶26;8M2AS/Nw+ARk EzG/F^zBɹUZ(mٖ1gėh+"w8p@?8ڪ< wT/toaܾK5rI`{Ps,: ݹ9ֶld2$D?Jw\XϸEdvIs&իW;z{(~c߻jعdggbJ332(gmh!ErO v XYY1؇5]Z>{_2fcmW-By [si+ݏh~"@bN9SR(u;%1*0 ʋ!qƄr%EY` 93 rщѭ:f2>wk(v)Tw0tzm'h h~'4Z;fҟ,mAcyOs&#u bȤWV$⸘QiiaZy??BҨ{Fes8G{u@ut(OJcz) U !zsj//{JH$g 9l9*QdGyzgr F&9r2suy`ĵ87tϞcWԥEowa~H9PQYvS6Iƕ4:٘P/)baƅ:bjח ȩbx!GH>U ns&_gKڜ[j! Pe6A/w;csGXd[%F>"(29*:9^1HVp42ATXXgm= DbddOI& #+a7XAtc*>`z# XYh?5J~g+ϋv V̖?~T|jƃؽcWaz.^njއB]#Yx":BoIfMiKJ%q,θD;䂮T0\|uNsl~:i_ĽN'Ӊ>EnVhC-QC_51:f舎5;|?y`} DGz;,~Gu#^9;ͳ3?t ~ф 7o?)t hؔxŮ<=r ~"ӡC!"s/OE st 5)ڰU4CKSkfxc 꺻v smR.x*dhtq4(t \ըR/,$3U!zx Ik NrY@l>}42kXJM9ao-g(82? g,V [þ; &K(*" 5otW- 5ܿ~<404mT8sݛI6 en&'!tS{bF$eHS[[N`RB萨Cɮ~oILݎ~ +++|v}|m]-sl:ae0(}#C#ū\xHQQ0*!pA\@\lfO$<}=Dn1MMadnnP4&Vв-//*D6mg+#4ey*6k[Ci&GJ?';zX(dgt a`_v۷A:J1*7 Xҏ 74AAݻwuy>K. ȈfF;A؟Xn7[+]icc[wׯLk $AqypA4&pg cA@n=N'PEeP=t(DX Ԡ:g"7ZrNI-$;58 |]S#4Q.AS~h*{&d9`ɱM_/%Tާ6Nx%]2Wv1'kEjq|敶4h { mǝO~f.ۚ~p'@U>qA$:z}Q ^ #%ٔ}"+.!GQ<҈݆|q͏ԆdlYvd|sZeZL \.Z;9>A>sxxx۷>0=t'Aۙu_~1Fy W +||_fm!_Ks ٔەzW+X "g gdd4mz']St"QF# ]2dWu8я[%8l٩$$2$m32pEh:.!nKWHBtfM0 tVe%p@_?g6ax(瘆]/$лo=h;!~CETi]UEtJi# ޅp{.bK@HU"58/}:鯍)+lY WuZ^ }} - tdgOlF~Yy )6][;Q2r M] !_EU_uTWGµ;?0Y!uqG*y D!֌FX#:D3*YɉB@`QfhiZ02HtpZ`W]>dJU :fJu! Riس?Pz]˘-0]a9OA}Juu` j)]7Z%&&v]ܳw8*''bQ33g[|Nơ2k~oġ UzgN?(9peʺ+GrC;||8|>8<0{hl4= 9_7]k4˜zd4;X`&e/,AH.~Rܨ`/55q[Wmkbf$~x8448-i/ܾ?l]>t'I҅GƠZ$ؖg T )hrH*INZXk)lb͢61EFFh&18g$#|裺âo499OssY\X67ݖϱZUƖ/\C$/*6|2 8)򪼌JjonK|2Zl1҇$JJ㲂QQbwYҨ2I@Γopr G^J|NgQ>k/#м{"G_7~SZw |SjQ{:oyOuFk/|u |?3VW;x4JGo{5RƷ]1L7UG]3)nbRR(r4"]~lܜؙ,CbBDs \ scE!`Mٽ\>cdMF'$C4o&?yḏ7o`L:OHKHL<,raY)]\Suǜ|7nD}GPP*x̨3T5%M>gU_b+TS.7oQJF!r o7ץeC] 4E&zcV e1 b'W p_*Lۿ6 4tu 4[[\31yo }0gOyuG;ZڢA?;SrFT4֞'284OHVh45pVZ6%%-͌Sؐ4+j̒ :əᆔWhsSxqZnw#N*` %]EFGFސkM%;fBs i僻6]g|[l58WXځɶj kl 7yt5$vPG{æ'|ƲǛ7oAa2lD͛rm 49VSJRXB&cQ̒WGMj1ӑB g0Rgهcžd1!p'dM1JuX uf=_iaGG {'3;޽KH(Q#"(&#Q(lI]U = 9:K;T޿?BO2=7|/ ɜ(yYC]-D!j6ĉcGܚDi?Gd.'9 ²։ H$, uqa%δ=Ѧ͞%'jo=/ V ᥛ7$ضy+#mUN-y֌<'j^7Ҹ';IeQ|hDdΙ3TL7RrHyw?,NjfbbB 52 )8BjJj=G]]A _K\lɓ'8?0@VdZB{&,yl V>{DXCeoW*7^W^8y%eأvIJr}3X}gՀ+%71$B]x877&hN-Si[# ,V@'KGƾiͱDgs15i\@MePͅ^ 3̬'KےO m@-:R͐>bnCixND"5/vbt1;@uw &Ph.G*[䃲WfÝؐ͜nq[ؕ0D4]c.w7v=&k 6V.pڕSPZ]:0P X\|У#;^ xA `&4mr&~"5>"o0_u&7-P@,b<Ec-/R{3W r1_{w Kk>(R}N_|.9