Mercurial > repos > iuc > bcftools_view

annotate macros.xml @ 7:d1f8f55f564d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:07:33 -0500
parents 3a233c8eb814
children ed94a3dccad0
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1 <macros>
7
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2 <token name="@TOOL_VERSION@">1.9</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="@TOOL_VERSION@">bcftools</requirement>
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14 <requirement type="package" version="1.9">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="1.9">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" 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 #if $input_file.metadata.tabix_index:
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54 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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55 #else
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56 bcftools index $input_vcf &&
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57 #end if
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58 #elif $input_file.is_of_type('bcf')
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59 #set $input_vcf = 'input.bcf'
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60 ln -s '$input_file' $input_vcf &&
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61 #if $input_file.metadata.bcf_index:
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62 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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63 #else
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64 bcftools index $input_vcf &&
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65 #end if
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66 #end if
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67 ]]>
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68 </token>
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69 <token name="@INPUT_FILE@">
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70 $input_vcf
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71 </token>
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73 <xml name="macro_inputs">
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74 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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75 </xml>
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76 <token name="@PREPARE_INPUT_FILES@">
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77 <![CDATA[
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78 ## May need to symlink input if there is an associated
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79 #set $input_vcfs = []
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80 #set $vcfs_list_file = 'vcfs_list'
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81 #for (i, input_file) in enumerate($input_files):
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82 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
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83 #if $input_file.is_of_type('vcf')
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84 bgzip -c '$input_file' > $input_vcf &&
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85 bcftools index $input_vcf &&
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86 #elif $input_file.is_of_type('vcf_bgzip')
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87 ln -s '$input_file' $input_vcf &&
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88 #if $input_file.metadata.tabix_index:
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89 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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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('bcf')
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94 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
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95 ln -s '$input_file' $input_vcf &&
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96 #if $input_file.metadata.bcf_index:
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97 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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98 #else
0
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99 bcftools index $input_vcf &&
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100 #end if
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101 #end if
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102 echo '$input_vcf' >> $vcfs_list_file &&
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103 $input_vcfs.append($input_vcf)
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104 #end for
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105 ]]>
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106 </token>
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107 <token name="@INPUT_FILES@">
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108 #echo ' '.join($input_vcfs)#
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109 </token>
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110 <token name="@INPUT_LIST_FILE@">
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111 $vcfs_list_file
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112 </token>
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113
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114 <xml name="macro_fasta_ref">
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115 <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />
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116 </xml>
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117 <token name="@PREPARE_FASTA_REF@">
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118 <![CDATA[
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119 #set $input_fa_ref = None
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120 #if 'fasta_ref' in $section and $section.fasta_ref:
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121 #set $input_fa_ref = 'ref.fa'
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122 ln -s '$section.fasta_ref' $input_fa_ref &&
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123 samtools faidx $input_fa_ref &&
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124 #end if
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125 ]]>
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126 </token>
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127 <token name="@FASTA_REF@">
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128 #if $input_fa_ref is not None:
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129 --fasta-ref $input_fa_ref
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130 #elif 'fasta_ref' in $section and $section.fasta_ref:
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131 --fasta-ref '${section.fasta_ref}'
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132 #end if
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133 </token>
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134
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135 <xml name="macro_ref_fasta">
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136 <conditional name="reference_source">
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137 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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138 <option value="cached">Locally cached</option>
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139 <option value="history">History</option>
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140 </param>
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141 <when value="cached">
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142 <param name="ref_file" type="select" label="Select reference genome">
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143 <options from_data_table="fasta_indexes">
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144 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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145 </options>
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146 <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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147 </param>
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148 </when>
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149 <when value="history"> <!-- FIX ME!!!! -->
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150 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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151 </when>
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152 </conditional>
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153 </xml>
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154
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155
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156 <xml name="macro_AF_file">
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157 <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
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158 </xml>
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159 <!-- This may need to bgzip and tabix the file -->
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160 <token name="@PREPARE_AF_FILE@">
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161 <![CDATA[
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162 #if 'AF_file' in $section and $section.AF_file:
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163 #pass
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164 #end if
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165 ]]>
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166 </token>
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167 <token name="@AF_FILE@">
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168 #if 'AF_file' in $section and $section.AF_file:
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169 --AF-file '${section.AF_file}'
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170 #end if
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171 </token>
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172
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173 <xml name="macro_estimate_AF">
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174 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" 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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175 </xml>
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176 <token name="@ESTIMATE_AF@">
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177 #if 'estimate_AF' in $section and $section.estimate_AF:
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178 --estimate-AF "${section.estimate_AF}"
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179 #end if
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180 </token>
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181
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182 <xml name="macro_exons_file">
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183 <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
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184 </xml>
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185 <token name="@PREPARE_EXONS_FILE@">
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186 <![CDATA[
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187 #set $exons_path = None
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188 #if 'exons_file' in $section and $section.exons_file:
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189 #set $exons_path = 'exons_file.tab.gz'
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190 bgzip -c "$section.exons_file" > $exons_path &&
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191 tabix -s 1 -b 2 -e 3 $exons_path &&
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192 #end if
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193 ]]>
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194 </token>
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195 <token name="@EXONS_FILE@">
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196 #if 'exons_file' in $section and $section.exons_file:
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197 --exons $exons_path
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198 #end if
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199 </token>
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200
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201 <xml name="macro_ploidy_file">
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202 <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
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203 </xml>
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204 <token name="@PLOIDY_FILE@">
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205 #if 'ploidy_file' in $section and $section.ploidy_file:
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206 --ploidy "${section.ploidy_file}"
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207 #end if
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208 </token>
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209
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210 <xml name="macro_collapse_opt_none">
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211 <option value="none">none - require the exact same set of alleles in all files</option>
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212 </xml>
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213 <xml name="macro_collapse_opt_id">
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214 <option value="id">id - only records with identical ID column are compatible. </option>
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215 </xml>
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216 <xml name="macro_collapse">
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217 <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
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218 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
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219 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
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220 <option value="both">both - indels and snps </option>
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221 <option value="some">some - at least some of the ALTs must match</option>
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222 <option value="any">any - any combination of alleles</option>
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223 <yield/>
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224 </param>
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225 </xml>
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226 <token name="@COLLAPSE@">
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227 #if $section.collapse:
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228 --collapse ${section.collapse}
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229 #end if
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230 </token>
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231
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232 <xml name="macro_apply_filters">
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233 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
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234 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
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235 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
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236 </param>
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237 </xml>
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238 <token name="@APPLY_FILTERS@">
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239 #if $section.apply_filters:
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240 --apply-filters '${section.apply_filters}'
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241 #end if
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242 </token>
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243
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244 <xml name="macro_select_output_type">
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245 <param name="output_type" type="select">
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246 <option value="b">compressed BCF</option>
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247 <!-- no galaxy datatypes for these
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248 <option value="u">uncompressed BCF</option>
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249 <option value="z">compressed VCF</option>
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250 -->
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251 <option value="v">uncompressed VCF</option>
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252 </param>
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253 </xml>
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254 <token name="@OUTPUT_TYPE@">
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255 #if str($output_type) != "__none__":
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256 --output-type '${output_type}'
0
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257 #end if
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258 </token>
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259
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260 <xml name="macro_vcf_output">
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261 <data name="output_file" format="vcf">
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262 <change_format>
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263 <when input="output_type" value="b" format="bcf" />
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264 <when input="output_type" value="u" format="bcf" />
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265 <when input="output_type" value="z" format="vcf_bgzip" />
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266 <when input="output_type" value="v" format="vcf" />
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267 </change_format>
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268 </data>
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269 </xml>
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270
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271 <xml name="macro_regions">
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272 <conditional name="regions">
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273 <param name="regions_src" type="select" label="Regions">
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274 <option value="__none__">None</option>
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275 <option value="regions">regions</option>
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276 <option value="regions_file">regions-file</option>
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277 </param>
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278 <when value="__none__"/>
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279 <when value="regions">
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280 <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions"
0
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281 help="Each region is specifed as: chr or chr:pos or chr:from-to">
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282 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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283 </param>
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284 </when>
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285 <when value="regions_file">
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286 <param name="regions_file" type="data" format="vcf,bed,tabular" optional="true" label="Regions file" help="Restrict to regions listed in a file" />
0
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287 </when>
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288 </conditional>
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289 </xml>
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290 <token name="@PREPARE_REGIONS_FILE@">
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291 <![CDATA[
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292 #set $regions_path = None
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293 #if 'regions' in $section
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294 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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295 #if $section.regions.regions_file.ext.startswith('bed'):
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296 #set $regions_path = 'regions_file.bed'
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297 ln -s '$section.regions.regions_file' $regions_path &&
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298 #end if
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299 #end if
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300 #end if
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301 ]]>
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302 </token>
0
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303 <token name="@REGIONS@">
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304 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
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305 --regions '$section.regions.regions'
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306 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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307 #if $regions_path is not None:
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308 --regions-file '$regions_path'
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309 #else:
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310 --regions-file '$section.regions.regions_file'
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311 #end if
0
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312 #end if
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313 </token>
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314 <xml name="macro_targets_file">
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315 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
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316 <yield/>
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317 </param>
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318 <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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319 </xml>
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320 <token name="@PREPARE_TARGETS_FILE@">
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321 <![CDATA[
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322 #set $targets_path = None
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323 #if 'targets' in $section
0
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324 #if $section.targets.targets_src == 'targets_file':
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325 #set $targets_path = 'targets_file.tab.gz'
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326 bgzip -c "$section.targets.targets_file" > $targets_path &&
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327 tabix -s 1 -b 2 -e 2 $targets_path &&
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328 #end if
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329 #elif $tgts_sec.targets_file:
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330 #set $targets_path = 'targets_file.tab.gz'
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331 bgzip -c "$section.targets_file" > $targets_path &&
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332 tabix -s 1 -b 2 -e 2 $targets_path &&
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333 #end if
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334 ]]>
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335 </token>
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336 <token name="@TARGETS_FILE@">
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337 <![CDATA[
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338 #if $targets_path is not None:
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339 --targets-file "${section.invert_targets_file}${targets_path}"
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340 #elif $section.targets_file:
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341 --targets-file "${section.invert_targets_file}${section.targets_file}"
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342 #end if
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343 ]]>
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344 </token>
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345
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346 <xml name="macro_targets">
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347 <conditional name="targets">
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348 <param name="targets_src" type="select" label="Targets">
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349 <option value="__none__">None</option>
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350 <option value="targets">targets</option>
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351 <option value="targets_file">targets-file</option>
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352 </param>
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353 <when value="__none__"/>
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354 <when value="targets">
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355 <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"
0
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356 help="Each target is specifed as: chr or chr:pos or chr:from-to">
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357 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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358 </param>
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359 <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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360 </when>
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361 <when value="targets_file">
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362 <expand macro="macro_targets_file">
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363 </expand>
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364 </when>
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365 </conditional>
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366 </xml>
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367 <token name="@TARGETS@">
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368 <![CDATA[
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369 #if $targets_path:
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370 --targets-file "${section.targets.invert_targets_file}${targets_path}"
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371 #else:
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372 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
4
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373 --targets '${section.targets.invert_targets_file}${section.targets.targets}'
0
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374 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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375 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
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376 #end if
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377 #end if
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378 ]]>
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379 </token>
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380
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381 <xml name="macro_samples">
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382 <param argument="--samples" type="text" value="" optional="true" label="Samples"
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383 help="Comma separated list of samples to annotate (or exclude)">
0
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384 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
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385 </param>
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386 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
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387 help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
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388 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
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389 help="File of samples to include" />
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390 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
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391 help="inverts the query/filtering applied by Samples file" />
0
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392 </xml>
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393 <token name="@SAMPLES@">
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394 #set $samples_defined = False
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395 #if str($section.samples) != '':
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396 #set $samples_defined = True
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397 --samples '${section.invert_samples}${section.samples}'
0
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398 #end if
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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399 #if $section.samples_file:
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400 #set $samples_defined = True
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401 --samples-file "${section.invert_samples_file}${section.samples_file}"
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402 #end if
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403 </token>
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404
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405 <xml name="macro_sample">
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406 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
0
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407 </xml>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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408 <token name="@SAMPLE@">
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409 #if $section.sample:
4
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410 --sample '${section.sample}'
0
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411 #end if
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412 </token>
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413
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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414
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415 <xml name="macro_include">
7
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diff changeset
416 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
0
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417 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
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418 <sanitizer sanitize="False"/>
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419 </param>
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420 </xml>
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421 <token name="@INCLUDE@">
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422 #if $section.include:
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423 --include '${section.include}'
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424 #end if
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diff changeset
425 </token>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
426
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427 <xml name="macro_exclude">
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428 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
0
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429 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
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430 <sanitizer sanitize="False"/>
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431 </param>
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432 </xml>
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433 <token name="@EXCLUDE@">
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434 #if $section.exclude:
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435 --exclude '${section.exclude}'
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436 #end if
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437 </token>
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parents:
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438
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439 <xml name="macro_columns">
7
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440 <param name="columns" type="text" value="" optional="true" label="Columns"
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diff changeset
441 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
0
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442 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
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diff changeset
443 </param>
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diff changeset
444 </xml>
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parents:
diff changeset
445 <token name="@COLUMNS@">
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446 #if $section.columns != '':
4
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parents: 3
diff changeset
447 --columns '${section.columns}'
0
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diff changeset
448 #end if
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
449 </token>
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parents:
diff changeset
450
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parents:
diff changeset
451 <xml name="macro_haploid2diploid">
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452 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
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diff changeset
453 </xml>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
454
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
455 <xml name="macro_vcf_ids">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
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456 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
457 </xml>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
458 <token name="@VCF_IDS@">
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diff changeset
459 ${section.vcf_ids}
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parents:
diff changeset
460 </token>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
461
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
462 <token name="@OUTPUT_HELP@">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
463 <![CDATA[
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
464 Output Type
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
465 -----------
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
466
3
cde34352778e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents: 2
diff changeset
467 Output compressed BCF (b), or uncompressed VCF (v).
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
468 Use the BCF option when piping between bcftools subcommands to speed up
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
469 performance by removing unecessary compression/decompression
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
470 and VCF<->BCF conversion.
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
471
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
472 This Galaxy tool recommends using the compressed BCF format
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
473 as piping is not implemented, and uncompressed data would
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
474 use unnecessary amounts of space.
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
475 ]]></token>
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
476 <token name="@REGIONS_HELP@">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
477 <![CDATA[
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
478 Region Selections
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
479 -----------------
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
480
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
481 Regions can be specified in a VCF,
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
482 BED, or tab-delimited file (the default). The columns of the
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
483 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
484 where positions are 1-based and inclusive. Uncompressed
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
485 files are stored in memory, while bgzip-compressed and
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
486 tabix-indexed region files are streamed. Note that sequence
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
487 names must match exactly, "chr20" is not the same as "20".
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
488 Also note that chromosome ordering in FILE will be
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
489 respected, the VCF will be processed in the order in which
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
490 chromosomes first appear in FILE. However, within
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
491 chromosomes, the VCF will always be processed in ascending
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
492 genomic coordinate order no matter what order they appear in
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
493 FILE. Note that overlapping regions in FILE can result in
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
494 duplicated out of order positions in the output. This option
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
495 requires indexed VCF/BCF files.
4
993ed534cc38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
496 ]]></token>
0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
497 <token name="@TARGETS_HELP@"><![CDATA[
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
498 Targets
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
499 -------
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
500
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
501 Similar to regions, but the next position is accessed by streaming the whole
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
502 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
503 applied simultaneously: regions uses the index to jump to a region and targets discards
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
504 positions which are not in the targets. Unlike regions, targets can be prefixed with
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
505 "^" to request logical complement. For example, "^X,Y,MT" indicates that
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
506 sequences X, Y and MT should be skipped. Yet another difference between the two
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
507 is that regions checks both start and end positions of indels, whereas targets checks
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
508 start positions only.
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
509
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
510 For the bcftools call command, with the option -C alleles, third column of the
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
511 targets file must be comma-separated list of alleles, starting with the
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
512 reference allele. Note that the file must be compressed and index. Such a file
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
513 can be easily created from a VCF using::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
514
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
515 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
516 ]]>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
517 <!-- TODO: galaxy-ify -->
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
518 </token>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
519
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
520
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
521 <token name="@COLLAPSE_HELP@">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
522 Collapse
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
523 --------
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
524
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
525 Controls how to treat records with duplicate positions and defines compatible
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
526 records across multiple input files. Here by "compatible" we mean records which
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
527 should be considered as identical by the tools. For example, when performing
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
528 line intersections, the desire may be to consider as identical all sites with
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
529 matching positions (bcftools isec -c all), or only sites with matching variant
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
530 type (bcftools isec -c snps -c indels), or only sites with all alleles
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
531 identical (bcftools isec -c none).
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
532
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
533
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
534 +------------+----------------------------------------------------------------+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
535 | Flag value | Result |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
536 +============+================================================================+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
537 | none | only records with identical REF and ALT alleles are compatible |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
538 +------------+----------------------------------------------------------------+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
539 | some | only records where some subset of ALT alleles match are |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
540 | | compatible |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
541 +------------+----------------------------------------------------------------+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
542 | all | all records are compatible, regardless of whether the ALT |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
543 | | alleles match or not. In the case of records with the same |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
544 | | position, only the first wil lbe considered and appear on |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
545 | | output. |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
546 +------------+----------------------------------------------------------------+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
547 | snps | any SNP records are compatible, regardless of whether the ALT |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
548 | | alleles match or not. For duplicate positions, only the first |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
549 | | SNP record will be considered and appear on output. |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
550 +------------+----------------------------------------------------------------+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
551 | indels | all indel records are compatible, regardless of whether the |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
552 | | REF and ALT alleles match or not. For duplicate positions, |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
553 | | only the first indel record will be considered and appear on |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
554 | | output. |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
555 +------------+----------------------------------------------------------------+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
556 | both | abbreviation of "-c indels -c snps" |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
557 +------------+----------------------------------------------------------------+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
558 | id | only records with identical ID column are compatible. |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
559 | | Supportedby bcftools merge only. |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
560 +------------+----------------------------------------------------------------+
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
561 </token>
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
562
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
563 <token name="@EXPRESSIONS_HELP@">
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
564 <![CDATA[
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
565 Expressions
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
566 -----------
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
567
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
568 Valid expressions may contain:
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
569
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
570 - numerical constants, string constants
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
571
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
572 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
573
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
574 1, 1.0, 1e-4
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
575 "String"
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
576
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
577 - arithmetic operators
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
578
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
579 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
580
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
581 +,*,-,/
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
582
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
583 - comparison operators
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
584
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
585 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
586
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
587 == (same as =), >, >=, <=, <, !=
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
588
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
589 - regex operators "~" and its negation "!~"
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
590
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
591 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
592
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
593 INFO/HAYSTACK ~ "needle"
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
594
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
595 - parentheses
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
596
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
597 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
598
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
599 (, )
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
600
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
601 - logical operators
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
602
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
603 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
604
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
605 && (same as &), ||, |
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
606
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
607 - INFO tags, FORMAT tags, column names
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
608
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
609 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
610
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
611 INFO/DP or DP
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
612 FORMAT/DV, FMT/DV, or DV
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
613 FILTER, QUAL, ID, REF, ALT[0]
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
614
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
615 - 1 (or 0) to test the presence (or absence) of a flag
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
616
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
617 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
618
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
619 FlagA=1 && FlagB=0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
620
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
621 - "." to test missing values
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
622
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
623 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
624
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
625 DP=".", DP!=".", ALT="."
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
626
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
627 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
628
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
629 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
630
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
631 GT="."
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
632
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
633 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
634
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
635 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
636
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
637 TYPE="indel" | TYPE="snp"
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
638
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
639 - array subscripts, "*" for any field
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
640
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
641 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
642
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
643 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
644 DP4[*] == 0
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
645 CSQ[*] ~ "missense_variant.*deleterious"
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
646
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
647 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
648
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
649 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
650
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
651 MAX, MIN, AVG, SUM, STRLEN, ABS
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
652
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
653 - 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
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
654
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
655 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
656
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
657 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
658
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
659 **Notes:**
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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660
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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661 - String comparisons and regular expressions are case-insensitive
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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662 - If the subscript "*" is used in regular expression search, the whole field
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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663 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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664 true for the string vector INFO/STR=AB,CD.
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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665 - Variables and function names are case-insensitive, but not tag names. For
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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666 example, "qual" can be used instead of "QUAL", "strlen()" instead of
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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667 "STRLEN()" , but not "dp" instead of "DP".
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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668
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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669 **Examples:**
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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670
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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671 ::
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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672
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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673 MIN(DV)>5
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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674 MIN(DV/DP)>0.3
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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675 MIN(DP)>10 & MIN(DV)>3
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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676 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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677 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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678 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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679 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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680 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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681 MIN(DP)>35 && AVG(GQ)>50
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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682 ID=@file .. selects lines with ID present in the file
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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683 ID!=@~/file .. skip lines with ID present in the ~/file
94f98eb08abc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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684 MAF[0]<0.05 .. select rare variants at 5% cutoff
4
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685 ]]></token>
0
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686 </macros>