Mercurial > repos > iuc > bcftools_plugin_fixploidy

annotate macros.xml @ 4:b7dc6f8084ce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
author iuc
date Sat, 11 Mar 2017 18:01:42 -0500
parents f6a06fcdebdc
children aec8cc772e0c
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1 <macros>
4
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2 <token name="@VERSION@">1.3.1</token>
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3 <xml name="stdio">
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4 <stdio>
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5 <exit_code range="1:" />
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6 <exit_code range=":-1" />
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7 <regex match="Error:" />
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8 <regex match="Exception:" />
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9 </stdio>
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10 </xml>
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="1.3.1">bcftools</requirement>
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14 <!-- conda dependency -->
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15 <requirement type="package" version="1.3.2">htslib</requirement>
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16 <yield />
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17 </requirements>
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18 </xml>
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19 <xml name="version_command">
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20 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
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21 </xml>
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22
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23 <xml name="citations">
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24 <citations>
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25 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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26 <yield />
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27 </citations>
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28 </xml>
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29 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
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30 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
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31 <token name="@THREADS@">
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32 --threads \${GALAXY_SLOTS:-4}
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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33 </token>
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34 <token name="@PREPARE_ENV@">
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35 <![CDATA[
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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36 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
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37 ]]>
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38 </token>
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39 <xml name="macro_input">
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41 </xml>
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42 <token name="@PREPARE_INPUT_FILE@">
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43 <![CDATA[
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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44 ## May need to symlink input if there is an associated
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45 #set $input_vcf = 'input.vcf.gz'
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46 #if $input_file.is_of_type('vcf')
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47 bgzip -c '$input_file' > $input_vcf &&
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48 bcftools index $input_vcf &&
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49 #elif $input_file.is_of_type('vcf_bgzip')
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50 ln -s '$input_file' $input_vcf
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51 #elif $input_file.is_of_type('bcf')
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52 #set $input_vcf = 'input.bcf'
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53 ln -s '$input_file' $input_vcf &&
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54 #if $input_file.metadata.bcf_index:
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55 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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56 #else
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57 bcftools index $input_vcf &&
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58 #end if
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59 #elif $input_file.is_of_type('bcf_bgzip')
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60 ln -s '$input_file' $input_vcf
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61 #end if
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62 ]]>
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63 </token>
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64 <token name="@INPUT_FILE@">
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65 $input_vcf
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66 </token>
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67
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68 <xml name="macro_inputs">
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69 <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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70 </xml>
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71 <token name="@PREPARE_INPUT_FILES@">
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72 <![CDATA[
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73 ## May need to symlink input if there is an associated
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74 #set $input_vcfs = []
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75 #set $vcfs_list_file = 'vcfs_list'
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76 #for (i, input_file) in enumerate($input_files):
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77 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
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78 #if $input_file.is_of_type('vcf')
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79 bgzip -c '$input_file' > $input_vcf &&
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80 bcftools index $input_vcf &&
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81 #elif $input_file.is_of_type('vcf_bgz')
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82 ln -s '$input_file' $input_vcf
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83 #elif $input_file.is_of_type('bcf')
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84 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
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85 ln -s '$input_file' $input_vcf &&
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86 #if $input_file.metadata.bcf_index:
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87 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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88 #else
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89 bcftools index $input_vcf &&
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90 #end if
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91 #elif $input_file.is_of_type('bcfvcf_bgz')
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92 ln -s '$input_file' $input_vcf &&
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93 #end if
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94 echo '$input_vcf' >> $vcfs_list_file &&
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95 $input_vcfs.append($input_vcf)
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96 #end for
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97 ]]>
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98 </token>
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99 <token name="@INPUT_FILES@">
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100 #echo ' '.join($input_vcfs)#
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101 </token>
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102 <token name="@INPUT_LIST_FILE@">
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103 $vcfs_list_file
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104 </token>
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105
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106 <xml name="macro_fasta_ref">
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107 <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />
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108 </xml>
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109 <token name="@PREPARE_FASTA_REF@">
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110 <![CDATA[
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111 #set $input_fa_ref = None
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112 #if 'fasta_ref' in $section and $section.fasta_ref:
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113 #set $input_fa_ref = 'ref.fa'
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114 ln -s '$section.fasta_ref' $input_fa_ref &&
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115 samtools faidx $input_fa_ref &&
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116 #end if
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117 ]]>
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118 </token>
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119 <token name="@FASTA_REF@">
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120 #if $input_fa_ref is not None:
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121 --fasta-ref $input_fa_ref
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122 #elif 'fasta_ref' in $section and $section.fasta_ref:
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123 --fasta-ref '${section.fasta_ref}'
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124 #end if
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125 </token>
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126
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127 <xml name="macro_ref_fasta">
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128 <conditional name="reference_source">
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129 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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130 <option value="cached">Locally cached</option>
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131 <option value="history">History</option>
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132 </param>
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133 <when value="cached">
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134 <param name="ref_file" type="select" label="Select reference genome">
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135 <options from_data_table="fasta_indexes">
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136 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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137 </options>
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138 <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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139 </param>
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140 </when>
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141 <when value="history"> <!-- FIX ME!!!! -->
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142 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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143 </when>
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144 </conditional>
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145 </xml>
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146
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147
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148 <xml name="macro_AF_file">
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149 <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
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150 </xml>
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151 <!-- This may need to bgzip and tabix the file -->
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152 <token name="@PREPARE_AF_FILE@">
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153 <![CDATA[
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154 #if 'AF_file' in $section and $section.AF_file:
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155 #pass
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156 #end if
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157 ]]>
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158 </token>
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159 <token name="@AF_FILE@">
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160 #if 'AF_file' in $section and $section.AF_file:
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161 --AF-file '${section.AF_file}'
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162 #end if
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163 </token>
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164
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165 <xml name="macro_estimate_AF">
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166 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
0
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167 </xml>
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168 <token name="@ESTIMATE_AF@">
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169 #if 'estimate_AF' in $section and $section.estimate_AF:
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170 --estimate-AF "${section.estimate_AF}"
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171 #end if
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172 </token>
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173
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174 <xml name="macro_exons_file">
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175 <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
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176 </xml>
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177 <token name="@PREPARE_EXONS_FILE@">
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178 <![CDATA[
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179 #set $exons_path = None
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180 #if 'exons_file' in $section and $section.exons_file:
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181 #set $exons_path = 'exons_file.tab.gz'
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182 bgzip -c "$section.exons_file" > $exons_path &&
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183 tabix -s 1 -b 2 -e 3 $exons_path &&
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184 #end if
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185 ]]>
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186 </token>
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187 <token name="@EXONS_FILE@">
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188 #if 'exons_file' in $section and $section.exons_file:
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189 --exons $exons_path
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190 #end if
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191 </token>
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192
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193 <xml name="macro_ploidy_file">
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194 <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
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195 </xml>
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196 <token name="@PLOIDY_FILE@">
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197 #if 'ploidy_file' in $section and $section.ploidy_file:
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198 --ploidy "${section.ploidy_file}"
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199 #end if
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200 </token>
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201
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202 <xml name="macro_collapse_opt_none">
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203 <option value="none">none - require the exact same set of alleles in all files</option>
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204 </xml>
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205 <xml name="macro_collapse_opt_id">
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206 <option value="id">id - only records with identical ID column are compatible. </option>
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207 </xml>
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208 <xml name="macro_collapse">
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209 <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
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210 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
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211 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
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212 <option value="both">both - indels and snps </option>
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213 <option value="some">some - at least some of the ALTs must match</option>
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214 <option value="any">any - any combination of alleles</option>
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215 <yield/>
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216 </param>
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217 </xml>
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218 <token name="@COLLAPSE@">
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219 #if $section.collapse:
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220 --collapse ${section.collapse}
0
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221 #end if
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222 </token>
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223
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224 <xml name="macro_apply_filters">
3
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225 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
0
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226 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
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227 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
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228 </param>
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229 </xml>
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230 <token name="@APPLY_FILTERS@">
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231 #if $section.apply_filters:
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232 --apply-filters '${section.apply_filters}'
0
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233 #end if
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234 </token>
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235
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236 <xml name="macro_select_output_type">
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237 <param name="output_type" type="select">
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238 <option value="b">compressed BCF</option>
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239 <!-- no galaxy datatypes for these
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240 <option value="u">uncompressed BCF</option>
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241 <option value="z">compressed VCF</option>
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242 -->
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243 <option value="v">uncompressed VCF</option>
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244 </param>
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245 </xml>
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246 <token name="@OUTPUT_TYPE@">
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247 #if str($output_type) != "__none__":
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248 --output-type "${output_type}"
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249 #end if
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250 </token>
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251
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252 <xml name="macro_vcf_output">
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253 <data name="output_file" format="vcf">
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254 <change_format>
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255 <when input="output_type" value="b" format="bcf" />
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256 <when input="output_type" value="u" format="bcf" />
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257 <when input="output_type" value="z" format="vcf_bgzip" />
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258 <when input="output_type" value="v" format="vcf" />
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259 </change_format>
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260 </data>
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261 </xml>
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262
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263 <xml name="macro_regions">
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264 <conditional name="regions">
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265 <param name="regions_src" type="select" label="Regions">
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266 <option value="__none__">None</option>
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267 <option value="regions">regions</option>
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268 <option value="regions_file">regions-file</option>
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269 </param>
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270 <when value="__none__"/>
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271 <when value="regions">
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272 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
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273 help="Each region is specifed as: chr or chr:pos or chr:from-to">
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274 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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275 </param>
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276 </when>
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277 <when value="regions_file">
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278 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
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279 </when>
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280 </conditional>
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281 </xml>
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282 <token name="@REGIONS@">
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283 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
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284 --regions '$section.regions.regions'
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285 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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286 --regions-file '$section.regions.regions_file'
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287 #end if
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288 </token>
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289
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290 <xml name="macro_targets_file">
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291 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
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292 <yield/>
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293 </param>
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294 <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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295 </xml>
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296 <token name="@PREPARE_TARGETS_FILE@">
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297 <![CDATA[
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298 #set $targets_path = None
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299 #if 'targets' in $section
0
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300 #if $section.targets.targets_src == 'targets_file':
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301 #set $targets_path = 'targets_file.tab.gz'
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302 bgzip -c "$section.targets.targets_file" > $targets_path &&
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303 tabix -s 1 -b 2 -e 2 $targets_path &&
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304 #end if
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305 #elif $tgts_sec.targets_file:
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306 #set $targets_path = 'targets_file.tab.gz'
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307 bgzip -c "$section.targets_file" > $targets_path &&
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308 tabix -s 1 -b 2 -e 2 $targets_path &&
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309 #end if
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310 ]]>
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311 </token>
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312 <token name="@TARGETS_FILE@">
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313 <![CDATA[
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314 #if $targets_path is not None:
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315 --targets-file "${section.invert_targets_file}${targets_path}"
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316 #elif $section.targets_file:
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317 --targets-file "${section.invert_targets_file}${section.targets_file}"
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318 #end if
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319 ]]>
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320 </token>
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321
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322 <xml name="macro_targets">
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323 <conditional name="targets">
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324 <param name="targets_src" type="select" label="Targets">
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325 <option value="__none__">None</option>
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326 <option value="targets">targets</option>
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327 <option value="targets_file">targets-file</option>
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328 </param>
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329 <when value="__none__"/>
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330 <when value="targets">
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331 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
0
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332 help="Each target is specifed as: chr or chr:pos or chr:from-to">
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333 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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334 </param>
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335 <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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336 </when>
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337 <when value="targets_file">
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338 <expand macro="macro_targets_file">
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339 </expand>
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340 </when>
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341 </conditional>
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342 </xml>
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343 <token name="@TARGETS@">
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344 <![CDATA[
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345 #if $targets_path:
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346 --targets-file "${section.targets.invert_targets_file}${targets_path}"
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347 #else:
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348 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
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349 --targets '${section.targets.invert_targets_file}${section.targets.targets}'
0
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350 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
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351 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
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352 #end if
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353 #end if
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354 ]]>
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355 </token>
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356
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357 <xml name="macro_samples">
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358 <param name="samples" type="text" value="" label="Samples" optional="true"
0
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359 help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
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360 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
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361 </param>
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362 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
0
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363 help="inverts the query/filtering applied by Samples" />
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364 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
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365 help="(-S) file of samples to include" />
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366 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
0
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367 help="inverts the query/filtering applied by Samples File" />
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368 </xml>
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369 <token name="@SAMPLES@">
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370 #set $samples_defined = False
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371 #if str($section.samples) != '':
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372 #set $samples_defined = True
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373 --samples '${section.invert_samples}${section.samples}'
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374 #end if
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375 #if $section.samples_file:
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376 #set $samples_defined = True
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377 --samples-file "${section.invert_samples_file}${section.samples_file}"
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378 #end if
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379 </token>
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380
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381 <xml name="macro_sample">
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382 <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
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383 </xml>
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384 <token name="@SAMPLE@">
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385 #if $section.sample:
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386 --sample '${section.sample}'
0
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387 #end if
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388 </token>
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389
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diff changeset
390
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391 <xml name="macro_include">
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392 <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">
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393 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
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394 <sanitizer sanitize="False"/>
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395 </param>
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396 </xml>
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397 <token name="@INCLUDE@">
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398 #if $section.include:
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399 --include '${section.include}'
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400 #end if
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diff changeset
401 </token>
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402
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403 <xml name="macro_exclude">
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404 <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">
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405 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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406 <sanitizer sanitize="False"/>
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407 </param>
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408 </xml>
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409 <token name="@EXCLUDE@">
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410 #if $section.exclude:
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411 --exclude '${section.exclude}'
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412 #end if
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413 </token>
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414
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415 <xml name="macro_columns">
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416 <param name="columns" type="text" value="" label="Columns" optional="true"
0
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417 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
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418 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
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419 </param>
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420 </xml>
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421 <token name="@COLUMNS@">
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422 #if $section.columns != '':
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423 --columns '${section.columns}'
0
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424 #end if
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425 </token>
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426
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427 <xml name="macro_haploid2diploid">
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428 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
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429 </xml>
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430
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431 <xml name="macro_vcf_ids">
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432 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
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433 </xml>
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434 <token name="@VCF_IDS@">
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435 ${section.vcf_ids}
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436 </token>
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diff changeset
437
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438 <token name="@OUTPUT_HELP@">
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439 <![CDATA[
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440 Output Type
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441 -----------
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442
3
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443 Output compressed BCF (b), or uncompressed VCF (v).
0
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444 Use the BCF option when piping between bcftools subcommands to speed up
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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445 performance by removing unecessary compression/decompression
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446 and VCF<->BCF conversion.
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447
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448 This Galaxy tool recommends using the compressed BCF format
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diff changeset
449 as piping is not implemented, and uncompressed data would
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
450 use unnecessary amounts of space.
4
b7dc6f8084ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
451 ]]></token>
0
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
452 <token name="@REGIONS_HELP@">
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
453 <![CDATA[
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
454 Region Selections
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
455 -----------------
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
456
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
457 Regions can be specified in a VCF,
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
458 BED, or tab-delimited file (the default). The columns of the
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
459 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
460 where positions are 1-based and inclusive. Uncompressed
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
461 files are stored in memory, while bgzip-compressed and
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
462 tabix-indexed region files are streamed. Note that sequence
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
463 names must match exactly, "chr20" is not the same as "20".
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
464 Also note that chromosome ordering in FILE will be
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
465 respected, the VCF will be processed in the order in which
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
466 chromosomes first appear in FILE. However, within
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
467 chromosomes, the VCF will always be processed in ascending
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
468 genomic coordinate order no matter what order they appear in
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
469 FILE. Note that overlapping regions in FILE can result in
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
470 duplicated out of order positions in the output. This option
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
471 requires indexed VCF/BCF files.
4
b7dc6f8084ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
472 ]]></token>
0
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
473 <token name="@TARGETS_HELP@"><![CDATA[
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
474 Targets
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
475 -------
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
476
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
477 Similar to regions, but the next position is accessed by streaming the whole
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
478 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
479 applied simultaneously: regions uses the index to jump to a region and targets discards
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
480 positions which are not in the targets. Unlike regions, targets can be prefixed with
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
481 "^" to request logical complement. For example, "^X,Y,MT" indicates that
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
482 sequences X, Y and MT should be skipped. Yet another difference between the two
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
483 is that regions checks both start and end positions of indels, whereas targets checks
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
484 start positions only.
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
485
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
486 For the bcftools call command, with the option -C alleles, third column of the
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
487 targets file must be comma-separated list of alleles, starting with the
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
488 reference allele. Note that the file must be compressed and index. Such a file
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
489 can be easily created from a VCF using::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
490
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
491 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
492 ]]>
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
493 <!-- TODO: galaxy-ify -->
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
494 </token>
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
495
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
496
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
497 <token name="@COLLAPSE_HELP@">
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
498 Collapse
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
499 --------
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
500
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
501 Controls how to treat records with duplicate positions and defines compatible
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
502 records across multiple input files. Here by "compatible" we mean records which
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
503 should be considered as identical by the tools. For example, when performing
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
504 line intersections, the desire may be to consider as identical all sites with
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
505 matching positions (bcftools isec -c all), or only sites with matching variant
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
506 type (bcftools isec -c snps -c indels), or only sites with all alleles
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
507 identical (bcftools isec -c none).
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
508
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
509
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
510 +------------+----------------------------------------------------------------+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
511 | Flag value | Result |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
512 +============+================================================================+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
513 | none | only records with identical REF and ALT alleles are compatible |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
514 +------------+----------------------------------------------------------------+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
515 | some | only records where some subset of ALT alleles match are |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
516 | | compatible |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
517 +------------+----------------------------------------------------------------+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
518 | all | all records are compatible, regardless of whether the ALT |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
519 | | alleles match or not. In the case of records with the same |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
520 | | position, only the first wil lbe considered and appear on |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
521 | | output. |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
522 +------------+----------------------------------------------------------------+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
523 | snps | any SNP records are compatible, regardless of whether the ALT |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
524 | | alleles match or not. For duplicate positions, only the first |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
525 | | SNP record will be considered and appear on output. |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
526 +------------+----------------------------------------------------------------+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
527 | indels | all indel records are compatible, regardless of whether the |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
528 | | REF and ALT alleles match or not. For duplicate positions, |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
529 | | only the first indel record will be considered and appear on |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
530 | | output. |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
531 +------------+----------------------------------------------------------------+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
532 | both | abbreviation of "-c indels -c snps" |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
533 +------------+----------------------------------------------------------------+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
534 | id | only records with identical ID column are compatible. |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
535 | | Supportedby bcftools merge only. |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
536 +------------+----------------------------------------------------------------+
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
537 </token>
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
538
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
539 <token name="@EXPRESSIONS_HELP@">
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
540 <![CDATA[
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
541 Expressions
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
542 -----------
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
543
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
544 Valid expressions may contain:
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
545
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
546 - numerical constants, string constants
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
547
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
548 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
549
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
550 1, 1.0, 1e-4
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
551 "String"
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
552
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
553 - arithmetic operators
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
554
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
555 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
556
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
557 +,*,-,/
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
558
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
559 - comparison operators
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
560
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
561 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
562
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
563 == (same as =), >, >=, <=, <, !=
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
564
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
565 - regex operators "~" and its negation "!~"
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
566
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
567 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
568
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
569 INFO/HAYSTACK ~ "needle"
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
570
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
571 - parentheses
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
572
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
573 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
574
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
575 (, )
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
576
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
577 - logical operators
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
578
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
579 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
580
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
581 && (same as &), ||, |
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
582
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
583 - INFO tags, FORMAT tags, column names
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
584
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
585 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
586
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
587 INFO/DP or DP
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
588 FORMAT/DV, FMT/DV, or DV
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
589 FILTER, QUAL, ID, REF, ALT[0]
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
590
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
591 - 1 (or 0) to test the presence (or absence) of a flag
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
592
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
593 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
594
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
595 FlagA=1 && FlagB=0
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
596
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
597 - "." to test missing values
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
598
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
599 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
600
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
601 DP=".", DP!=".", ALT="."
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
602
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
603 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
604
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
605 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
606
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
607 GT="."
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
608
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
609 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
610
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
611 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
612
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
613 TYPE="indel" | TYPE="snp"
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
614
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
615 - array subscripts, "*" for any field
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
616
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
617 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
618
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
619 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
620 DP4[*] == 0
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
621 CSQ[*] ~ "missense_variant.*deleterious"
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
622
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
623 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
624
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
625 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
626
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
627 MAX, MIN, AVG, SUM, STRLEN, ABS
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
628
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
629 - 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
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
630
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
631 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
632
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
633 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
634
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
635 **Notes:**
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
636
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
637 - String comparisons and regular expressions are case-insensitive
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
638 - If the subscript "*" is used in regular expression search, the whole field
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
639 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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640 true for the string vector INFO/STR=AB,CD.
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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641 - Variables and function names are case-insensitive, but not tag names. For
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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642 example, "qual" can be used instead of "QUAL", "strlen()" instead of
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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643 "STRLEN()" , but not "dp" instead of "DP".
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644
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645 **Examples:**
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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646
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647 ::
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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648
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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649 MIN(DV)>5
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650 MIN(DV/DP)>0.3
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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651 MIN(DP)>10 & MIN(DV)>3
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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652 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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653 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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654 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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655 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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656 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
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657 MIN(DP)>35 && AVG(GQ)>50
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658 ID=@file .. selects lines with ID present in the file
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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659 ID!=@~/file .. skip lines with ID present in the ~/file
7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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660 MAF[0]<0.05 .. select rare variants at 5% cutoff
4
b7dc6f8084ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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661 ]]></token>
0
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662 </macros>