Mercurial > repos > iuc > bcftools_query

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 08:06:21 +0000
parents 31a1b89eab9b
children
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2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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1 <macros>
23
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2 <token name="@TOOL_VERSION@">1.22</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">24.1</token>
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3b1b51e1fcba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
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5 <xml name="bio_tools">
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6 <xrefs>
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7 <xref type="bio.tools">bcftools</xref>
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8 </xrefs>
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9 </xml>
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
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13 <requirement type="package" version="1.22.1">htslib</requirement>
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14 <yield />
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15 </requirements>
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16 </xml>
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17 <xml name="samtools_requirement">
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18 <requirement type="package" version="1.22.1">samtools</requirement>
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19 </xml>
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20 <xml name="matplotlib_requirement">
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21 <requirement type="package" version="3.10.7">matplotlib</requirement>
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22 </xml>
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23 <xml name="version_command">
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24 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
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25 </xml>
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26
0
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27 <xml name="citations">
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28 <citations>
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29 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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30 <yield />
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31 </citations>
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32 </xml>
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33 <token name="@BCFTOOLS_HOWTOS@">https://samtools.github.io/bcftools/howtos/index.html</token>
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34 <token name="@BCFTOOLS_MANPAGE@">https://www.htslib.org/doc/bcftools.html</token>
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35 <token name="@THREADS@">
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36 --threads \${GALAXY_SLOTS:-4}
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37 </token>
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38 <xml name="macro_input">
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39 <!--
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40 REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
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41 <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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42 -->
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43 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
0
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44 </xml>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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45 <token name="@PREPARE_INPUT_FILE@">
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46 <![CDATA[
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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47 ## May need to symlink input if there is an associated
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48 #set $input_vcf = 'input.vcf.gz'
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49 #if $input_file.is_of_type('vcf')
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50 bgzip -c '$input_file' > $input_vcf &&
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51 bcftools index $input_vcf &&
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52 ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
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53 #elif $input_file.is_of_type('vcf_bgzip')
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54 ln -s '$input_file' $input_vcf &&
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55 #if $input_file.metadata.tabix_index:
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56 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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57 #else
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58 bcftools index $input_vcf &&
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59 #end if
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60 #elif $input_file.is_of_type('bcf')
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61 #set $input_vcf = 'input.bcf'
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62 ln -s '$input_file' $input_vcf &&
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63 #if $input_file.metadata.bcf_index:
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64 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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65 #else
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66 bcftools index $input_vcf &&
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67 #end if
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68 #end if
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69 ]]>
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70 </token>
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71 <token name="@INPUT_FILE@">
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72 $input_vcf
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73 </token>
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74
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75 <xml name="macro_inputs">
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76 <!--
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77 REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
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78 <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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79 -->
7
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80 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
0
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81 </xml>
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82 <token name="@PREPARE_INPUT_FILES@">
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83 <![CDATA[
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84 ## May need to symlink input if there is an associated
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85 #set $input_vcfs = []
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86 #set $vcfs_list_file = 'vcfs_list'
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87 #for (i, input_file) in enumerate($input_files):
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88 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
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89 #if $input_file.is_of_type('vcf')
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90 bgzip -c '$input_file' > $input_vcf &&
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91 bcftools index $input_vcf &&
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92 ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
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93 #elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
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94 ln -s '$input_file' $input_vcf &&
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95 #if $input_file.metadata.tabix_index:
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96 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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97 #else
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98 bcftools index $input_vcf &&
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99 #end if
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100 #elif $input_file.is_of_type('bcf')
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101 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
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102 ln -s '$input_file' $input_vcf &&
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103 #if $input_file.metadata.bcf_index:
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104 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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105 #else
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106 bcftools index $input_vcf &&
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107 #end if
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108 #end if
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109 echo '$input_vcf' >> $vcfs_list_file &&
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110 $input_vcfs.append($input_vcf)
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111 #end for
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112 ]]>
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113 </token>
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114 <token name="@INPUT_FILES@">
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115 #echo ' '.join($input_vcfs)#
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116 </token>
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117 <token name="@INPUT_LIST_FILE@">
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118 $vcfs_list_file
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119 </token>
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120
8
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121 <xml name="test_using_reference" token_select_from="history" token_ref="">
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122 <conditional name="reference_source">
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123 <param name="reference_source_selector" value="@SELECT_FROM@" />
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124 <param name="fasta_ref" ftype="fasta" value="@REF@" />
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125 </conditional>
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126 </xml>
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127
0
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128 <xml name="macro_fasta_ref">
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129 <conditional name="reference_source">
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130 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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131 <option value="cached">Use a built-in genome</option>
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132 <option value="history">Use a genome from the history</option>
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133 </param>
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134 <when value="cached">
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135 <param name="fasta_ref" type="select" label="Reference genome">
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136 <options from_data_table="fasta_indexes">
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137 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_file" />
8
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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 </options>
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140 </param>
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141 </when>
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142 <when value="history">
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143 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
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144 </when>
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145 </conditional>
0
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146 </xml>
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147 <token name="@PREPARE_FASTA_REF@">
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148 <![CDATA[
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149 #set $input_fa_ref = None
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150 #if 'fasta_ref' in $section and $section.fasta_ref:
8
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151 #if 'reference_source_selector' in $section:
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152 #if str($section.reference_source_selector) == "history":
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153 #set $input_fa_ref = 'ref.fa'
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154 ln -s '$section.fasta_ref' $input_fa_ref &&
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155 samtools faidx $input_fa_ref &&
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156 #else:
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157 #set $input_fa_ref = str($section.fasta_ref.fields.path)
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158 #end if
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159 #end if
0
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160 #end if
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161 ]]>
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162 </token>
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163 <token name="@FASTA_REF@">
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164 #if $input_fa_ref is not None:
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165 --fasta-ref $input_fa_ref
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166 #elif 'fasta_ref' in $section and $section.fasta_ref:
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167 --fasta-ref '${section.fasta_ref}'
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168 #end if
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169 </token>
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170
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171 <xml name="macro_AF_file">
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172 <param 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" />
0
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173 </xml>
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174 <!-- This may need to bgzip and tabix the file -->
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175 <token name="@PREPARE_AF_FILE@">
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176 <![CDATA[
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177 #if 'AF_file' in $section and $section.AF_file:
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178 #pass
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179 #end if
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180 ]]>
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181 </token>
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182 <token name="@AF_FILE@">
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183 #if 'AF_file' in $section and $section.AF_file:
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184 --AF-file '${section.AF_file}'
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185 #end if
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186 </token>
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187
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188 <xml name="macro_estimate_AF">
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189 <param 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
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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190 </xml>
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191 <token name="@ESTIMATE_AF@">
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192 #if 'estimate_AF' in $section and $section.estimate_AF:
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193 --estimate-AF "${section.estimate_AF}"
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194 #end if
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195 </token>
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196
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197 <xml name="macro_exons_file">
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198 <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)" />
0
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199 </xml>
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200 <token name="@PREPARE_EXONS_FILE@">
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201 <![CDATA[
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202 #set $exons_path = None
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203 #if 'exons_file' in $section and $section.exons_file:
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204 #set $exons_path = 'exons_file.tab.gz'
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205 bgzip -c "$section.exons_file" > $exons_path &&
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206 tabix -s 1 -b 2 -e 3 $exons_path &&
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207 #end if
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208 ]]>
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209 </token>
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210 <token name="@EXONS_FILE@">
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211 #if 'exons_file' in $section and $section.exons_file:
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212 --exons $exons_path
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213 #end if
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214 </token>
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215
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216 <xml name="macro_ploidy_file">
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217 <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
0
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218 </xml>
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219 <token name="@PLOIDY_FILE@">
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220 #if 'ploidy_file' in $section and $section.ploidy_file:
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221 --ploidy "${section.ploidy_file}"
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222 #end if
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223 </token>
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224
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225 <xml name="macro_collapse_opt_none">
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226 <option value="none">none - require the exact same set of alleles in all files</option>
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227 </xml>
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228 <xml name="macro_collapse_opt_id">
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229 <option value="id">id - only records with identical ID column are compatible. </option>
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230 </xml>
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231 <xml name="macro_collapse">
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232 <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">
0
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233 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
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234 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
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235 <option value="both">both - indels and snps </option>
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236 <option value="some">some - at least some of the ALTs must match</option>
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237 <option value="any">any - any combination of alleles</option>
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238 <yield/>
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239 </param>
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240 </xml>
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241 <token name="@COLLAPSE@">
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242 #if $section.collapse:
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243 --collapse ${section.collapse}
0
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244 #end if
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245 </token>
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246
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247 <xml name="macro_apply_filters">
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248 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
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249 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
0
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250 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
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251 </param>
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252 </xml>
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253 <token name="@APPLY_FILTERS@">
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254 #if $section.apply_filters:
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255 --apply-filters '${section.apply_filters}'
0
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256 #end if
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257 </token>
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258
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259 <xml name="macro_select_output_type">
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260 <param name="output_type" type="select">
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261 <option value="b">compressed BCF</option>
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262 <!-- no galaxy datatypes for these
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263 <option value="u">uncompressed BCF</option>
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264 <option value="z">compressed VCF</option>
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265 -->
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266 <option value="v">uncompressed VCF</option>
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267 </param>
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268 </xml>
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269 <token name="@OUTPUT_TYPE@">
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270 #if str($output_type) != "__none__":
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271 --output-type '${output_type}'
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272 #end if
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273 </token>
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274
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275 <xml name="macro_vcf_output">
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276 <data name="output_file" format="vcf">
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277 <change_format>
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278 <when input="output_type" value="b" format="bcf" />
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279 <when input="output_type" value="u" format="bcf" />
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280 <when input="output_type" value="z" format="vcf_bgzip" />
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281 <when input="output_type" value="v" format="vcf" />
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282 </change_format>
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283 </data>
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284 </xml>
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285
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286 <xml name="macro_invert_targets">
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287 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
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288 label="Invert Targets"
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289 help="inverts the query/filtering applied by the targets" />
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290 </xml>
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291
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292 <xml name="macro_restriction_spec" tokens="type,label_type">
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293 <repeat name="@TYPE@_specs" title="@LABEL_TYPE@ Filter" default="1" min="1">
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294 <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
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295 <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
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296 </param>
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297 <param name="start" type="text" label="@LABEL_TYPE@ start position">
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298 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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299 </param>
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300 <param name="stop" type="text" label="@LABEL_TYPE@ end position">
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301 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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302 </param>
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303 </repeat>
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304 </xml>
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305
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306 <xml name="macro_restrictions_file" tokens="type,label_type">
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307 <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" />
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308 </xml>
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309
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310 <xml name="__macro_restrict__" tokens="type,label_select,label_type,pos_is_default,rec_is_default">
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311 <conditional name="@TYPE@s">
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312 <param name="@TYPE@s_src" type="select" label="@LABEL_SELECT@">
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313 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
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314 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
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315 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
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316 </param>
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317 <when value="__none__"/>
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318 <when value="@TYPE@s">
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319 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
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320 <yield />
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321 <param argument="--@TYPE@s-overlap" type="select" label="Consider variant calls with partial overlap with @LABEL_TYPE@(s) if ..." help="Set to 0 if the record has to have POS inside a region; set to 1 if also overlapping records with POS outside a region should be included (this includes indels with POS at the end of a region, which are technically outside the region); or set to 2 to include only true overlapping variation (compare the full VCF representation 'TA>T-' vs the true sequence variation 'A>-').">
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322 <option value="0" selected="@POS_IS_DEFAULT@">0: the variant's POS falls in the region</option>
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323 <option value="1" selected="@REC_IS_DEFAULT@">1: any part of the variant's representation overlaps the region</option>
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324 <option value="2">2: the variant's actual sequence change falls in the region</option>
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325 </param>
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326 </when>
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327 <when value="@TYPE@s_file">
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328 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
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329 <yield />
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330 <param argument="--@TYPE@s-overlap" type="select" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)">
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331 <option value="0" selected="@POS_IS_DEFAULT@">0: POS in the region</option>
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332 <option value="1" selected="@REC_IS_DEFAULT@">1: Record overlaps</option>
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333 <option value="2">2: Variant overlaps</option>
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334 </param>
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335 </when>
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336 </conditional>
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337 </xml>
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338
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339 <xml name="__macro_restrict_simple__" tokens="type,label_select,label_type">
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340 <conditional name="@TYPE@s">
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341 <param name="@TYPE@s_src" type="select" label="@LABEL_SELECT@">
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342 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
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343 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
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344 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
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345 </param>
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346 <when value="__none__"/>
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347 <when value="@TYPE@s">
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348 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
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349 <yield />
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350 </when>
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351 <when value="@TYPE@s_file">
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352 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
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353 <yield />
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354 </when>
0
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355 </conditional>
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356 </xml>
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357
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358 <xml name="macro_region_restrict" token_label_select="Regions">
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359 <expand macro="__macro_restrict__" type="region" label_select="@LABEL_SELECT@" label_type="Region" pos_is_default="false" rec_is_default="true" />
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360 </xml>
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361
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362 <xml name="macro_region_restrict_simple" token_label_select="Regions">
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363 <!-- To be used with subcommands that don't support the 'regions-overlap' option. Currently only mpileup? -->
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364 <expand macro="__macro_restrict_simple__" type="region" label_select="@LABEL_SELECT@" label_type="Region" />
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365 </xml>
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366
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367 <xml name="macro_target_restrict">
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368 <expand macro="__macro_restrict__" type="target" label_select="Target" label_type="Target" pos_is_default="true" rec_is_default="false">
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369 <expand macro="macro_invert_targets" />
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370 </expand>
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371 </xml>
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372
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373 <xml name="macro_target_restrict_simple">
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374 <!-- To be used with subcommands that don't support the 'regions-overlap' option. Currently only mpileup and call? -->
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375 <expand macro="__macro_restrict_simple__" type="target" label_select="Target" label_type="Target">
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376 <expand macro="macro_invert_targets" />
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377 </expand>
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378 </xml>
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379
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380 <xml name="macro_mask_restrict">
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381 <expand macro="__macro_restrict__" type="mask" label_select="Mask" label_type="Mask" pos_is_default="false" rec_is_default="true" />
0
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382 </xml>
8
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383
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384 <token name="@PARSE_INTERVALS@">
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385 <![CDATA[
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386 #set $components = []
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387 #for $i in $intervals:
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388 #set $chrom = str($i.chrom).strip()
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389 #set $start = str($i.start).strip()
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390 #set $stop = str($i.stop).strip()
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391 #if $start or $stop:
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392 $components.append($chrom + ':' + ($start or '1') + '-' + $stop)
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393 #else:
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394 $components.append($chrom)
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395 #end if
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396 #end for
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397 #set $intervals_spec = ','.join($components)
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398 ]]>
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399 </token>
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400
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401 <token name="@MASK@">
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402 <![CDATA[
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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403 #if $section.conditional_soft_filter.selector == 'enabled' and $section.conditional_soft_filter.soft_filter
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404 #if $section.conditional_soft_filter.masks.masks_src != '__none__':
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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405 #if $section.conditional_soft_filter.masks.masks_src == 'masks':
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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406 #set $intervals = $section.conditional_soft_filter.masks.mask_specs
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407 @PARSE_INTERVALS@
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408 --mask '$intervals_spec'
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409 #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file':
16
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410 --mask-file '$section.conditional_soft_filter.masks.masks_file'
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411 #end if
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412 --mask-overlap $section.conditional_soft_filter.masks_overlap
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413 #end if
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414 #end if
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415
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416 ]]>
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417 </token>
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418
8
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419 <token name="@REGIONS@">
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420 <![CDATA[
23
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421 #if $section.regions.regions_src != '__none__':
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422 #if $section.regions.regions_src == 'regions':
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423 #set $intervals = $section.regions.region_specs
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424 @PARSE_INTERVALS@
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425 --regions '$intervals_spec'
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426 #elif $section.regions.regions_src == 'regions_file':
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427 #if $regions_path is not None:
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428 --regions-file '$regions_path'
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429 #else:
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430 --regions-file '$section.regions.regions_file'
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431 #end if
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432 #end if
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433 #if 'regions_overlap' in $section.regions:
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434 --regions-overlap $section.regions.regions_overlap
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435 #end if
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436 #end if
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437 ]]>
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438 </token>
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diff changeset
439
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440 <token name="@TARGETS@">
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441 <![CDATA[
23
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442 #if $section.targets.targets_src != '__none__':
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443 #if $section.targets.targets_src == 'targets':
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444 #set $intervals = $section.targets.target_specs
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445 @PARSE_INTERVALS@
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446 --targets '${section.targets.invert_targets_file}$intervals_spec'
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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diff changeset
447 #elif $section.targets.targets_src == 'targets_file':
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
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448 #if $targets_path:
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449 --targets-file '${section.targets.invert_targets_file}${targets_path}'
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
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450 #else:
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
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451 --targets-file '${section.targets.invert_targets_file}${section.targets.targets_file}'
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
452 #end if
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parents: 22
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453 #end if
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
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454 #if 'targets_overlap' in $section.targets:
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
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455 --targets-overlap $section.targets.targets_overlap
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
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456 #end if
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457 #end if
8
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parents: 7
diff changeset
458 ]]>
0770b1203e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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parents: 7
diff changeset
459 </token>
0770b1203e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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parents: 7
diff changeset
460
5
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parents: 4
diff changeset
461 <token name="@PREPARE_REGIONS_FILE@">
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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parents: 4
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462 <![CDATA[
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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463 #set $regions_path = None
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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464 #if 'regions' in $section
23
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465 #if $section.regions.regions_src == 'regions_file':
5
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diff changeset
466 #if $section.regions.regions_file.ext.startswith('bed'):
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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467 #set $regions_path = 'regions_file.bed'
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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468 ln -s '$section.regions.regions_file' $regions_path &&
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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parents: 4
diff changeset
469 #end if
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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parents: 4
diff changeset
470 #end if
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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parents: 4
diff changeset
471 #end if
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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parents: 4
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472 ]]>
24ff7b989329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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parents: 4
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473 </token>
8
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parents: 7
diff changeset
474
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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475 <token name="@PREPARE_TARGETS_FILE@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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476 <![CDATA[
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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477 #set $targets_path = None
3
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parents: 2
diff changeset
478 #if 'targets' in $section
0
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479 #if $section.targets.targets_src == 'targets_file':
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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480 #set $targets_path = 'targets_file.tab.gz'
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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481 bgzip -c "$section.targets.targets_file" > $targets_path &&
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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482 tabix -s 1 -b 2 -e 2 $targets_path &&
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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483 #end if
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parents: 20
diff changeset
484 #elif $section.targets_file:
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
485 #set $targets_path = 'targets_file.tab.gz'
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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486 bgzip -c "$section.targets_file" > $targets_path &&
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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487 tabix -s 1 -b 2 -e 2 $targets_path &&
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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488 #end if
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
489 ]]>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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490 </token>
8
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parents: 7
diff changeset
491
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
492 <token name="@TARGETS_FILE@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
493 <![CDATA[
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
494 #if $targets_path is not None:
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
495 --targets-file "${section.invert_targets_file}${targets_path}"
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
496 #elif $section.targets_file:
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
497 --targets-file "${section.invert_targets_file}${section.targets_file}"
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
498 #end if
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
499 ]]>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
500 </token>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
501
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
502 <xml name="macro_samples">
7
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parents: 6
diff changeset
503 <param argument="--samples" type="text" value="" optional="true" label="Samples"
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parents: 13
diff changeset
504 help="Comma-separated list of samples to annotate (or exclude) or - to include all samples">
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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parents: 13
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505 <validator type="regex" message="Comma-separated list of samples or - to include all samples">^(-|\w+(,\w+)*)?$</validator>
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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506 </param>
3
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parents: 2
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507 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
7
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diff changeset
508 help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
23
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parents: 22
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509 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file" help="File of samples to include" />
7
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parents: 6
diff changeset
510 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
e0ad88dec40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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diff changeset
511 help="inverts the query/filtering applied by Samples file" />
0
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diff changeset
512 </xml>
23
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parents: 22
diff changeset
513
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
514 <xml name="macro_samples_enhanced" token_all_samples="" token_file_help="File listing samples to include one per line.">
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
515 <conditional name="specify_samples">
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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516 <param name="how" type="select" label="How do you want to select samples?">
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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diff changeset
517 <option value="-s">Specify samples manually</option>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
518 <option value="-S">Provide sample file</option>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
519 <option value="@ALL_SAMPLES@" selected="true">No selection; just use all samples found in input</option>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
520 </param>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
521 <when value="-s">
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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diff changeset
522 <param argument="--samples" name="samples_spec" type="text" optional="false" label="Sample(s)" help="Specify a single sample by name or a comma-separated list of sample names.">
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
523 <validator type="expression" message="Please specify a single sample by name or a comma-separated list of sample names">value.strip() and value[0] not in "^," and ",," not in value</validator>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
524 </param>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
525 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude these samples instead of including them?" help="Equivalent to prefixing the list of samples with &quot;^&quot; on the command line."/>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
526 </when>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
527 <when value="-S">
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
528 <param argument="--samples_file" type="data" format="tabular" optional="@IS_OPTIONAL@" label="Samples file" help="@FILE_HELP@" />
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
529 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude the samples listed in the file instead of including them?" help="Equivalent to prefixing the file with &quot;^&quot; on the command line."/>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
530 </when>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
531 <when value="@ALL_SAMPLES@" />
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
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parents: 22
diff changeset
532 </conditional>
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
533 </xml>
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
534 <token name="@SAMPLES@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
535 #set $samples_defined = False
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
536 #if str($section.samples) != '':
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
537 #set $samples_defined = True
4
5476360ed9db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
538 --samples '${section.invert_samples}${section.samples}'
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
539 #end if
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
540 #if $section.samples_file:
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
541 #set $samples_defined = True
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
542 --samples-file "${section.invert_samples_file}${section.samples_file}"
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
543 #end if
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
544 </token>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
545
23
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
546 <xml name="macro_sample" token_help="Apply variants of the given sample">
1dc6f1ac7f32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
547 <param name="sample" type="text" optional="true" label="Sample" help="@HELP@" />
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
548 </xml>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
549 <token name="@SAMPLE@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
550 #if $section.sample:
4
5476360ed9db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
551 --sample '${section.sample}'
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
552 #end if
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
553 </token>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
554
12
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
555 <xml name="macro_include_exclude_validate_sanitize">
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
556 <validator type="expression" message="Single quote or trailing backslash not allowed">"'" not in value and value[-1] != "\\"</validator>
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
557 <sanitizer>
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
558 <valid initial="string.ascii_letters,string.digits,string.whitespace,string.punctuation">
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
559 <remove value="@" />
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
560 <remove value="'" />
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
561 </valid>
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
562 </sanitizer>
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
563 </xml>
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
564
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
565 <xml name="macro_include">
7
e0ad88dec40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
566 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
12
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
567 <expand macro="macro_include_exclude_validate_sanitize" />
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
568 </param>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
569 </xml>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
570 <token name="@INCLUDE@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
571 #if $section.include:
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
572 --include '${section.include}'
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
573 #end if
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
574 </token>
12
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
575
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
576 <xml name="macro_exclude">
7
e0ad88dec40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
577 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
12
c9c5718edc19 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
578 <expand macro="macro_include_exclude_validate_sanitize" />
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
579 </param>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
580 </xml>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
581 <token name="@EXCLUDE@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
582 #if $section.exclude:
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
583 --exclude '${section.exclude}'
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
584 #end if
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
585 </token>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
586
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
587 <xml name="macro_columns">
7
e0ad88dec40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
588 <param name="columns" type="text" value="" optional="true" label="Columns"
e0ad88dec40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
589 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
16
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
590 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
591 </param>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
592 </xml>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
593 <token name="@COLUMNS@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
594 #if $section.columns != '':
4
5476360ed9db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
595 --columns '${section.columns}'
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
596 #end if
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
597 </token>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
598
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
599 <xml name="macro_haploid2diploid">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
600 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
601 </xml>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
602
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
603 <xml name="macro_vcf_ids">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
604 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
605 </xml>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
606 <token name="@VCF_IDS@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
607 ${section.vcf_ids}
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
608 </token>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
609
16
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
610 <xml name="macro_output_tags">
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
611 <param name="output_tags" argument="--annotate" type="select" optional="true" multiple="True" display="checkboxes" label="Optional tags to output" help="--annotate">
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
612 <yield />
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
613 </param>
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
614 </xml>
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
615
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
616 <xml name="macro_overlap" token_argument="" token_label="">
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
617 </xml>
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
618
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
619
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
620 <token name="@OUTPUT_HELP@">
16
3ce32adc55b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 13
diff changeset
621
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
622 <![CDATA[
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
623 Output Type
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
624 -----------
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
625
3
f4f3013287a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents: 2
diff changeset
626 Output compressed BCF (b), or uncompressed VCF (v).
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
627 Use the BCF option when piping between bcftools subcommands to speed up
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
628 performance by removing unecessary compression/decompression
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
629 and VCF<->BCF conversion.
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
630
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
631 This Galaxy tool recommends using the compressed BCF format
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
632 as piping is not implemented, and uncompressed data would
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
633 use unnecessary amounts of space.
4
5476360ed9db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
634 ]]></token>
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
635 <token name="@REGIONS_HELP@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
636 <![CDATA[
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
637 Region Selections
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
638 -----------------
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
639
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
640 Regions can be specified in a VCF,
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
641 BED, or tab-delimited file (the default). The columns of the
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
642 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
643 where positions are 1-based and inclusive. Uncompressed
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
644 files are stored in memory, while bgzip-compressed and
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
645 tabix-indexed region files are streamed. Note that sequence
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
646 names must match exactly, "chr20" is not the same as "20".
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
647 Also note that chromosome ordering in FILE will be
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
648 respected, the VCF will be processed in the order in which
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
649 chromosomes first appear in FILE. However, within
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
650 chromosomes, the VCF will always be processed in ascending
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
651 genomic coordinate order no matter what order they appear in
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
652 FILE. Note that overlapping regions in FILE can result in
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
653 duplicated out of order positions in the output. This option
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
654 requires indexed VCF/BCF files.
4
5476360ed9db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
655 ]]></token>
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
656 <token name="@TARGETS_HELP@"><![CDATA[
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
657 Targets
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
658 -------
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
659
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
660 Similar to regions, but the next position is accessed by streaming the whole
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
661 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
662 applied simultaneously: regions uses the index to jump to a region and targets discards
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
663 positions which are not in the targets. Unlike regions, targets can be prefixed with
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
664 "^" to request logical complement. For example, "^X,Y,MT" indicates that
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
665 sequences X, Y and MT should be skipped. Yet another difference between the two
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
666 is that regions checks both start and end positions of indels, whereas targets checks
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
667 start positions only.
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
668
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
669 For the bcftools call command, with the option -C alleles, third column of the
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
670 targets file must be comma-separated list of alleles, starting with the
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
671 reference allele. Note that the file must be compressed and index. Such a file
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
672 can be easily created from a VCF using::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
673
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
674 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
675 ]]>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
676 <!-- TODO: galaxy-ify -->
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
677 </token>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
678
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
679
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
680 <token name="@COLLAPSE_HELP@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
681 Collapse
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
682 --------
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
683
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
684 Controls how to treat records with duplicate positions and defines compatible
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
685 records across multiple input files. Here by "compatible" we mean records which
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
686 should be considered as identical by the tools. For example, when performing
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
687 line intersections, the desire may be to consider as identical all sites with
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
688 matching positions (bcftools isec -c all), or only sites with matching variant
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
689 type (bcftools isec -c snps -c indels), or only sites with all alleles
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
690 identical (bcftools isec -c none).
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
691
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
692
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
693 +------------+----------------------------------------------------------------+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
694 | Flag value | Result |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
695 +============+================================================================+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
696 | none | only records with identical REF and ALT alleles are compatible |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
697 +------------+----------------------------------------------------------------+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
698 | some | only records where some subset of ALT alleles match are |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
699 | | compatible |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
700 +------------+----------------------------------------------------------------+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
701 | all | all records are compatible, regardless of whether the ALT |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
702 | | alleles match or not. In the case of records with the same |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
703 | | position, only the first wil lbe considered and appear on |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
704 | | output. |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
705 +------------+----------------------------------------------------------------+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
706 | snps | any SNP records are compatible, regardless of whether the ALT |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
707 | | alleles match or not. For duplicate positions, only the first |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
708 | | SNP record will be considered and appear on output. |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
709 +------------+----------------------------------------------------------------+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
710 | indels | all indel records are compatible, regardless of whether the |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
711 | | REF and ALT alleles match or not. For duplicate positions, |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
712 | | only the first indel record will be considered and appear on |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
713 | | output. |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
714 +------------+----------------------------------------------------------------+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
715 | both | abbreviation of "-c indels -c snps" |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
716 +------------+----------------------------------------------------------------+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
717 | id | only records with identical ID column are compatible. |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
718 | | Supportedby bcftools merge only. |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
719 +------------+----------------------------------------------------------------+
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
720 </token>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
721
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
722 <token name="@EXPRESSIONS_HELP@">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
723 <![CDATA[
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
724 Expressions
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
725 -----------
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
726
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
727 Valid expressions may contain:
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
728
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
729 - numerical constants, string constants
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
730
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
731 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
732
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
733 1, 1.0, 1e-4
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
734 "String"
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
735
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
736 - arithmetic operators
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
737
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
738 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
739
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
740 +,*,-,/
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
741
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
742 - comparison operators
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
743
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
744 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
745
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
746 == (same as =), >, >=, <=, <, !=
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
747
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
748 - regex operators "~" and its negation "!~"
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
749
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
750 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
751
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
752 INFO/HAYSTACK ~ "needle"
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
753
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
754 - parentheses
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
755
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
756 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
757
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
758 (, )
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
759
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
760 - logical operators
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
761
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
762 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
763
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
764 && (same as &), ||, |
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
765
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
766 - INFO tags, FORMAT tags, column names
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
767
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
768 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
769
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
770 INFO/DP or DP
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
771 FORMAT/DV, FMT/DV, or DV
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
772 FILTER, QUAL, ID, REF, ALT[0]
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
773
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
774 - 1 (or 0) to test the presence (or absence) of a flag
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
775
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
776 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
777
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
778 FlagA=1 && FlagB=0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
779
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
780 - "." to test missing values
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
781
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
782 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
783
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
784 DP=".", DP!=".", ALT="."
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
785
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
786 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
787
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
788 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
789
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
790 GT="."
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
791
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
792 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
793
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
794 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
795
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
796 TYPE="indel" | TYPE="snp"
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
797
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
798 - array subscripts, "*" for any field
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
799
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
800 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
801
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
802 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
803 DP4[*] == 0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
804 CSQ[*] ~ "missense_variant.*deleterious"
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
805
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
806 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
807
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
808 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
809
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
810 MAX, MIN, AVG, SUM, STRLEN, ABS
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
811
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
812 - 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
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
813
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
814 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
815
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
816 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
817
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
818 **Notes:**
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
819
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
820 - String comparisons and regular expressions are case-insensitive
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
821 - If the subscript "*" is used in regular expression search, the whole field
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
822 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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823 true for the string vector INFO/STR=AB,CD.
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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824 - Variables and function names are case-insensitive, but not tag names. For
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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825 example, "qual" can be used instead of "QUAL", "strlen()" instead of
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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826 "STRLEN()" , but not "dp" instead of "DP".
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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827
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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828 **Examples:**
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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829
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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830 ::
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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831
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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832 MIN(DV)>5
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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833 MIN(DV/DP)>0.3
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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834 MIN(DP)>10 & MIN(DV)>3
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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835 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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836 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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837 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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838 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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839 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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840 MIN(DP)>35 && AVG(GQ)>50
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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841 ID=@file .. selects lines with ID present in the file
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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842 ID!=@~/file .. skip lines with ID present in the ~/file
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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843 MAF[0]<0.05 .. select rare variants at 5% cutoff
4
5476360ed9db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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844 ]]></token>
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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845 </macros>