Mercurial > repos > iuc > bcftools_plugin_fixploidy

annotate macros.xml @ 13:e6d3f7bfd4cf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
author iuc
date Fri, 05 Feb 2021 18:43:01 +0000
parents 381f0ac51b6a
children 71268fcea042
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.10</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
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6 <requirement type="package" version="1.10">htslib</requirement>
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7 <yield />
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8 </requirements>
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9 </xml>
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10 <xml name="samtools_requirement">
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11 <requirement type="package" version="1.10">samtools</requirement>
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12 </xml>
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13 <xml name="matplotlib_requirement">
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14 <requirement type="package" version="3.1.0">matplotlib</requirement>
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15 </xml>
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16 <xml name="version_command">
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17 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
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18 </xml>
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19
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20 <xml name="citations">
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21 <citations>
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22 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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23 <yield />
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24 </citations>
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25 </xml>
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26 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
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27 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
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28 <token name="@THREADS@">
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29 --threads \${GALAXY_SLOTS:-4}
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30 </token>
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31 <token name="@PREPARE_ENV@">
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32 <![CDATA[
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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33 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
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34 ]]>
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35 </token>
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36 <xml name="macro_input">
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37 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
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38 </xml>
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39 <token name="@PREPARE_INPUT_FILE@">
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40 <![CDATA[
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41 ## May need to symlink input if there is an associated
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42 #set $input_vcf = 'input.vcf.gz'
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43 #if $input_file.is_of_type('vcf')
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44 bgzip -c '$input_file' > $input_vcf &&
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45 bcftools index $input_vcf &&
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46 #elif $input_file.is_of_type('vcf_bgzip')
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47 ln -s '$input_file' $input_vcf &&
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48 #if $input_file.metadata.tabix_index:
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49 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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50 #else
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51 bcftools index $input_vcf &&
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52 #end if
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53 #elif $input_file.is_of_type('bcf')
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54 #set $input_vcf = 'input.bcf'
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55 ln -s '$input_file' $input_vcf &&
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56 #if $input_file.metadata.bcf_index:
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57 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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58 #else
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59 bcftools index $input_vcf &&
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60 #end if
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61 #end if
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62 ]]>
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63 </token>
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64 <token name="@INPUT_FILE@">
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65 $input_vcf
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66 </token>
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67
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68 <xml name="macro_inputs">
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69 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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70 </xml>
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71 <token name="@PREPARE_INPUT_FILES@">
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72 <![CDATA[
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73 ## May need to symlink input if there is an associated
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74 #set $input_vcfs = []
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75 #set $vcfs_list_file = 'vcfs_list'
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76 #for (i, input_file) in enumerate($input_files):
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77 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
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78 #if $input_file.is_of_type('vcf')
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79 bgzip -c '$input_file' > $input_vcf &&
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80 bcftools index $input_vcf &&
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81 #elif $input_file.is_of_type('vcf_bgzip')
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82 ln -s '$input_file' $input_vcf &&
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83 #if $input_file.metadata.tabix_index:
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84 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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85 #else
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86 bcftools index $input_vcf &&
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87 #end if
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88 #elif $input_file.is_of_type('bcf')
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89 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
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90 ln -s '$input_file' $input_vcf &&
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91 #if $input_file.metadata.bcf_index:
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92 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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93 #else
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94 bcftools index $input_vcf &&
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95 #end if
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96 #end if
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97 echo '$input_vcf' >> $vcfs_list_file &&
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98 $input_vcfs.append($input_vcf)
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99 #end for
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100 ]]>
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101 </token>
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102 <token name="@INPUT_FILES@">
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103 #echo ' '.join($input_vcfs)#
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104 </token>
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105 <token name="@INPUT_LIST_FILE@">
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106 $vcfs_list_file
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107 </token>
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108
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109 <xml name="test_using_reference" token_select_from="history" token_ref="">
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110 <conditional name="reference_source">
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111 <param name="reference_source_selector" value="@SELECT_FROM@" />
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112 <param name="fasta_ref" ftype="fasta" value="@REF@" />
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113 </conditional>
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114 </xml>
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115
0
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116 <xml name="macro_fasta_ref">
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117 <conditional name="reference_source">
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118 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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119 <option value="cached">Use a built-in genome</option>
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120 <option value="history">Use a genome from the history</option>
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121 </param>
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122 <when value="cached">
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123 <param name="fasta_ref" type="select" label="Reference genome">
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124 <options from_data_table="fasta_indexes">
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125 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_file" />
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126 <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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127 </options>
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128 </param>
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129 </when>
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130 <when value="history">
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131 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
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132 </when>
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133 </conditional>
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134 </xml>
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135 <token name="@PREPARE_FASTA_REF@">
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136 <![CDATA[
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137 #set $input_fa_ref = None
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138 #if 'fasta_ref' in $section and $section.fasta_ref:
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139 #if 'reference_source_selector' in $section:
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140 #if str($section.reference_source_selector) == "history":
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141 #set $input_fa_ref = 'ref.fa'
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142 ln -s '$section.fasta_ref' $input_fa_ref &&
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143 samtools faidx $input_fa_ref &&
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144 #else:
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145 #set $input_fa_ref = str($section.fasta_ref.fields.path)
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146 #end if
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147 #end if
0
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148 #end if
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149 ]]>
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150 </token>
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151 <token name="@FASTA_REF@">
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152 #if $input_fa_ref is not None:
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153 --fasta-ref $input_fa_ref
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154 #elif 'fasta_ref' in $section and $section.fasta_ref:
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155 --fasta-ref '${section.fasta_ref}'
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156 #end if
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157 </token>
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158
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159 <xml name="macro_AF_file">
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160 <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
0
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161 </xml>
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162 <!-- This may need to bgzip and tabix the file -->
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163 <token name="@PREPARE_AF_FILE@">
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164 <![CDATA[
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165 #if 'AF_file' in $section and $section.AF_file:
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166 #pass
0
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167 #end if
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168 ]]>
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169 </token>
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170 <token name="@AF_FILE@">
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171 #if 'AF_file' in $section and $section.AF_file:
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172 --AF-file '${section.AF_file}'
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173 #end if
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174 </token>
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175
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176 <xml name="macro_estimate_AF">
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177 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
0
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178 </xml>
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179 <token name="@ESTIMATE_AF@">
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180 #if 'estimate_AF' in $section and $section.estimate_AF:
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181 --estimate-AF "${section.estimate_AF}"
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182 #end if
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183 </token>
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184
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185 <xml name="macro_exons_file">
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186 <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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187 </xml>
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188 <token name="@PREPARE_EXONS_FILE@">
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189 <![CDATA[
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190 #set $exons_path = None
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191 #if 'exons_file' in $section and $section.exons_file:
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192 #set $exons_path = 'exons_file.tab.gz'
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193 bgzip -c "$section.exons_file" > $exons_path &&
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194 tabix -s 1 -b 2 -e 3 $exons_path &&
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195 #end if
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196 ]]>
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197 </token>
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198 <token name="@EXONS_FILE@">
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199 #if 'exons_file' in $section and $section.exons_file:
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200 --exons $exons_path
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201 #end if
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202 </token>
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203
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204 <xml name="macro_ploidy_file">
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205 <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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206 </xml>
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207 <token name="@PLOIDY_FILE@">
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208 #if 'ploidy_file' in $section and $section.ploidy_file:
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209 --ploidy "${section.ploidy_file}"
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210 #end if
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211 </token>
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212
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213 <xml name="macro_collapse_opt_none">
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214 <option value="none">none - require the exact same set of alleles in all files</option>
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215 </xml>
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216 <xml name="macro_collapse_opt_id">
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217 <option value="id">id - only records with identical ID column are compatible. </option>
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218 </xml>
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219 <xml name="macro_collapse">
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220 <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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221 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
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222 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
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223 <option value="both">both - indels and snps </option>
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224 <option value="some">some - at least some of the ALTs must match</option>
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225 <option value="any">any - any combination of alleles</option>
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226 <yield/>
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227 </param>
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228 </xml>
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229 <token name="@COLLAPSE@">
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230 #if $section.collapse:
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231 --collapse ${section.collapse}
0
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232 #end if
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233 </token>
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234
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235 <xml name="macro_apply_filters">
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236 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
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237 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
0
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238 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
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239 </param>
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240 </xml>
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241 <token name="@APPLY_FILTERS@">
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242 #if $section.apply_filters:
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243 --apply-filters '${section.apply_filters}'
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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_select_output_type">
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248 <param name="output_type" type="select">
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249 <option value="b">compressed BCF</option>
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250 <!-- no galaxy datatypes for these
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251 <option value="u">uncompressed BCF</option>
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252 <option value="z">compressed VCF</option>
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253 -->
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254 <option value="v">uncompressed VCF</option>
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255 </param>
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256 </xml>
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257 <token name="@OUTPUT_TYPE@">
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258 #if str($output_type) != "__none__":
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259 --output-type '${output_type}'
0
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260 #end if
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261 </token>
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262
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263 <xml name="macro_vcf_output">
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264 <data name="output_file" format="vcf">
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265 <change_format>
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266 <when input="output_type" value="b" format="bcf" />
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267 <when input="output_type" value="u" format="bcf" />
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268 <when input="output_type" value="z" format="vcf_bgzip" />
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269 <when input="output_type" value="v" format="vcf" />
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270 </change_format>
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271 </data>
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272 </xml>
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273
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274 <xml name="macro_invert_targets">
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275 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
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276 label="Invert Targets"
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277 help="inverts the query/filtering applied by the targets" />
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278 </xml>
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279
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280 <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">
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281 <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">
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282 <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
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283 <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
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284 </param>
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285 <param name="start" type="text" label="@LABEL_TYPE@ start position">
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286 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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287 </param>
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288 <param name="stop" type="text" label="@LABEL_TYPE@ end position">
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289 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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290 </param>
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291 <yield />
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292 </repeat>
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293 </xml>
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294
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295 <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">
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296 <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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297 </xml>
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298
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299 <xml name="macro_restrict" token_type="region" token_label_type="Region" >
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300 <conditional name="@TYPE@s">
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301 <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">
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302 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
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303 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
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304 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
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305 </param>
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306 <when value="__none__"/>
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307 <when value="@TYPE@s">
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308 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
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309 <yield />
0
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310 </when>
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311 <when value="@TYPE@s_file">
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312 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
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313 <yield />
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314 </when>
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315 </conditional>
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316 </xml>
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317
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318 <token name="@PARSE_INTERVALS@">
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319 <![CDATA[
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320 #set $components = []
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321 #for $i in $intervals:
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322 #set $chrom = str($i.chrom).strip()
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323 #set $start = str($i.start).strip()
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324 #set $stop = str($i.stop).strip()
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325 #if $start or $stop:
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326 $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
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327 #else:
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328 $components.append($chrom)
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329 #end if
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330 #end for
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331 #set $intervals_spec = ','.join($components)
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332 ]]>
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333 </token>
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334
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335 <token name="@REGIONS@">
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336 <![CDATA[
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337 #if $section.regions.regions_src == 'regions':
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338 #set $intervals = $section.regions.regions
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339 @PARSE_INTERVALS@
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340 --regions '$intervals_spec'
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341 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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342 #if $regions_path is not None:
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343 --regions-file '$regions_path'
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344 #else:
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345 --regions-file '$section.regions.regions_file'
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346 #end if
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347 #end if
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348 ]]>
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349 </token>
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350
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351 <token name="@TARGETS@">
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352 <![CDATA[
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353 #if $targets_path:
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354 --targets-file "${section.targets.invert_targets_file}${targets_path}"
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355 #elif $section.targets.targets_src == 'targets':
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356 #set $intervals = $section.targets.targets
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357 @PARSE_INTERVALS@
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358 --targets '${section.targets.invert_targets_file}$intervals_spec'
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359 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
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360 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
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361 #end if
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362 ]]>
f4199f9f7de8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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363 </token>
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364
5
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diff changeset
365 <token name="@PREPARE_REGIONS_FILE@">
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366 <![CDATA[
11b5b774005c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
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367 #set $regions_path = None
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368 #if 'regions' in $section
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369 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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370 #if $section.regions.regions_file.ext.startswith('bed'):
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371 #set $regions_path = 'regions_file.bed'
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372 ln -s '$section.regions.regions_file' $regions_path &&
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373 #end if
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374 #end if
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375 #end if
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376 ]]>
11b5b774005c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
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377 </token>
9
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378
0
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379 <token name="@PREPARE_TARGETS_FILE@">
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380 <![CDATA[
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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381 #set $targets_path = None
2
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382 #if 'targets' in $section
0
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383 #if $section.targets.targets_src == 'targets_file':
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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384 #set $targets_path = 'targets_file.tab.gz'
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385 bgzip -c "$section.targets.targets_file" > $targets_path &&
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386 tabix -s 1 -b 2 -e 2 $targets_path &&
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387 #end if
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388 #elif $tgts_sec.targets_file:
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389 #set $targets_path = 'targets_file.tab.gz'
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390 bgzip -c "$section.targets_file" > $targets_path &&
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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391 tabix -s 1 -b 2 -e 2 $targets_path &&
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392 #end if
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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393 ]]>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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394 </token>
9
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diff changeset
395
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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396 <token name="@TARGETS_FILE@">
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397 <![CDATA[
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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398 #if $targets_path is not None:
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399 --targets-file "${section.invert_targets_file}${targets_path}"
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
400 #elif $section.targets_file:
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401 --targets-file "${section.invert_targets_file}${section.targets_file}"
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diff changeset
402 #end if
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
403 ]]>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
404 </token>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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405
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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406 <xml name="macro_samples">
8
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407 <param argument="--samples" type="text" value="" optional="true" label="Samples"
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diff changeset
408 help="Comma separated list of samples to annotate (or exclude)">
0
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409 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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410 </param>
2
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411 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
8
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diff changeset
412 help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
228d79b799dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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413 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
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diff changeset
414 help="File of samples to include" />
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diff changeset
415 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
228d79b799dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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diff changeset
416 help="inverts the query/filtering applied by Samples file" />
0
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diff changeset
417 </xml>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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418 <token name="@SAMPLES@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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419 #set $samples_defined = False
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420 #if str($section.samples) != '':
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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421 #set $samples_defined = True
4
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diff changeset
422 --samples '${section.invert_samples}${section.samples}'
0
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423 #end if
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
424 #if $section.samples_file:
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
425 #set $samples_defined = True
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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426 --samples-file "${section.invert_samples_file}${section.samples_file}"
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diff changeset
427 #end if
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
428 </token>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
429
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430 <xml name="macro_sample">
8
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diff changeset
431 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
432 </xml>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
433 <token name="@SAMPLE@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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434 #if $section.sample:
4
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diff changeset
435 --sample '${section.sample}'
0
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diff changeset
436 #end if
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
437 </token>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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438
13
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
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diff changeset
439 <xml name="macro_include_exclude_validate_sanitize">
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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diff changeset
440 <validator type="expression" message="Single quote or trailing backslash not allowed">"'" not in value and value[-1] != "\\"</validator>
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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diff changeset
441 <sanitizer>
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
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diff changeset
442 <valid initial="string.ascii_letters,string.digits,string.whitespace,string.punctuation">
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
443 <remove value="@" />
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
444 <remove value="'" />
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
445 </valid>
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
446 </sanitizer>
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
447 </xml>
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
448
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents:
diff changeset
449 <xml name="macro_include">
8
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parents: 7
diff changeset
450 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
13
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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diff changeset
451 <expand macro="macro_include_exclude_validate_sanitize" />
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
452 </param>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
453 </xml>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
454 <token name="@INCLUDE@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
455 #if $section.include:
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
456 --include '${section.include}'
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
457 #end if
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
458 </token>
13
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
459
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
460 <xml name="macro_exclude">
8
228d79b799dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
461 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
13
e6d3f7bfd4cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
462 <expand macro="macro_include_exclude_validate_sanitize" />
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
463 </param>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
464 </xml>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
465 <token name="@EXCLUDE@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
466 #if $section.exclude:
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
467 --exclude '${section.exclude}'
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
468 #end if
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
469 </token>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
470
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
471 <xml name="macro_columns">
8
228d79b799dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
472 <param name="columns" type="text" value="" optional="true" label="Columns"
228d79b799dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
473 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
474 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
475 </param>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
476 </xml>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
477 <token name="@COLUMNS@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
478 #if $section.columns != '':
4
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iuc
parents: 3
diff changeset
479 --columns '${section.columns}'
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
480 #end if
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
481 </token>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
482
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
483 <xml name="macro_haploid2diploid">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
484 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
485 </xml>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
486
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
487 <xml name="macro_vcf_ids">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
488 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
489 </xml>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
490 <token name="@VCF_IDS@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
491 ${section.vcf_ids}
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
492 </token>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
493
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
494 <token name="@OUTPUT_HELP@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
495 <![CDATA[
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
496 Output Type
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
497 -----------
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
498
2
7fad90ade0b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094
iuc
parents: 1
diff changeset
499 Output compressed BCF (b), or uncompressed VCF (v).
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
500 Use the BCF option when piping between bcftools subcommands to speed up
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
501 performance by removing unecessary compression/decompression
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
502 and VCF<->BCF conversion.
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
503
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
504 This Galaxy tool recommends using the compressed BCF format
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
505 as piping is not implemented, and uncompressed data would
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
506 use unnecessary amounts of space.
4
5a4073ad1140 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
507 ]]></token>
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
508 <token name="@REGIONS_HELP@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
509 <![CDATA[
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
510 Region Selections
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
511 -----------------
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
512
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
513 Regions can be specified in a VCF,
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
514 BED, or tab-delimited file (the default). The columns of the
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
515 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
516 where positions are 1-based and inclusive. Uncompressed
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
517 files are stored in memory, while bgzip-compressed and
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
518 tabix-indexed region files are streamed. Note that sequence
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
519 names must match exactly, "chr20" is not the same as "20".
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
520 Also note that chromosome ordering in FILE will be
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
521 respected, the VCF will be processed in the order in which
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
522 chromosomes first appear in FILE. However, within
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
523 chromosomes, the VCF will always be processed in ascending
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
524 genomic coordinate order no matter what order they appear in
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
525 FILE. Note that overlapping regions in FILE can result in
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
526 duplicated out of order positions in the output. This option
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
527 requires indexed VCF/BCF files.
4
5a4073ad1140 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
528 ]]></token>
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
529 <token name="@TARGETS_HELP@"><![CDATA[
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
530 Targets
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
531 -------
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
532
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
533 Similar to regions, but the next position is accessed by streaming the whole
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
534 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
535 applied simultaneously: regions uses the index to jump to a region and targets discards
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
536 positions which are not in the targets. Unlike regions, targets can be prefixed with
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
537 "^" to request logical complement. For example, "^X,Y,MT" indicates that
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
538 sequences X, Y and MT should be skipped. Yet another difference between the two
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
539 is that regions checks both start and end positions of indels, whereas targets checks
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
540 start positions only.
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
541
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
542 For the bcftools call command, with the option -C alleles, third column of the
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
543 targets file must be comma-separated list of alleles, starting with the
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
544 reference allele. Note that the file must be compressed and index. Such a file
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
545 can be easily created from a VCF using::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
546
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
547 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
548 ]]>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
549 <!-- TODO: galaxy-ify -->
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
550 </token>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
551
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
552
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
553 <token name="@COLLAPSE_HELP@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
554 Collapse
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
555 --------
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
556
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
557 Controls how to treat records with duplicate positions and defines compatible
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
558 records across multiple input files. Here by "compatible" we mean records which
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
559 should be considered as identical by the tools. For example, when performing
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
560 line intersections, the desire may be to consider as identical all sites with
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
561 matching positions (bcftools isec -c all), or only sites with matching variant
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
562 type (bcftools isec -c snps -c indels), or only sites with all alleles
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
563 identical (bcftools isec -c none).
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
564
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
565
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
566 +------------+----------------------------------------------------------------+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
567 | Flag value | Result |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
568 +============+================================================================+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
569 | none | only records with identical REF and ALT alleles are compatible |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
570 +------------+----------------------------------------------------------------+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
571 | some | only records where some subset of ALT alleles match are |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
572 | | compatible |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
573 +------------+----------------------------------------------------------------+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
574 | all | all records are compatible, regardless of whether the ALT |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
575 | | alleles match or not. In the case of records with the same |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
576 | | position, only the first wil lbe considered and appear on |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
577 | | output. |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
578 +------------+----------------------------------------------------------------+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
579 | snps | any SNP records are compatible, regardless of whether the ALT |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
580 | | alleles match or not. For duplicate positions, only the first |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
581 | | SNP record will be considered and appear on output. |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
582 +------------+----------------------------------------------------------------+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
583 | indels | all indel records are compatible, regardless of whether the |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
584 | | REF and ALT alleles match or not. For duplicate positions, |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
585 | | only the first indel record will be considered and appear on |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
586 | | output. |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
587 +------------+----------------------------------------------------------------+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
588 | both | abbreviation of "-c indels -c snps" |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
589 +------------+----------------------------------------------------------------+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
590 | id | only records with identical ID column are compatible. |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
591 | | Supportedby bcftools merge only. |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
592 +------------+----------------------------------------------------------------+
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
593 </token>
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
594
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
595 <token name="@EXPRESSIONS_HELP@">
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
596 <![CDATA[
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
597 Expressions
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
598 -----------
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
599
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
600 Valid expressions may contain:
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
601
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
602 - numerical constants, string constants
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
603
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
604 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
605
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
606 1, 1.0, 1e-4
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
607 "String"
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
608
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
609 - arithmetic operators
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
610
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
611 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
612
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
613 +,*,-,/
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
614
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
615 - comparison operators
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
616
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
617 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
618
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
619 == (same as =), >, >=, <=, <, !=
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
620
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
621 - regex operators "~" and its negation "!~"
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
622
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
623 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
624
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
625 INFO/HAYSTACK ~ "needle"
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
626
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
627 - parentheses
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
628
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
629 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
630
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
631 (, )
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
632
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
633 - logical operators
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
634
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
635 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
636
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
637 && (same as &), ||, |
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
638
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
639 - INFO tags, FORMAT tags, column names
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
640
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
641 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
642
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
643 INFO/DP or DP
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
644 FORMAT/DV, FMT/DV, or DV
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
645 FILTER, QUAL, ID, REF, ALT[0]
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
646
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
647 - 1 (or 0) to test the presence (or absence) of a flag
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
648
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
649 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
650
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
651 FlagA=1 && FlagB=0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
652
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
653 - "." to test missing values
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
654
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
655 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
656
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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657 DP=".", DP!=".", ALT="."
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
658
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
659 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
660
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
661 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
662
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
663 GT="."
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
664
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
665 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
666
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
667 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
668
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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669 TYPE="indel" | TYPE="snp"
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
670
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
671 - array subscripts, "*" for any field
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
672
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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673 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
674
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
675 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
676 DP4[*] == 0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
677 CSQ[*] ~ "missense_variant.*deleterious"
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
678
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
679 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
680
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
681 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
682
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
683 MAX, MIN, AVG, SUM, STRLEN, ABS
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
684
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
685 - 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
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
686
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
687 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
688
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
689 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
690
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
691 **Notes:**
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
692
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
693 - String comparisons and regular expressions are case-insensitive
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
694 - If the subscript "*" is used in regular expression search, the whole field
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
695 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
696 true for the string vector INFO/STR=AB,CD.
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
697 - Variables and function names are case-insensitive, but not tag names. For
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
698 example, "qual" can be used instead of "QUAL", "strlen()" instead of
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
699 "STRLEN()" , but not "dp" instead of "DP".
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
700
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
701 **Examples:**
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
702
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
703 ::
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
704
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
705 MIN(DV)>5
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
706 MIN(DV/DP)>0.3
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
707 MIN(DP)>10 & MIN(DV)>3
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
708 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
709 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
710 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
711 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
712 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
713 MIN(DP)>35 && AVG(GQ)>50
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
714 ID=@file .. selects lines with ID present in the file
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
715 ID!=@~/file .. skip lines with ID present in the ~/file
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
716 MAF[0]<0.05 .. select rare variants at 5% cutoff
4
5a4073ad1140 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
717 ]]></token>
0
8eb720e59e15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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718 </macros>