annotate macros.xml @ 15:cbe39e530cbf draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
author iuc
date Sat, 23 Jul 2022 13:41:51 +0000
parents dcf130f10ca5
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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="bio_tools">
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4 <xrefs>
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5 <xref type="bio.tools">bcftools</xref>
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6 </xrefs>
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7 </xml>
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8 <xml name="requirements">
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
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11 <requirement type="package" version="1.10">htslib</requirement>
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12 <yield />
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13 </requirements>
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14 </xml>
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15 <xml name="samtools_requirement">
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16 <requirement type="package" version="1.10">samtools</requirement>
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17 </xml>
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18 <xml name="matplotlib_requirement">
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19 <requirement type="package" version="3.4.3">matplotlib</requirement>
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20 </xml>
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21 <xml name="version_command">
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22 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
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23 </xml>
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24
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25 <xml name="citations">
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26 <citations>
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27 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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28 <yield />
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29 </citations>
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30 </xml>
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31 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
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32 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
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33 <token name="@THREADS@">
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34 --threads \${GALAXY_SLOTS:-4}
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35 </token>
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36 <token name="@PREPARE_ENV@">
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37 <![CDATA[
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38 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
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39 ]]>
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40 </token>
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41 <xml name="macro_input">
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42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
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43 </xml>
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44 <token name="@PREPARE_INPUT_FILE@">
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45 <![CDATA[
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46 ## May need to symlink input if there is an associated
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47 #set $input_vcf = 'input.vcf.gz'
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48 #if $input_file.is_of_type('vcf')
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49 bgzip -c '$input_file' > $input_vcf &&
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50 bcftools index $input_vcf &&
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51 #elif $input_file.is_of_type('vcf_bgzip')
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52 ln -s '$input_file' $input_vcf &&
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53 #if $input_file.metadata.tabix_index:
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54 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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55 #else
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56 bcftools index $input_vcf &&
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57 #end if
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58 #elif $input_file.is_of_type('bcf')
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59 #set $input_vcf = 'input.bcf'
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60 ln -s '$input_file' $input_vcf &&
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61 #if $input_file.metadata.bcf_index:
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62 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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63 #else
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64 bcftools index $input_vcf &&
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65 #end if
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66 #end if
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67 ]]>
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68 </token>
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69 <token name="@INPUT_FILE@">
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70 $input_vcf
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71 </token>
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72
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73 <xml name="macro_inputs">
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74 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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75 </xml>
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76 <token name="@PREPARE_INPUT_FILES@">
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77 <![CDATA[
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78 ## May need to symlink input if there is an associated
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79 #set $input_vcfs = []
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80 #set $vcfs_list_file = 'vcfs_list'
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81 #for (i, input_file) in enumerate($input_files):
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82 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
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83 #if $input_file.is_of_type('vcf')
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84 bgzip -c '$input_file' > $input_vcf &&
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85 bcftools index $input_vcf &&
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86 #elif $input_file.is_of_type('vcf_bgzip')
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87 ln -s '$input_file' $input_vcf &&
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88 #if $input_file.metadata.tabix_index:
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89 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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90 #else
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91 bcftools index $input_vcf &&
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92 #end if
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93 #elif $input_file.is_of_type('bcf')
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94 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
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95 ln -s '$input_file' $input_vcf &&
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96 #if $input_file.metadata.bcf_index:
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97 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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98 #else
0
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99 bcftools index $input_vcf &&
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100 #end if
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101 #end if
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102 echo '$input_vcf' >> $vcfs_list_file &&
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103 $input_vcfs.append($input_vcf)
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104 #end for
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105 ]]>
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106 </token>
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107 <token name="@INPUT_FILES@">
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108 #echo ' '.join($input_vcfs)#
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109 </token>
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110 <token name="@INPUT_LIST_FILE@">
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111 $vcfs_list_file
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112 </token>
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113
8
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114 <xml name="test_using_reference" token_select_from="history" token_ref="">
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115 <conditional name="reference_source">
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116 <param name="reference_source_selector" value="@SELECT_FROM@" />
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117 <param name="fasta_ref" ftype="fasta" value="@REF@" />
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118 </conditional>
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119 </xml>
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120
0
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121 <xml name="macro_fasta_ref">
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122 <conditional name="reference_source">
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123 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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124 <option value="cached">Use a built-in genome</option>
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125 <option value="history">Use a genome from the history</option>
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126 </param>
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127 <when value="cached">
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128 <param name="fasta_ref" type="select" label="Reference genome">
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129 <options from_data_table="fasta_indexes">
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130 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_file" />
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131 <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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132 </options>
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133 </param>
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134 </when>
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135 <when value="history">
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136 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
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137 </when>
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138 </conditional>
0
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139 </xml>
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140 <token name="@PREPARE_FASTA_REF@">
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141 <![CDATA[
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142 #set $input_fa_ref = None
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143 #if 'fasta_ref' in $section and $section.fasta_ref:
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144 #if 'reference_source_selector' in $section:
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145 #if str($section.reference_source_selector) == "history":
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146 #set $input_fa_ref = 'ref.fa'
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147 ln -s '$section.fasta_ref' $input_fa_ref &&
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148 samtools faidx $input_fa_ref &&
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149 #else:
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150 #set $input_fa_ref = str($section.fasta_ref.fields.path)
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151 #end if
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152 #end if
0
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153 #end if
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154 ]]>
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155 </token>
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156 <token name="@FASTA_REF@">
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157 #if $input_fa_ref is not None:
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158 --fasta-ref $input_fa_ref
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159 #elif 'fasta_ref' in $section and $section.fasta_ref:
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160 --fasta-ref '${section.fasta_ref}'
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161 #end if
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162 </token>
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163
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164 <xml name="macro_AF_file">
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165 <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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166 </xml>
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167 <!-- This may need to bgzip and tabix the file -->
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168 <token name="@PREPARE_AF_FILE@">
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169 <![CDATA[
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170 #if 'AF_file' in $section and $section.AF_file:
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171 #pass
0
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172 #end if
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173 ]]>
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174 </token>
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175 <token name="@AF_FILE@">
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176 #if 'AF_file' in $section and $section.AF_file:
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177 --AF-file '${section.AF_file}'
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178 #end if
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179 </token>
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180
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181 <xml name="macro_estimate_AF">
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182 <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;" />
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183 </xml>
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184 <token name="@ESTIMATE_AF@">
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185 #if 'estimate_AF' in $section and $section.estimate_AF:
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186 --estimate-AF "${section.estimate_AF}"
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187 #end if
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188 </token>
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189
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190 <xml name="macro_exons_file">
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191 <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
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192 </xml>
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193 <token name="@PREPARE_EXONS_FILE@">
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194 <![CDATA[
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195 #set $exons_path = None
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196 #if 'exons_file' in $section and $section.exons_file:
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197 #set $exons_path = 'exons_file.tab.gz'
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198 bgzip -c "$section.exons_file" > $exons_path &&
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199 tabix -s 1 -b 2 -e 3 $exons_path &&
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200 #end if
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201 ]]>
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202 </token>
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203 <token name="@EXONS_FILE@">
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204 #if 'exons_file' in $section and $section.exons_file:
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205 --exons $exons_path
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206 #end if
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207 </token>
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208
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209 <xml name="macro_ploidy_file">
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210 <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
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211 </xml>
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212 <token name="@PLOIDY_FILE@">
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213 #if 'ploidy_file' in $section and $section.ploidy_file:
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214 --ploidy "${section.ploidy_file}"
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215 #end if
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216 </token>
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217
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218 <xml name="macro_collapse_opt_none">
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219 <option value="none">none - require the exact same set of alleles in all files</option>
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220 </xml>
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221 <xml name="macro_collapse_opt_id">
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222 <option value="id">id - only records with identical ID column are compatible. </option>
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223 </xml>
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224 <xml name="macro_collapse">
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225 <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
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226 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
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227 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
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228 <option value="both">both - indels and snps </option>
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229 <option value="some">some - at least some of the ALTs must match</option>
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230 <option value="any">any - any combination of alleles</option>
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231 <yield/>
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232 </param>
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233 </xml>
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234 <token name="@COLLAPSE@">
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235 #if $section.collapse:
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236 --collapse ${section.collapse}
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237 #end if
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238 </token>
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239
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240 <xml name="macro_apply_filters">
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241 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
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242 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
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243 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
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244 </param>
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245 </xml>
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246 <token name="@APPLY_FILTERS@">
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247 #if $section.apply_filters:
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248 --apply-filters '${section.apply_filters}'
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249 #end if
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250 </token>
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251
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252 <xml name="macro_select_output_type">
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253 <param name="output_type" type="select">
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254 <option value="b">compressed BCF</option>
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255 <!-- no galaxy datatypes for these
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256 <option value="u">uncompressed BCF</option>
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257 <option value="z">compressed VCF</option>
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258 -->
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259 <option value="v">uncompressed VCF</option>
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260 </param>
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261 </xml>
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262 <token name="@OUTPUT_TYPE@">
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263 #if str($output_type) != "__none__":
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264 --output-type '${output_type}'
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265 #end if
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266 </token>
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267
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268 <xml name="macro_vcf_output">
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269 <data name="output_file" format="vcf">
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270 <change_format>
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271 <when input="output_type" value="b" format="bcf" />
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272 <when input="output_type" value="u" format="bcf" />
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273 <when input="output_type" value="z" format="vcf_bgzip" />
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274 <when input="output_type" value="v" format="vcf" />
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275 </change_format>
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276 </data>
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277 </xml>
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278
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279 <xml name="macro_invert_targets">
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280 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
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281 label="Invert Targets"
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282 help="inverts the query/filtering applied by the targets" />
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283 </xml>
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284
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285 <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">
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286 <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">
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287 <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
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288 <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
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289 </param>
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290 <param name="start" type="text" label="@LABEL_TYPE@ start position">
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291 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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292 </param>
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293 <param name="stop" type="text" label="@LABEL_TYPE@ end position">
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294 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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295 </param>
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296 <yield />
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297 </repeat>
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298 </xml>
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299
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300 <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">
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301 <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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302 </xml>
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303
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304 <xml name="macro_restrict" token_type="region" token_label_type="Region" >
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305 <conditional name="@TYPE@s">
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306 <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">
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307 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
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308 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
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309 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
0
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310 </param>
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311 <when value="__none__"/>
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312 <when value="@TYPE@s">
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313 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
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314 <yield />
0
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315 </when>
8
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316 <when value="@TYPE@s_file">
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317 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
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318 <yield />
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319 </when>
0
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320 </conditional>
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321 </xml>
8
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322
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323 <token name="@PARSE_INTERVALS@">
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324 <![CDATA[
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325 #set $components = []
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326 #for $i in $intervals:
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327 #set $chrom = str($i.chrom).strip()
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328 #set $start = str($i.start).strip()
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329 #set $stop = str($i.stop).strip()
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330 #if $start or $stop:
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331 $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
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332 #else:
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333 $components.append($chrom)
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334 #end if
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335 #end for
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336 #set $intervals_spec = ','.join($components)
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337 ]]>
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338 </token>
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339
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340 <token name="@REGIONS@">
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341 <![CDATA[
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342 #if $section.regions.regions_src == 'regions':
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343 #set $intervals = $section.regions.regions
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344 @PARSE_INTERVALS@
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345 --regions '$intervals_spec'
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346 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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347 #if $regions_path is not None:
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348 --regions-file '$regions_path'
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349 #else:
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350 --regions-file '$section.regions.regions_file'
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351 #end if
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352 #end if
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353 ]]>
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354 </token>
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355
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356 <token name="@TARGETS@">
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357 <![CDATA[
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358 #if $targets_path:
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359 --targets-file "${section.targets.invert_targets_file}${targets_path}"
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360 #elif $section.targets.targets_src == 'targets':
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361 #set $intervals = $section.targets.targets
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362 @PARSE_INTERVALS@
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363 --targets '${section.targets.invert_targets_file}$intervals_spec'
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364 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
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365 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
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366 #end if
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367 ]]>
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368 </token>
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369
5
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370 <token name="@PREPARE_REGIONS_FILE@">
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371 <![CDATA[
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372 #set $regions_path = None
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373 #if 'regions' in $section
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374 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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375 #if $section.regions.regions_file.ext.startswith('bed'):
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376 #set $regions_path = 'regions_file.bed'
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377 ln -s '$section.regions.regions_file' $regions_path &&
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378 #end if
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379 #end if
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380 #end if
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381 ]]>
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382 </token>
8
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383
0
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384 <token name="@PREPARE_TARGETS_FILE@">
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385 <![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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386 #set $targets_path = None
3
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387 #if 'targets' in $section
0
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388 #if $section.targets.targets_src == 'targets_file':
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389 #set $targets_path = 'targets_file.tab.gz'
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390 bgzip -c "$section.targets.targets_file" > $targets_path &&
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391 tabix -s 1 -b 2 -e 2 $targets_path &&
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392 #end if
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393 #elif $tgts_sec.targets_file:
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394 #set $targets_path = 'targets_file.tab.gz'
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395 bgzip -c "$section.targets_file" > $targets_path &&
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396 tabix -s 1 -b 2 -e 2 $targets_path &&
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397 #end if
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398 ]]>
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399 </token>
8
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400
0
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401 <token name="@TARGETS_FILE@">
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402 <![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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403 #if $targets_path is not None:
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404 --targets-file "${section.invert_targets_file}${targets_path}"
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405 #elif $section.targets_file:
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406 --targets-file "${section.invert_targets_file}${section.targets_file}"
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407 #end if
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408 ]]>
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409 </token>
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410
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411 <xml name="macro_samples">
7
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412 <param argument="--samples" type="text" value="" optional="true" label="Samples"
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413 help="Comma separated list of samples to annotate (or exclude)">
0
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414 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
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415 </param>
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416 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
7
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417 help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
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418 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
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419 help="File of samples to include" />
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420 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
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diff changeset
421 help="inverts the query/filtering applied by Samples file" />
0
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422 </xml>
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423 <token name="@SAMPLES@">
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424 #set $samples_defined = False
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425 #if str($section.samples) != '':
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426 #set $samples_defined = True
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427 --samples '${section.invert_samples}${section.samples}'
0
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428 #end if
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429 #if $section.samples_file:
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430 #set $samples_defined = True
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431 --samples-file "${section.invert_samples_file}${section.samples_file}"
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432 #end if
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433 </token>
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434
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435 <xml name="macro_sample">
7
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diff changeset
436 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
0
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437 </xml>
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438 <token name="@SAMPLE@">
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439 #if $section.sample:
4
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440 --sample '${section.sample}'
0
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441 #end if
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442 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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443
12
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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diff changeset
444 <xml name="macro_include_exclude_validate_sanitize">
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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445 <validator type="expression" message="Single quote or trailing backslash not allowed">"'" not in value and value[-1] != "\\"</validator>
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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446 <sanitizer>
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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447 <valid initial="string.ascii_letters,string.digits,string.whitespace,string.punctuation">
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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diff changeset
448 <remove value="@" />
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
449 <remove value="'" />
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
450 </valid>
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
451 </sanitizer>
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
452 </xml>
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
453
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
454 <xml name="macro_include">
7
6f8e223f78f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
455 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
12
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
456 <expand macro="macro_include_exclude_validate_sanitize" />
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
457 </param>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
458 </xml>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
459 <token name="@INCLUDE@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
460 #if $section.include:
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
461 --include '${section.include}'
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
462 #end if
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
463 </token>
12
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
464
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
465 <xml name="macro_exclude">
7
6f8e223f78f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
466 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
12
776ad0b21536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 11
diff changeset
467 <expand macro="macro_include_exclude_validate_sanitize" />
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
468 </param>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
469 </xml>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
470 <token name="@EXCLUDE@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
471 #if $section.exclude:
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
472 --exclude '${section.exclude}'
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
473 #end if
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
474 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
475
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
476 <xml name="macro_columns">
7
6f8e223f78f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
477 <param name="columns" type="text" value="" optional="true" label="Columns"
6f8e223f78f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
478 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
479 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
480 </param>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
481 </xml>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
482 <token name="@COLUMNS@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
483 #if $section.columns != '':
4
c6071203aaa0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
484 --columns '${section.columns}'
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
485 #end if
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
486 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
487
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
488 <xml name="macro_haploid2diploid">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
489 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
490 </xml>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
491
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
492 <xml name="macro_vcf_ids">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
493 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
494 </xml>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
495 <token name="@VCF_IDS@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
496 ${section.vcf_ids}
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
497 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
498
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
499 <token name="@OUTPUT_HELP@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
500 <![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
501 Output Type
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
502 -----------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
503
3
35f66846632e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents: 2
diff changeset
504 Output compressed BCF (b), or uncompressed VCF (v).
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
505 Use the BCF option when piping between bcftools subcommands to speed up
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
506 performance by removing unecessary compression/decompression
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
507 and VCF<->BCF conversion.
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
508
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
509 This Galaxy tool recommends using the compressed BCF format
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
510 as piping is not implemented, and uncompressed data would
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
511 use unnecessary amounts of space.
4
c6071203aaa0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
512 ]]></token>
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
513 <token name="@REGIONS_HELP@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
514 <![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
515 Region Selections
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
516 -----------------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
517
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
518 Regions can be specified in a VCF,
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
519 BED, or tab-delimited file (the default). The columns of the
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
520 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
521 where positions are 1-based and inclusive. Uncompressed
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
522 files are stored in memory, while bgzip-compressed and
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
523 tabix-indexed region files are streamed. Note that sequence
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
524 names must match exactly, "chr20" is not the same as "20".
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
525 Also note that chromosome ordering in FILE will be
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
526 respected, the VCF will be processed in the order in which
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
527 chromosomes first appear in FILE. However, within
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
528 chromosomes, the VCF will always be processed in ascending
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
529 genomic coordinate order no matter what order they appear in
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
530 FILE. Note that overlapping regions in FILE can result in
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
531 duplicated out of order positions in the output. This option
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
532 requires indexed VCF/BCF files.
4
c6071203aaa0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
533 ]]></token>
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
534 <token name="@TARGETS_HELP@"><![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
535 Targets
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
536 -------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
537
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
538 Similar to regions, but the next position is accessed by streaming the whole
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
539 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
540 applied simultaneously: regions uses the index to jump to a region and targets discards
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
541 positions which are not in the targets. Unlike regions, targets can be prefixed with
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
542 "^" to request logical complement. For example, "^X,Y,MT" indicates that
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
543 sequences X, Y and MT should be skipped. Yet another difference between the two
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
544 is that regions checks both start and end positions of indels, whereas targets checks
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
545 start positions only.
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
546
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
547 For the bcftools call command, with the option -C alleles, third column of the
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
548 targets file must be comma-separated list of alleles, starting with the
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
549 reference allele. Note that the file must be compressed and index. Such a file
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
550 can be easily created from a VCF using::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
551
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
552 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
553 ]]>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
554 <!-- TODO: galaxy-ify -->
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
555 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
556
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
557
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
558 <token name="@COLLAPSE_HELP@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
559 Collapse
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
560 --------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
561
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
562 Controls how to treat records with duplicate positions and defines compatible
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
563 records across multiple input files. Here by "compatible" we mean records which
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
564 should be considered as identical by the tools. For example, when performing
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
565 line intersections, the desire may be to consider as identical all sites with
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
566 matching positions (bcftools isec -c all), or only sites with matching variant
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
567 type (bcftools isec -c snps -c indels), or only sites with all alleles
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
568 identical (bcftools isec -c none).
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
569
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
570
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
571 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
572 | Flag value | Result |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
573 +============+================================================================+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
574 | none | only records with identical REF and ALT alleles are compatible |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
575 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
576 | some | only records where some subset of ALT alleles match are |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
577 | | compatible |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
578 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
579 | all | all records are compatible, regardless of whether the ALT |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
580 | | alleles match or not. In the case of records with the same |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
581 | | position, only the first wil lbe considered and appear on |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
582 | | output. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
583 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
584 | snps | any SNP records are compatible, regardless of whether the ALT |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
585 | | alleles match or not. For duplicate positions, only the first |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
586 | | SNP record will be considered and appear on output. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
587 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
588 | indels | all indel records are compatible, regardless of whether the |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
589 | | REF and ALT alleles match or not. For duplicate positions, |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
590 | | only the first indel record will be considered and appear on |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
591 | | output. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
592 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
593 | both | abbreviation of "-c indels -c snps" |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
594 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
595 | id | only records with identical ID column are compatible. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
596 | | Supportedby bcftools merge only. |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
597 +------------+----------------------------------------------------------------+
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
598 </token>
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
599
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
600 <token name="@EXPRESSIONS_HELP@">
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
601 <![CDATA[
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
602 Expressions
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
603 -----------
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
604
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
605 Valid expressions may contain:
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
606
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
607 - numerical constants, string constants
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
608
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
609 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
610
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
611 1, 1.0, 1e-4
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
612 "String"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
613
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
614 - arithmetic operators
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
615
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
616 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
617
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
618 +,*,-,/
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
619
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
620 - comparison operators
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
621
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
622 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
623
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
624 == (same as =), >, >=, <=, <, !=
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
625
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
626 - regex operators "~" and its negation "!~"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
627
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
628 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
629
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
630 INFO/HAYSTACK ~ "needle"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
631
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
632 - parentheses
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
633
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
634 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
635
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
636 (, )
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
637
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
638 - logical operators
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
639
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
640 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
641
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
642 && (same as &), ||, |
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
643
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
644 - INFO tags, FORMAT tags, column names
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
645
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
646 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
647
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
648 INFO/DP or DP
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
649 FORMAT/DV, FMT/DV, or DV
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
650 FILTER, QUAL, ID, REF, ALT[0]
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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651
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
652 - 1 (or 0) to test the presence (or absence) of a flag
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
653
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
654 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
655
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
656 FlagA=1 && FlagB=0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
657
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
658 - "." to test missing values
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
659
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
660 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
661
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
662 DP=".", DP!=".", ALT="."
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
663
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
664 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
665
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
666 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
667
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
668 GT="."
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
669
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
670 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
671
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
672 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
673
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
674 TYPE="indel" | TYPE="snp"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
675
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
676 - array subscripts, "*" for any field
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
677
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
678 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
679
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
680 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
681 DP4[*] == 0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
682 CSQ[*] ~ "missense_variant.*deleterious"
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
683
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
684 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
685
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
686 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
687
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
688 MAX, MIN, AVG, SUM, STRLEN, ABS
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
689
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
690 - variables calculated on the fly if not present: number of alternate alleles; number of samples; count of alternate alleles; minor allele count (similar to AC but is always smaller than 0.5); frequency of alternate alleles (AF=AC/AN); frequency of minor alleles (MAF=MAC/AN); number of alleles in called genotypes
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
691
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
692 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
693
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
694 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
695
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
696 **Notes:**
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
697
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
698 - String comparisons and regular expressions are case-insensitive
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
699 - If the subscript "*" is used in regular expression search, the whole field
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
700 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
701 true for the string vector INFO/STR=AB,CD.
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
702 - Variables and function names are case-insensitive, but not tag names. For
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
703 example, "qual" can be used instead of "QUAL", "strlen()" instead of
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
704 "STRLEN()" , but not "dp" instead of "DP".
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
705
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
706 **Examples:**
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
707
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
708 ::
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
709
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
710 MIN(DV)>5
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
711 MIN(DV/DP)>0.3
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
712 MIN(DP)>10 & MIN(DV)>3
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
713 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
714 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
715 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
716 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
717 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
718 MIN(DP)>35 && AVG(GQ)>50
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
719 ID=@file .. selects lines with ID present in the file
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
720 ID!=@~/file .. skip lines with ID present in the ~/file
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
721 MAF[0]<0.05 .. select rare variants at 5% cutoff
4
c6071203aaa0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 3
diff changeset
722 ]]></token>
0
981086ab0e3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
723 </macros>