Mercurial > repos > iuc > bcftools_call

annotate macros.xml @ 23:07396b423218 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author iuc
date Sun, 18 Aug 2024 10:21:29 +0000
parents 1001172b5089
children
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a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.15.1</token>
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3 <token name="@VERSION_SUFFIX@">4</token>
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4 <token name="@PROFILE@">20.01</token>
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5 <xml name="bio_tools">
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6 <xrefs>
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7 <xref type="bio.tools">bcftools</xref>
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8 </xrefs>
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9 </xml>
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
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13 <requirement type="package" version="1.15.1">htslib</requirement>
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14 <yield />
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15 </requirements>
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16 </xml>
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17 <xml name="samtools_requirement">
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18 <requirement type="package" version="1.15.1">samtools</requirement>
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19 </xml>
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20 <xml name="matplotlib_requirement">
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21 <requirement type="package" version="3.5.3">matplotlib</requirement>
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22 </xml>
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23 <xml name="version_command">
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24 <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
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25 </xml>
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26
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27 <xml name="citations">
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28 <citations>
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29 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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30 <yield />
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31 </citations>
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32 </xml>
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33 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
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34 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
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35 <token name="@THREADS@">
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36 --threads \${GALAXY_SLOTS:-4}
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37 </token>
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38 <token name="@PREPARE_ENV@">
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39 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
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41 ]]>
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42 </token>
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43 <xml name="macro_input">
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44 <!--
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45 REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
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46 <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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47 -->
8
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48 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
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49 </xml>
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50 <token name="@PREPARE_INPUT_FILE@">
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51 <![CDATA[
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52 ## May need to symlink input if there is an associated
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53 #set $input_vcf = 'input.vcf.gz'
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54 #if $input_file.is_of_type('vcf')
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55 bgzip -c '$input_file' > $input_vcf &&
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56 bcftools index $input_vcf &&
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57 ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
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58 #elif $input_file.is_of_type('vcf_bgzip')
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59 ln -s '$input_file' $input_vcf &&
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60 #if $input_file.metadata.tabix_index:
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61 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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62 #else
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63 bcftools index $input_vcf &&
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64 #end if
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65 #elif $input_file.is_of_type('bcf')
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66 #set $input_vcf = 'input.bcf'
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67 ln -s '$input_file' $input_vcf &&
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68 #if $input_file.metadata.bcf_index:
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69 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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70 #else
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71 bcftools index $input_vcf &&
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72 #end if
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73 #end if
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74 ]]>
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75 </token>
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76 <token name="@INPUT_FILE@">
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77 $input_vcf
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78 </token>
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79
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80 <xml name="macro_inputs">
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81 <!--
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82 REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
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83 <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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84 -->
8
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85 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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86 </xml>
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87 <token name="@PREPARE_INPUT_FILES@">
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88 <![CDATA[
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89 ## May need to symlink input if there is an associated
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90 #set $input_vcfs = []
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91 #set $vcfs_list_file = 'vcfs_list'
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92 #for (i, input_file) in enumerate($input_files):
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93 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
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94 #if $input_file.is_of_type('vcf')
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95 bgzip -c '$input_file' > $input_vcf &&
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96 bcftools index $input_vcf &&
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97 ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
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98 #elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
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99 ln -s '$input_file' $input_vcf &&
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100 #if $input_file.metadata.tabix_index:
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101 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
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102 #else
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103 bcftools index $input_vcf &&
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104 #end if
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105 #elif $input_file.is_of_type('bcf')
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106 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
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107 ln -s '$input_file' $input_vcf &&
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108 #if $input_file.metadata.bcf_index:
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109 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
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110 #else
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111 bcftools index $input_vcf &&
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112 #end if
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113 #end if
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114 echo '$input_vcf' >> $vcfs_list_file &&
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115 $input_vcfs.append($input_vcf)
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116 #end for
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117 ]]>
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118 </token>
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119 <token name="@INPUT_FILES@">
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120 #echo ' '.join($input_vcfs)#
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121 </token>
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122 <token name="@INPUT_LIST_FILE@">
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123 $vcfs_list_file
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124 </token>
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125
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126 <xml name="test_using_reference" token_select_from="history" token_ref="">
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127 <conditional name="reference_source">
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128 <param name="reference_source_selector" value="@SELECT_FROM@" />
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129 <param name="fasta_ref" ftype="fasta" value="@REF@" />
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130 </conditional>
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131 </xml>
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132
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133 <xml name="macro_fasta_ref">
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134 <conditional name="reference_source">
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135 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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136 <option value="cached">Use a built-in genome</option>
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137 <option value="history">Use a genome from the history</option>
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138 </param>
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139 <when value="cached">
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140 <param name="fasta_ref" type="select" label="Reference genome">
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141 <options from_data_table="fasta_indexes">
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142 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_file" />
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143 <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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144 </options>
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145 </param>
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146 </when>
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147 <when value="history">
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148 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
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149 </when>
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150 </conditional>
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151 </xml>
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152 <token name="@PREPARE_FASTA_REF@">
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153 <![CDATA[
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154 #set $input_fa_ref = None
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155 #if 'fasta_ref' in $section and $section.fasta_ref:
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156 #if 'reference_source_selector' in $section:
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157 #if str($section.reference_source_selector) == "history":
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158 #set $input_fa_ref = 'ref.fa'
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159 ln -s '$section.fasta_ref' $input_fa_ref &&
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160 samtools faidx $input_fa_ref &&
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161 #else:
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162 #set $input_fa_ref = str($section.fasta_ref.fields.path)
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163 #end if
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164 #end if
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165 #end if
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166 ]]>
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167 </token>
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168 <token name="@FASTA_REF@">
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169 #if $input_fa_ref is not None:
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170 --fasta-ref $input_fa_ref
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171 #elif 'fasta_ref' in $section and $section.fasta_ref:
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172 --fasta-ref '${section.fasta_ref}'
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173 #end if
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174 </token>
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175
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176 <xml name="macro_AF_file">
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177 <param argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
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178 </xml>
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179 <!-- This may need to bgzip and tabix the file -->
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180 <token name="@PREPARE_AF_FILE@">
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181 <![CDATA[
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182 #if 'AF_file' in $section and $section.AF_file:
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183 #pass
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184 #end if
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185 ]]>
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186 </token>
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187 <token name="@AF_FILE@">
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188 #if 'AF_file' in $section and $section.AF_file:
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189 --AF-file '${section.AF_file}'
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190 #end if
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191 </token>
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192
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193 <xml name="macro_estimate_AF">
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194 <param argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
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195 </xml>
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196 <token name="@ESTIMATE_AF@">
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197 #if 'estimate_AF' in $section and $section.estimate_AF:
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198 --estimate-AF "${section.estimate_AF}"
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199 #end if
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200 </token>
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201
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202 <xml name="macro_exons_file">
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203 <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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204 </xml>
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205 <token name="@PREPARE_EXONS_FILE@">
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206 <![CDATA[
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207 #set $exons_path = None
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208 #if 'exons_file' in $section and $section.exons_file:
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209 #set $exons_path = 'exons_file.tab.gz'
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210 bgzip -c "$section.exons_file" > $exons_path &&
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211 tabix -s 1 -b 2 -e 3 $exons_path &&
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212 #end if
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213 ]]>
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214 </token>
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215 <token name="@EXONS_FILE@">
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216 #if 'exons_file' in $section and $section.exons_file:
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217 --exons $exons_path
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218 #end if
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219 </token>
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220
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221 <xml name="macro_ploidy_file">
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222 <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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223 </xml>
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224 <token name="@PLOIDY_FILE@">
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225 #if 'ploidy_file' in $section and $section.ploidy_file:
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226 --ploidy "${section.ploidy_file}"
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227 #end if
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228 </token>
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229
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230 <xml name="macro_collapse_opt_none">
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231 <option value="none">none - require the exact same set of alleles in all files</option>
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232 </xml>
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233 <xml name="macro_collapse_opt_id">
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234 <option value="id">id - only records with identical ID column are compatible. </option>
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235 </xml>
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236 <xml name="macro_collapse">
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237 <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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238 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
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239 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
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240 <option value="both">both - indels and snps </option>
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241 <option value="some">some - at least some of the ALTs must match</option>
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242 <option value="any">any - any combination of alleles</option>
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243 <yield/>
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244 </param>
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245 </xml>
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246 <token name="@COLLAPSE@">
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247 #if $section.collapse:
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248 --collapse ${section.collapse}
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249 #end if
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250 </token>
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251
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252 <xml name="macro_apply_filters">
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253 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
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254 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
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255 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
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256 </param>
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257 </xml>
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258 <token name="@APPLY_FILTERS@">
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259 #if $section.apply_filters:
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260 --apply-filters '${section.apply_filters}'
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261 #end if
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262 </token>
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263
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264 <xml name="macro_select_output_type">
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265 <param name="output_type" type="select">
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266 <option value="b">compressed BCF</option>
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267 <!-- no galaxy datatypes for these
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268 <option value="u">uncompressed BCF</option>
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269 <option value="z">compressed VCF</option>
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270 -->
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271 <option value="v">uncompressed VCF</option>
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272 </param>
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273 </xml>
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274 <token name="@OUTPUT_TYPE@">
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275 #if str($output_type) != "__none__":
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276 --output-type '${output_type}'
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277 #end if
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278 </token>
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279
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280 <xml name="macro_vcf_output">
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281 <data name="output_file" format="vcf">
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282 <change_format>
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283 <when input="output_type" value="b" format="bcf" />
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284 <when input="output_type" value="u" format="bcf" />
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285 <when input="output_type" value="z" format="vcf_bgzip" />
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286 <when input="output_type" value="v" format="vcf" />
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287 </change_format>
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288 </data>
0
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289 </xml>
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290
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291 <xml name="macro_invert_targets">
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292 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
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293 label="Invert Targets"
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294 help="inverts the query/filtering applied by the targets" />
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295 </xml>
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296
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297 <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">
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298 <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">
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299 <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
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300 <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
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301 </param>
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302 <param name="start" type="text" label="@LABEL_TYPE@ start position">
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303 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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304 </param>
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305 <param name="stop" type="text" label="@LABEL_TYPE@ end position">
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306 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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307 </param>
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308 <yield />
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309 </repeat>
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310 </xml>
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311
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312 <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">
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313 <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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314 </xml>
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315
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316 <xml name="macro_restrict" token_type="region" token_label_type="Region" >
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317 <conditional name="@TYPE@s">
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318 <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">
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319 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
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320 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
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321 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
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322 </param>
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323 <when value="__none__"/>
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324 <when value="@TYPE@s">
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325 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
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326 <yield />
1
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327 </when>
9
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328 <when value="@TYPE@s_file">
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329 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
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330 <yield />
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331 </when>
1
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332 </conditional>
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333 <param argument="--@TYPE@s-overlap" type="select" optional="true" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)">
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334 <option value="0">0: POS in the region</option>
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335 <option value="1">1: Record overlaps</option>
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336 <option value="2">2: Variant overlaps</option>
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337 </param>
1
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338 </xml>
9
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339
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340 <token name="@PARSE_INTERVALS@">
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341 <![CDATA[
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342 #set $components = []
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343 #for $i in $intervals:
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344 #set $chrom = str($i.chrom).strip()
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345 #set $start = str($i.start).strip()
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346 #set $stop = str($i.stop).strip()
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347 #if $start or $stop:
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348 $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
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349 #else:
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350 $components.append($chrom)
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351 #end if
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352 #end for
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353 #set $intervals_spec = ','.join($components)
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354 ]]>
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355 </token>
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356
17
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357 <token name="@MASK@">
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358 <![CDATA[
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359 #if $section.conditional_soft_filter.selector == 'enabled' and $section.conditional_soft_filter.soft_filter
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diff changeset
360 #if $section.conditional_soft_filter.masks.masks_src == 'regions':
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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diff changeset
361 #set $intervals = $section.conditional_soft_filter.masks.masks
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
362 @PARSE_INTERVALS@
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iuc
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diff changeset
363 --mask '$intervals_spec'
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
364 #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file' and $section.conditional_soft_filter.masks.masks_file:
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
365 #if $masks_path is not None:
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
366 --mask-file '$masks_path'
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
367 #else:
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
368 --mask-file '$section.conditional_soft_filter.masks.masks_file'
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
369 #end if
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
370 #end if
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
371 #if $section.conditional_soft_filter.masks_overlap
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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diff changeset
372 --mask-overlap $section.conditional_soft_filter.masks_overlap
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
373 #end if
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
374 #end if
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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parents: 14
diff changeset
375
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
376 ]]>
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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377 </token>
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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378
9
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
379 <token name="@REGIONS@">
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
380 <![CDATA[
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
381 #if $section.regions.regions_src == 'regions':
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
382 #set $intervals = $section.regions.regions
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
383 @PARSE_INTERVALS@
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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384 --regions '$intervals_spec'
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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diff changeset
385 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
386 #if $regions_path is not None:
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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387 --regions-file '$regions_path'
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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diff changeset
388 #else:
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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389 --regions-file '$section.regions.regions_file'
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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diff changeset
390 #end if
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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diff changeset
391 #end if
17
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parents: 14
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392 #if $section.regions_overlap
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iuc
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393 --regions-overlap $section.regions_overlap
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
394 #end if
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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395
9
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
396 ]]>
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
397 </token>
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
398
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
399 <token name="@TARGETS@">
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
400 <![CDATA[
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
401 #if $targets_path:
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
402 --targets-file "${section.targets.invert_targets_file}${targets_path}"
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
403 #elif $section.targets.targets_src == 'targets':
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
404 #set $intervals = $section.targets.targets
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
405 @PARSE_INTERVALS@
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
406 --targets '${section.targets.invert_targets_file}$intervals_spec'
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
407 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
408 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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409 #end if
17
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iuc
parents: 14
diff changeset
410 #if $section.targets_overlap
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iuc
parents: 14
diff changeset
411 --targets-overlap $section.targets_overlap
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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diff changeset
412 #end if
9
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
413 ]]>
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
414 </token>
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
415
6
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 5
diff changeset
416 <token name="@PREPARE_REGIONS_FILE@">
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 5
diff changeset
417 <![CDATA[
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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diff changeset
418 #set $regions_path = None
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iuc
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419 #if 'regions' in $section
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 5
diff changeset
420 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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diff changeset
421 #if $section.regions.regions_file.ext.startswith('bed'):
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 5
diff changeset
422 #set $regions_path = 'regions_file.bed'
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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423 ln -s '$section.regions.regions_file' $regions_path &&
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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parents: 5
diff changeset
424 #end if
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iuc
parents: 5
diff changeset
425 #end if
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 5
diff changeset
426 #end if
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 5
diff changeset
427 ]]>
3296c3680d96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 5
diff changeset
428 </token>
9
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
429
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
430 <token name="@PREPARE_TARGETS_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
431 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
432 #set $targets_path = None
4
6d2a5f0859cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
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parents: 3
diff changeset
433 #if 'targets' in $section
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
434 #if $section.targets.targets_src == 'targets_file':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
435 #set $targets_path = 'targets_file.tab.gz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
436 bgzip -c "$section.targets.targets_file" > $targets_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
437 tabix -s 1 -b 2 -e 2 $targets_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
438 #end if
23
07396b423218 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
iuc
parents: 21
diff changeset
439 #elif $section.targets_file:
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
440 #set $targets_path = 'targets_file.tab.gz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
441 bgzip -c "$section.targets_file" > $targets_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
442 tabix -s 1 -b 2 -e 2 $targets_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
443 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
444 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
445 </token>
9
cb30a39055d0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
446
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
447 <token name="@TARGETS_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
448 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
449 #if $targets_path is not None:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
450 --targets-file "${section.invert_targets_file}${targets_path}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
451 #elif $section.targets_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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452 --targets-file "${section.invert_targets_file}${section.targets_file}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
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453 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
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454 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
455 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
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456
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
457 <xml name="macro_samples">
8
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458 <param argument="--samples" type="text" value="" optional="true" label="Samples"
17
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parents: 14
diff changeset
459 help="Comma-separated list of samples to annotate (or exclude) or - to include all samples">
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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parents: 14
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460 <validator type="regex" message="Comma-separated list of samples or - to include all samples">^(-|\w+(,\w+)*)?$</validator>
1
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parents: 0
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461 </param>
4
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parents: 3
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462 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
8
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iuc
parents: 7
diff changeset
463 help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
0fba2c15b40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
464 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
0fba2c15b40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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parents: 7
diff changeset
465 help="File of samples to include" />
0fba2c15b40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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parents: 7
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466 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
0fba2c15b40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
467 help="inverts the query/filtering applied by Samples file" />
0
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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parents:
diff changeset
468 </xml>
1
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iuc
parents: 0
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469 <token name="@SAMPLES@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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470 #set $samples_defined = False
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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471 #if str($section.samples) != '':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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472 #set $samples_defined = True
5
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parents: 4
diff changeset
473 --samples '${section.invert_samples}${section.samples}'
1
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iuc
parents: 0
diff changeset
474 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
475 #if $section.samples_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
476 #set $samples_defined = True
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
477 --samples-file "${section.invert_samples_file}${section.samples_file}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
478 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
479 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
480
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
481 <xml name="macro_sample">
8
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parents: 7
diff changeset
482 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
1
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parents: 0
diff changeset
483 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
484 <token name="@SAMPLE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
485 #if $section.sample:
5
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parents: 4
diff changeset
486 --sample '${section.sample}'
1
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iuc
parents: 0
diff changeset
487 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
488 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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489
13
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iuc
parents: 12
diff changeset
490 <xml name="macro_include_exclude_validate_sanitize">
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
491 <validator type="expression" message="Single quote or trailing backslash not allowed">"'" not in value and value[-1] != "\\"</validator>
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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parents: 12
diff changeset
492 <sanitizer>
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
493 <valid initial="string.ascii_letters,string.digits,string.whitespace,string.punctuation">
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
494 <remove value="@" />
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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parents: 12
diff changeset
495 <remove value="'" />
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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diff changeset
496 </valid>
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
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parents: 12
diff changeset
497 </sanitizer>
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parents: 12
diff changeset
498 </xml>
1
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parents: 0
diff changeset
499
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
500 <xml name="macro_include">
8
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parents: 7
diff changeset
501 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
13
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
502 <expand macro="macro_include_exclude_validate_sanitize" />
1
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iuc
parents: 0
diff changeset
503 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
504 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
505 <token name="@INCLUDE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
506 #if $section.include:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
507 --include '${section.include}'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
508 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
509 </token>
13
072f606e2e69 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents: 12
diff changeset
510
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
511 <xml name="macro_exclude">
8
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parents: 7
diff changeset
512 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
13
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iuc
parents: 12
diff changeset
513 <expand macro="macro_include_exclude_validate_sanitize" />
1
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parents: 0
diff changeset
514 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
515 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
516 <token name="@EXCLUDE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
517 #if $section.exclude:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
518 --exclude '${section.exclude}'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
519 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
520 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
521
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
522 <xml name="macro_columns">
8
0fba2c15b40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
523 <param name="columns" type="text" value="" optional="true" label="Columns"
0fba2c15b40d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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parents: 7
diff changeset
524 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
17
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iuc
parents: 14
diff changeset
525 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
0
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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parents:
diff changeset
526 </param>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents:
diff changeset
527 </xml>
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
528 <token name="@COLUMNS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
529 #if $section.columns != '':
5
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iuc
parents: 4
diff changeset
530 --columns '${section.columns}'
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
531 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
532 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
533
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
534 <xml name="macro_haploid2diploid">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
535 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
536 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
537
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
538 <xml name="macro_vcf_ids">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
539 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
540 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
541 <token name="@VCF_IDS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
542 ${section.vcf_ids}
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
543 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
544
17
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
545 <xml name="macro_output_tags">
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
546 <param name="output_tags" argument="--annotate" type="select" optional="true" multiple="True" display="checkboxes" label="Optional tags to output" help="--annotate">
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
547 <yield />
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
548 </param>
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
549 </xml>
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
550
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
551 <xml name="macro_overlap" token_argument="" token_label="">
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
552 </xml>
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
553
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
554
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
555 <token name="@OUTPUT_HELP@">
17
22637b1a55bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
556
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
557 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
558 Output Type
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
559 -----------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
560
4
6d2a5f0859cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents: 3
diff changeset
561 Output compressed BCF (b), or uncompressed VCF (v).
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
562 Use the BCF option when piping between bcftools subcommands to speed up
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
563 performance by removing unecessary compression/decompression
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
564 and VCF<->BCF conversion.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
565
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
566 This Galaxy tool recommends using the compressed BCF format
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
567 as piping is not implemented, and uncompressed data would
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
568 use unnecessary amounts of space.
5
0a564427739d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 4
diff changeset
569 ]]></token>
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
570 <token name="@REGIONS_HELP@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
571 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
572 Region Selections
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
573 -----------------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
574
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
575 Regions can be specified in a VCF,
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
576 BED, or tab-delimited file (the default). The columns of the
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
577 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
578 where positions are 1-based and inclusive. Uncompressed
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
579 files are stored in memory, while bgzip-compressed and
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
580 tabix-indexed region files are streamed. Note that sequence
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
581 names must match exactly, "chr20" is not the same as "20".
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
582 Also note that chromosome ordering in FILE will be
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
583 respected, the VCF will be processed in the order in which
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
584 chromosomes first appear in FILE. However, within
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
585 chromosomes, the VCF will always be processed in ascending
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
586 genomic coordinate order no matter what order they appear in
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
587 FILE. Note that overlapping regions in FILE can result in
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
588 duplicated out of order positions in the output. This option
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
589 requires indexed VCF/BCF files.
5
0a564427739d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents: 4
diff changeset
590 ]]></token>
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
591 <token name="@TARGETS_HELP@"><![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
592 Targets
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
593 -------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
594
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
595 Similar to regions, but the next position is accessed by streaming the whole
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
596 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
597 applied simultaneously: regions uses the index to jump to a region and targets discards
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
598 positions which are not in the targets. Unlike regions, targets can be prefixed with
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
599 "^" to request logical complement. For example, "^X,Y,MT" indicates that
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
600 sequences X, Y and MT should be skipped. Yet another difference between the two
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
601 is that regions checks both start and end positions of indels, whereas targets checks
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
602 start positions only.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
603
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
604 For the bcftools call command, with the option -C alleles, third column of the
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
605 targets file must be comma-separated list of alleles, starting with the
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
606 reference allele. Note that the file must be compressed and index. Such a file
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
607 can be easily created from a VCF using::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
608
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
609 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
610 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
611 <!-- TODO: galaxy-ify -->
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
612 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
613
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
614
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
615 <token name="@COLLAPSE_HELP@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
616 Collapse
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
617 --------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
618
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
619 Controls how to treat records with duplicate positions and defines compatible
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
620 records across multiple input files. Here by "compatible" we mean records which
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
621 should be considered as identical by the tools. For example, when performing
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
622 line intersections, the desire may be to consider as identical all sites with
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
623 matching positions (bcftools isec -c all), or only sites with matching variant
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
624 type (bcftools isec -c snps -c indels), or only sites with all alleles
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
625 identical (bcftools isec -c none).
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
626
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
627
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
628 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
629 | Flag value | Result |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
630 +============+================================================================+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
631 | none | only records with identical REF and ALT alleles are compatible |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
632 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
633 | some | only records where some subset of ALT alleles match are |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
634 | | compatible |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
635 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
636 | all | all records are compatible, regardless of whether the ALT |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
637 | | alleles match or not. In the case of records with the same |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
638 | | position, only the first wil lbe considered and appear on |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
639 | | output. |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
640 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
641 | snps | any SNP records are compatible, regardless of whether the ALT |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
642 | | alleles match or not. For duplicate positions, only the first |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
643 | | SNP record will be considered and appear on output. |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
644 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
645 | indels | all indel records are compatible, regardless of whether the |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
646 | | REF and ALT alleles match or not. For duplicate positions, |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
647 | | only the first indel record will be considered and appear on |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
648 | | output. |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
649 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
650 | both | abbreviation of "-c indels -c snps" |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
651 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
652 | id | only records with identical ID column are compatible. |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
653 | | Supportedby bcftools merge only. |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
654 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
655 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
656
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
657 <token name="@EXPRESSIONS_HELP@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
658 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
659 Expressions
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
660 -----------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
661
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
662 Valid expressions may contain:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
663
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
664 - numerical constants, string constants
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
665
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
666 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
667
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
668 1, 1.0, 1e-4
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
669 "String"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
670
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
671 - arithmetic operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
672
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
673 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
674
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
675 +,*,-,/
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
676
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
677 - comparison operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
678
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
679 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
680
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
681 == (same as =), >, >=, <=, <, !=
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
682
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
683 - regex operators "~" and its negation "!~"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
684
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
685 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
686
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
687 INFO/HAYSTACK ~ "needle"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
688
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
689 - parentheses
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
690
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
691 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
692
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
693 (, )
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
694
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
695 - logical operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
696
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
697 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
698
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
699 && (same as &), ||, |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
700
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
701 - INFO tags, FORMAT tags, column names
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
702
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
703 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
704
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
705 INFO/DP or DP
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
706 FORMAT/DV, FMT/DV, or DV
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
707 FILTER, QUAL, ID, REF, ALT[0]
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
708
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
709 - 1 (or 0) to test the presence (or absence) of a flag
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
710
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
711 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
712
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
713 FlagA=1 && FlagB=0
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
714
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
715 - "." to test missing values
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
716
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
717 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
718
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
719 DP=".", DP!=".", ALT="."
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
720
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
721 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
722
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
723 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
724
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
725 GT="."
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
726
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
727 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
728
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
729 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
730
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
731 TYPE="indel" | TYPE="snp"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
732
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
733 - array subscripts, "*" for any field
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
734
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
735 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
736
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
737 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
diff changeset
738 DP4[*] == 0
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
739 CSQ[*] ~ "missense_variant.*deleterious"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
740
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
741 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
742
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
743 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
744
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
745 MAX, MIN, AVG, SUM, STRLEN, ABS
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
746
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
747 - 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
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
748
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
749 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
750
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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751 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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752
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
753 **Notes:**
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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754
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
755 - String comparisons and regular expressions are case-insensitive
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
756 - If the subscript "*" is used in regular expression search, the whole field
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
757 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
758 true for the string vector INFO/STR=AB,CD.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
759 - Variables and function names are case-insensitive, but not tag names. For
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
760 example, "qual" can be used instead of "QUAL", "strlen()" instead of
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
761 "STRLEN()" , but not "dp" instead of "DP".
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
762
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
763 **Examples:**
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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764
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
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765 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
766
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
767 MIN(DV)>5
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
768 MIN(DV/DP)>0.3
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
769 MIN(DP)>10 & MIN(DV)>3
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
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770 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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771 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
772 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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773 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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774 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
775 MIN(DP)>35 && AVG(GQ)>50
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
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776 ID=@file .. selects lines with ID present in the file
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
777 ID!=@~/file .. skip lines with ID present in the ~/file
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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parents: 0
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778 MAF[0]<0.05 .. select rare variants at 5% cutoff
5
0a564427739d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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779 ]]></token>
0
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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780 </macros>