Mercurial > repos > iuc > bcftools_call

annotate macros.xml @ 4:6d2a5f0859cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author iuc
date Tue, 31 Jan 2017 12:41:31 -0500
parents 5337db17a5f7
children 0a564427739d
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1
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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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2 <macros>
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3 <token name="@VERSION@">1.3</token>
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4 <xml name="stdio">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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5 <stdio>
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6 <exit_code range="1:" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 <exit_code range=":-1" />
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8 <regex match="Error:" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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9 <regex match="Exception:" />
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10 </stdio>
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11 </xml>
0
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12 <xml name="requirements">
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13 <requirements>
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14 <requirement type="package" version="1.3">bcftools</requirement>
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15 <!-- conda dependency -->
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16 <requirement type="package" version="1.3">htslib</requirement>
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17 <!-- htslib provides tabix and bgzip
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18 <requirement type="package" version="0.2.6">tabix</requirement>
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19 -->
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20 <requirement type="package" version="1.2">samtools</requirement>
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21 </requirements>
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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>
0
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25 </xml>
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26
0
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27 <xml name="citations">
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28 <citations>
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29 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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30 <yield />
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31 </citations>
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32 </xml>
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33 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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}
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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37 </token>
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38 <token name="@PREPARE_ENV@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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,'`;
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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42 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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43 <xml name="macro_input">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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44 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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45 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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46 <token name="@PREPARE_INPUT_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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47 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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48 ## May need to symlink input if there is an associated
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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49 #set $input_vcf = 'input.vcf.gz'
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50 #if $input_file.is_of_type('vcf')
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51 bgzip -c "$input_file" > $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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52 bcftools index $input_vcf &&
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53 #elif $input_file.is_of_type('vcf_bgzip')
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54 ln -s "$input_file" $input_vcf
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55 #elif $input_file.is_of_type('bcf')
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56 #set $input_vcf = 'input.bcf'
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57 ln -s "$input_file" $input_vcf &&
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58 #if $input_file.metadata.bcf_index:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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59 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
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60 #else
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61 bcftools index $input_vcf &&
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62 #end if
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63 #elif $input_file.is_of_type('bcf_bgzip')
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64 ln -s "$input_file" $input_vcf
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65 #end if
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66 ]]>
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67 </token>
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68 <token name="@INPUT_FILE@">
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69 $input_vcf
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70 </token>
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71
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72 <xml name="macro_inputs">
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73 <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />
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74 </xml>
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75 <token name="@PREPARE_INPUT_FILES@">
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76 <![CDATA[
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77 ## May need to symlink input if there is an associated
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78 #set $input_vcfs = []
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79 #set $vcfs_list_file = 'vcfs_list'
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80 #for (i,input_file) in enumerate($input_files):
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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81 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
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82 #if $input_file.is_of_type('vcf')
1
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83 bgzip -c "$input_file" > $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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84 bcftools index $input_vcf &&
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85 #elif $input_file.is_of_type('vcf_bgz')
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86 ln -s "$input_file" $input_vcf
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87 #elif $input_file.is_of_type('bcf')
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88 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
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89 ## bgzip -c "$input_file" > $input_vcf &&
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90 ln -s "$input_file" $input_vcf &&
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91 #if $input_file.metadata.bcf_index:
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92 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
4
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93 #else
1
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94 bcftools index $input_vcf &&
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95 #end if
4
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96 #elif $input_file.is_of_type('bcfvcf_bgz')
1
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97 ln -s "$input_file" $input_vcf &&
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98 #end if
2
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99 echo '$input_vcf' >> $vcfs_list_file &&
1
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100 $input_vcfs.append($input_vcf)
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101 #end for
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102 ]]>
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103 </token>
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104 <token name="@INPUT_FILES@">
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105 #echo ' '.join($input_vcfs)#
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106 </token>
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107 <token name="@INPUT_LIST_FILE@">
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108 $vcfs_list_file
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109 </token>
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110
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111 <xml name="macro_fasta_ref">
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112 <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="reference sequence in fasta format" />
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113 </xml>
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114 <token name="@PREPARE_FASTA_REF@">
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115 <![CDATA[
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116 #set $input_fa_ref = None
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117 #if 'fasta_ref' in $section and $section.fasta_ref:
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118 #set $input_fa_ref = 'ref.fa'
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119 ln -s $section.fasta_ref $input_fa_ref &&
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120 samtools faidx $input_fa_ref &&
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121 #end if
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122 ]]>
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123 </token>
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124 <token name="@FASTA_REF@">
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125 #if $input_fa_ref is not None:
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126 --fasta-ref "$input_fa_ref"
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127 #elif 'fasta_ref' in $section and $section.fasta_ref:
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128 --fasta-ref "${section.fasta_ref}"
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129 #end if
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130 </token>
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131
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132 <xml name="macro_ref_fasta">
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133 <conditional name="reference_source">
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134 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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135 <option value="cached">Locally cached</option>
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136 <option value="history">History</option>
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137 </param>
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138 <when value="cached">
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139 <param name="ref_file" type="select" label="Select reference genome">
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140 <options from_data_table="fasta_indexes">
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141 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
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142 </options>
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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 </param>
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145 </when>
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146 <when value="history"> <!-- FIX ME!!!! -->
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147 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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148 </when>
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149 </conditional>
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150 </xml>
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151
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152
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153 <xml name="macro_AF_file">
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154 <param name="AF_file" type="data" format="data" label="Af File" optional="True" help="read allele frequencies from file (CHR\tPOS\tREF,ALT\tAF)" />
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155 </xml>
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156 <!-- This may need to bgzip and tabix the file -->
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157 <token name="@PREPARE_AF_FILE@">
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158 <![CDATA[
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159 #if 'AF_file' in $section and $section.AF_file:
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160 #pass
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161 #end if
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162 ]]>
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163 </token>
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164 <token name="@AF_FILE@">
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165 #if 'AF_file' in $section and $section.AF_file:
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166 --AF-file "${section.AF_file}"
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167 #end if
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168 </token>
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169
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170 <xml name="macro_estimate_AF">
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171 <param name="estimate_AF" type="data" format="data" label="Estimate Af" optional="True" 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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172 </xml>
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173 <token name="@ESTIMATE_AF@">
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174 #if 'estimate_AF' in $section and $section.estimate_AF:
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175 --estimate-AF "${section.estimate_AF}"
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176 #end if
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177 </token>
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178
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179 <xml name="macro_exons_file">
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180 <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
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181 </xml>
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182 <token name="@PREPARE_EXONS_FILE@">
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183 <![CDATA[
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184 #set $exons_path = None
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185 #if 'exons_file' in $section and $section.exons_file:
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186 #set $exons_path = 'exons_file.tab.gz'
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187 bgzip -c "$section.exons_file" > $exons_path &&
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188 tabix -s 1 -b 2 -e 3 $exons_path &&
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189 #end if
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190 ]]>
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191 </token>
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192 <token name="@EXONS_FILE@">
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193 #if 'exons_file' in $section and $section.exons_file:
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194 --exons $exons_path
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195 #end if
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196 </token>
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197
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198 <xml name="macro_ploidy_file">
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199 <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
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200 </xml>
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201 <token name="@PLOIDY_FILE@">
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202 #if 'ploidy_file' in $section and $section.ploidy_file:
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203 --ploidy "${section.ploidy_file}"
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204 #end if
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205 </token>
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206
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207 <xml name="macro_collapse_opt_none">
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208 <option value="none">none - require the exact same set of alleles in all files</option>
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209 </xml>
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210 <xml name="macro_collapse_opt_id">
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211 <option value="id">id - only records with identical ID column are compatible. </option>
0
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212 </xml>
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213 <xml name="macro_collapse">
1
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214 <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
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215 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
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216 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
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217 <option value="both">both - indels and snps </option>
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218 <option value="some">some - at least some of the ALTs must match</option>
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219 <option value="any">any - any combination of alleles</option>
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220 <yield/>
0
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221 </param>
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222 </xml>
1
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223 <token name="@COLLAPSE@">
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224 #if $section.collapse:
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225 --collapse "${section.collapse}"
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226 #end if
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227 </token>
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228
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229 <xml name="macro_apply_filters">
4
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230 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
1
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231 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
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232 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
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233 </param>
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234 </xml>
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235 <token name="@APPLY_FILTERS@">
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236 #if $section.apply_filters:
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237 --apply-filters "${section.apply_filters}"
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238 #end if
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239 </token>
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240
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241 <xml name="macro_select_output_type">
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242 <param name="output_type" type="select">
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243 <option value="b">compressed BCF</option>
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244 <!-- no galaxy datatypes for these
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245 <option value="u">uncompressed BCF</option>
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246 <option value="z">compressed VCF</option>
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247 -->
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248 <option value="v">uncompressed VCF</option>
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249 </param>
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250 </xml>
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251 <token name="@OUTPUT_TYPE@">
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252 #if str($output_type) != "__none__":
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253 --output-type "${output_type}"
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254 #end if
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255 </token>
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256
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257 <xml name="macro_vcf_output">
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258 <data name="output_file" format="vcf">
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259 <change_format>
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260 <when input="output_type" value="b" format="bcf" />
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261 <when input="output_type" value="u" format="bcf" />
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262 <when input="output_type" value="z" format="vcf_bgzip" />
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263 <when input="output_type" value="v" format="vcf" />
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264 </change_format>
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265 </data>
0
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266 </xml>
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267
1
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268 <xml name="macro_regions">
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269 <conditional name="regions">
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270 <param name="regions_src" type="select" label="Regions">
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271 <option value="__none__">None</option>
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272 <option value="regions">regions</option>
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273 <option value="regions_file">regions-file</option>
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274 </param>
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275 <when value="__none__"/>
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276 <when value="regions">
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277 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
1
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278 help="Each region is specifed as: chr or chr:pos or chr:from-to">
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279 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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280 </param>
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281 </when>
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282 <when value="regions_file">
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283 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
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284 </when>
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285 </conditional>
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286 </xml>
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287 <token name="@REGIONS@">
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288 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
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289 --regions "$section.regions.regions"
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290 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
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291 --regions-file "$section.regions.regions_file"
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292 #end if
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293 </token>
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294
1
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295 <xml name="macro_targets_file">
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296 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
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297 <yield/>
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298 </param>
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299 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
0
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300 </xml>
1
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301 <token name="@PREPARE_TARGETS_FILE@">
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302 <![CDATA[
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303 #set $targets_path = None
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304 #if 'targets' in $section
1
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305 #if $section.targets.targets_src == 'targets_file':
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306 #set $targets_path = 'targets_file.tab.gz'
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307 bgzip -c "$section.targets.targets_file" > $targets_path &&
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308 tabix -s 1 -b 2 -e 2 $targets_path &&
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309 #end if
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310 #elif $tgts_sec.targets_file:
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311 #set $targets_path = 'targets_file.tab.gz'
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312 bgzip -c "$section.targets_file" > $targets_path &&
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313 tabix -s 1 -b 2 -e 2 $targets_path &&
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314 #end if
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315 ]]>
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316 </token>
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317 <token name="@TARGETS_FILE@">
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318 <![CDATA[
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319 #if $targets_path is not None:
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320 --targets-file "${section.invert_targets_file}${targets_path}"
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321 #elif $section.targets_file:
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322 --targets-file "${section.invert_targets_file}${section.targets_file}"
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323 #end if
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324 ]]>
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325 </token>
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326
0
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327 <xml name="macro_targets">
1
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328 <conditional name="targets">
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329 <param name="targets_src" type="select" label="Targets">
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330 <option value="__none__">None</option>
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331 <option value="targets">targets</option>
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332 <option value="targets_file">targets-file</option>
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333 </param>
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334 <when value="__none__"/>
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335 <when value="targets">
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336 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
1
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337 help="Each target is specifed as: chr or chr:pos or chr:from-to">
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338 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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339 </param>
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340 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
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341 </when>
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342 <when value="targets_file">
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343 <expand macro="macro_targets_file">
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344 </expand>
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345 </when>
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346 </conditional>
0
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347 </xml>
1
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348 <token name="@TARGETS@">
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349 <![CDATA[
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350 #if $targets_path:
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351 --targets-file "${section.targets.invert_targets_file}${targets_path}"
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352 #else:
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353 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
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354 --targets "${section.targets.invert_targets_file}${section.targets.targets}"
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355 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
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356 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
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357 #end if
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358 #end if
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359 ]]>
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360 </token>
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361
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362 <xml name="macro_samples">
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363 <param name="samples" type="text" value="" label="Samples" optional="true"
1
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364 help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
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365 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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366 </param>
4
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367 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
1
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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368 help="inverts the query/filtering applied by Samples" />
4
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369 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
1
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370 help="(-S) file of samples to include" />
4
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371 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
1
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372 help="inverts the query/filtering applied by Samples File" />
0
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373 </xml>
1
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374 <token name="@SAMPLES@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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375 #set $samples_defined = False
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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376 #if str($section.samples) != '':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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377 #set $samples_defined = True
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378 --samples "${section.invert_samples}${section.samples}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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379 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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380 #if $section.samples_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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381 #set $samples_defined = True
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382 --samples-file "${section.invert_samples_file}${section.samples_file}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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383 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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384 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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385
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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386 <xml name="macro_sample">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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387 <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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388 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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389 <token name="@SAMPLE@">
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390 #if $section.sample:
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391 --sample "${section.sample}"
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392 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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393 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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394
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395
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396 <xml name="macro_include">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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397 <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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398 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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399 <sanitizer sanitize="False"/>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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400 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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401 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
402 <token name="@INCLUDE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
403 #if $section.include:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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404 --include '${section.include}'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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405 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
406 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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407
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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408 <xml name="macro_exclude">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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409 <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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410 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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411 <sanitizer sanitize="False"/>
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412 </param>
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413 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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414 <token name="@EXCLUDE@">
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415 #if $section.exclude:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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416 --exclude '${section.exclude}'
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417 #end if
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418 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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419
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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420 <xml name="macro_columns">
4
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421 <param name="columns" type="text" value="" label="Columns" optional="true"
1
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422 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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423 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
0
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424 </param>
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425 </xml>
1
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426 <token name="@COLUMNS@">
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diff changeset
427 #if $section.columns != '':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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428 --columns "${section.columns}"
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diff changeset
429 #end if
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diff changeset
430 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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431
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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432 <xml name="macro_haploid2diploid">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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433 <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
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434 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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435
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
436 <xml name="macro_vcf_ids">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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437 <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
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438 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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439 <token name="@VCF_IDS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
440 ${section.vcf_ids}
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
441 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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442
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
443 <token name="@OUTPUT_HELP@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
444 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
445 Output Type
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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446 -----------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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447
4
6d2a5f0859cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents: 3
diff changeset
448 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
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449 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
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450 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
451 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
452
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
453 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
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diff changeset
454 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
455 use unnecessary amounts of space.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
456
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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diff changeset
457 ]]></token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
458 <token name="@REGIONS_HELP@">
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
459 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
460 Region Selections
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
461 -----------------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
462
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
463 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
464 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
465 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
466 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
467 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
468 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
469 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
470 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
471 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
472 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
473 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
474 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
475 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
476 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
477 requires indexed VCF/BCF files.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
478
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 <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
481 Targets
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
482 -------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
483
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
484 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
485 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
486 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
487 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
488 "^" 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
489 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
490 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
491 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
492
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
493 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
494 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
495 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
496 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
497
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
498 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
499 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
500 <!-- 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
501 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
502
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
503
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
504 <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
505 Collapse
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
506 --------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
507
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
508 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
509 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
510 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
511 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
512 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
513 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
514 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
515
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
516
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
517 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
518 | 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
519 +============+================================================================+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
520 | 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
521 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
522 | 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
523 | | compatible |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
524 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
525 | 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
526 | | 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
527 | | 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
528 | | output. |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
529 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
530 | 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
531 | | 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
532 | | 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
533 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
534 | 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
535 | | 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
536 | | 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
537 | | output. |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
538 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
539 | 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
540 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
541 | 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
542 | | 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
543 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
544
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
545 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
546
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
547 <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
548 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
549 Expressions
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
550 -----------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
551
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
552 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
553
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
554 - 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
555
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
556 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
557
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
558 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
559 "String"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
560
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
561 - arithmetic operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
562
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
563 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
564
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
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
567 - comparison operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
568
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
569 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
570
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
571 == (same as =), >, >=, <=, <, !=
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
572
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
573 - 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
574
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
575 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
576
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
577 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
578
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
579 - parentheses
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
580
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
581 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
582
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
583 (, )
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
584
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
585 - logical operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
586
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
587 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
588
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
589 && (same as &), ||, |
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
590
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
591 - 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
592
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 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
596 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
597 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
598
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
599 - 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
600
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
601 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
602
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
603 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
604
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
605 - "." 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
606
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
607 ::
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 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
610
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
611 - 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
612
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 GT="."
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
616
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
617 - 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
618
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
619 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
620
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
621 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
622
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
623 - 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
624
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
625 ::
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 (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
iuc
parents: 0
diff changeset
628 DP4[*] == 0
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
629 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
630
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
631 - 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
632
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
633 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
634
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
635 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
636
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
637 - 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
638
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
639 ::
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 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
diff changeset
642
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
643 **Notes:**
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 - 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
646 - 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
647 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
648 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
649 - 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
650 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
651 "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
652
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents: 0
diff changeset
653 **Examples:**
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
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655 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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656
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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657 MIN(DV)>5
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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658 MIN(DV/DP)>0.3
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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659 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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660 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
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661 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
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662 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
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663 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
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664 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
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665 MIN(DP)>35 && AVG(GQ)>50
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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666 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
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667 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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668 MAF[0]<0.05 .. select rare variants at 5% cutoff
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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669
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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670 ]]></token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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671
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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672
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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673
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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674
0
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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675 </macros>