Mercurial > repos > iuc > bcftools_norm

annotate bcftools_norm.xml @ 23:271965b55437 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author iuc
date Sun, 18 Aug 2024 09:59:16 +0000
parents 48291658fdf6
children
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">norm</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools" />
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8 <expand macro="requirements">
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9 <expand macro="samtools_requirement"/>
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10 <!-- gawk only required for current bcftools norm bug workaround
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11 Remove once fixed (see command section below -->
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12 <requirement type="package" version="5.0.1">gawk</requirement>
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13 </expand>
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14 <expand macro="version_command" />
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15 <command detect_errors="aggressive"><![CDATA[
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16 @PREPARE_ENV@
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17 @PREPARE_INPUT_FILE@
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18 #set $section = $reference_source
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19 @PREPARE_FASTA_REF@
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21 ## The next two lines are a workaround for a bug in bcftools norm up to version
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22 ## 1.9, which caused indel normalization to be case-sensitive
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23 ## see:
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24 ## https://github.com/samtools/bcftools/commit/65b211da1f5cdbf1c7c11eb610481a736fa88bda
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25 ## https://github.com/samtools/bcftools/commit/77b0a27a156803e382d60651ff94ea0bd95fad0f
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26 ## With the next release of bcftools, this should be fixed and, at that point,
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27 ## the time-consuming on-the-fly uppercasing should be removed again.
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28 awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' '$input_fa_ref' > ref_upper.fa &&
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29 #set $input_fa_ref = 'ref_upper.fa'
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30
0
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31 #set $section = $sec_restrict
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32 @PREPARE_TARGETS_FILE@
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33 @PREPARE_REGIONS_FILE@
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35 bcftools @EXECUTABLE@
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36
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37 #set $section = $reference_source
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38 @FASTA_REF@
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39 --check-ref $check_ref
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40 $normalize_indels
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41 #if $rm_dup:
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42 --rm-dup "$rm_dup"
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43 #end if
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44 $atomize
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45 #if $old_rec_tag
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46 --old-rec-tag '$old_rec_tag'
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47 #end if
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48 #if $multiallelics.mode:
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49 --multiallelics '${multiallelics.mode}${multiallelics.multiallelic_types}'
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50 #end if
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51 #if $multiallelics.mode == '+':
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52 ${multiallelics.strict_filter}
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53 #end if
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54
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55 #if $sec_default.site_win:
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56 --site-win ${sec_default.site_win}
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57 #end if
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59 #set $section = $sec_restrict
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60 @REGIONS@
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61 @TARGETS@
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63 @OUTPUT_TYPE@
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64 @THREADS@
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65
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66 ## Primary Input/Outputs
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67 @INPUT_FILE@
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68 > '$output_file'
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69 ]]>
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70 </command>
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71 <inputs>
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72 <expand macro="macro_input" />
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73 <expand macro="macro_fasta_ref" />
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74 <param name="check_ref" type="select" display="radio"
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75 label="When any REF allele does not match the reference genome base"
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76 help="Warnings about REF mismatches will be emitted to the standard
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77 error (stderr) stream, and it is recommended to check there for
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78 problems if you choose not to exit with an error immediately upon
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79 encountering a mismatch.">
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80 <option value="w">ignore the problem (-w)</option>
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81 <option value="wx">exclude the variant record from the output (-wx)</option>
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82 <option value="ws">fix the variant record using the reference genome information (-ws)</option>
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83 <option value="e">exit with an error (-e)</option>
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84 </param>
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85 <param argument="--atomize" type="boolean" truevalue="--atomize" falsevalue="" checked="false"
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86 label="Atomize" help="Decompose complex variants (e.g. MNVs become consecutive SNVs)" />
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87 <param argument="--do-not-normalize" name="normalize_indels" type="boolean" truevalue="" falsevalue="--do-not-normalize" checked="false"
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88 label="Left-align and normalize indels?" />
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89 <param argument="--old-rec-tag" type="text" value="" optional="true" label="Annotate modified records with INFO/STR indicating the original variant">
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90 <sanitizer invalid_char="">
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91 <valid initial="string.letters,string.digits">
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92 <add value="_" />
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93 <add value="/" />
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94 </valid>
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95 </sanitizer>
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96 <validator type="regex">[0-9a-zA-Z_/]+</validator>
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97 </param>
8
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98 <param name="rm_dup" type="select" display="radio"
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99 label="Perform deduplication for the folowing types of variant records">
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100 <option value="">do not deduplicate any records</option>
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101 <option value="snps">snps</option>
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102 <option value="indels">indels</option>
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103 <option value="both">both</option>
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104 <option value="any">any</option>
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105 </param>
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106 <conditional name="multiallelics">
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107 <param name="mode" type="select" label="~multiallelics">
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108 <option value="">preserve multiallelic/biallelic sites</option>
0
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109 <option value="-">split multiallelic sites into biallelic records (-)</option>
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110 <option value="+">join biallelic sites into multiallelic records (+)</option>
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111 </param>
8
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112 <when value="" />
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113 <when value="-">
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114 <param name="multiallelic_types" type="select" display="radio"
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115 label="split the following variant types">
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116 <option value="snps">SNPs</option>
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117 <option value="indels">indels</option>
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118 <option value="both" selected="true">both</option>
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119 </param>
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120 </when>
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121 <when value="+">
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122 <param name="multiallelic_types" type="select" display="radio"
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123 label="merge the following variant types">
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124 <option value="snps">SNPs</option>
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125 <option value="indels">indels</option>
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126 <option value="both" selected="true">SNPs and indels, but keep variants of the two types separate (both)</option>
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127 <option value="any">SNPs and indels, and merge variant records of different types (any)</option>
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128 </param>
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129 <param name="strict_filter" type="boolean" truevalue="--strict-filter" falsevalue=""
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130 label="Strict Filter"
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131 help="merged site is PASS only if all sites being merged PASS" />
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132 </when>
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133 </conditional>
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134 <section name="sec_restrict" expanded="false" title="Restrict all operations to">
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135 <expand macro="macro_restrict" type="region" label_type="Region" />
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136 <expand macro="macro_restrict" type="target" label_type="Target">
17
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137 <expand macro="macro_invert_targets" />
8
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138 </expand>
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139 </section>
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140
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141 <section name="sec_default" expanded="false" title="Other Options">
2
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142 <param name="site_win" type="integer" label="Site Window" value="1000" optional="True"
0
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143 help="(-w, --site-win) Buffer for sorting lines which changed position during realignment" />
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144 </section>
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145 <expand macro="macro_select_output_type" />
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146 </inputs>
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147 <outputs>
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148 <expand macro="macro_vcf_output"/>
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149 </outputs>
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150 <tests>
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151 <test>
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152 <param name="input_file" ftype="vcf" value="norm.vcf" />
8
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153 <expand macro="test_using_reference" ref="norm.fa" />
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154 <param name="normalize_indels" value="true" />
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155 <param name="output_type" value="v" />
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156 <output name="output_file">
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157 <assert_contents>
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158 <has_text text="T,TAACCCTA" />
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159 <not_has_text text="TAA,TAACCCTAAA" />
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160 </assert_contents>
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161 </output>
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162 </test>
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163
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164 <test>
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165 <param name="input_file" ftype="vcf" dbkey="?" value="norm.vcf" />
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166 <expand macro="test_using_reference" select_from="cached" ref="norm" />
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167 <param name="normalize_indels" value="true" />
0
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168 <param name="output_type" value="v" />
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169 <output name="output_file">
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170 <assert_contents>
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171 <has_text text="T,TAACCCTA" />
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172 <not_has_text text="TAA,TAACCCTAAA" />
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173 </assert_contents>
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174 </output>
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175 </test>
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176
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177 <test>
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178 <param name="input_file" ftype="vcf" value="norm.split.vcf" />
8
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179 <expand macro="test_using_reference" ref="norm.fa" />
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180 <conditional name="multiallelics">
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181 <param name="mode" value="-" />
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182 </conditional>
0
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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183 <param name="output_type" value="v" />
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184 <output name="output_file">
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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185 <assert_contents>
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186 <not_has_text text="TAA,TAACCCTAAA" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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187 <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAA\t"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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188 <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAACCCTAAA\t"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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189 </assert_contents>
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190 </output>
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iuc
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191 </test>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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192
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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193 <test>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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194 <param name="input_file" ftype="vcf" value="norm.split.vcf" />
8
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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195 <expand macro="test_using_reference" ref="norm.fa" />
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iuc
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196 <param name="normalize_indels" value="true" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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197 <conditional name="multiallelics">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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198 <param name="mode" value="-" />
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iuc
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199 </conditional>
0
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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200 <param name="output_type" value="v" />
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iuc
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201 <output name="output_file">
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202 <assert_contents>
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iuc
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203 <not_has_text text="TAA,TAACCCTAAA" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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204 <has_text_matching expression="1\t105\t.\tTAAACCCTA\tT\t"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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205 <has_text_matching expression="1\t105\t.\tTA\tT\t"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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206 </assert_contents>
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iuc
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207 </output>
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208 </test>
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209
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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210 <test>
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iuc
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211 <param name="input_file" ftype="vcf" value="norm.merge.vcf" />
8
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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212 <expand macro="test_using_reference" ref="norm.fa" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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213 <conditional name="multiallelics">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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214 <param name="mode" value="+" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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215 </conditional>
0
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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216 <param name="output_type" value="v" />
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217 <output name="output_file">
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218 <assert_contents>
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iuc
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219 <has_text text="TAA,TAACCCTAAA" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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220 <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tFAIL"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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221 </assert_contents>
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222 </output>
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223 </test>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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224 <test>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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225 <param name="input_file" ftype="vcf" value="norm.merge.vcf" />
8
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
226 <expand macro="test_using_reference" ref="norm.fa" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
227 <conditional name="multiallelics">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
228 <param name="mode" value="+" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
229 <param name="strict_filter" value="true" />
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iuc
parents: 7
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230 </conditional>
0
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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231 <param name="output_type" value="v" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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232 <output name="output_file">
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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233 <assert_contents>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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234 <has_text text="TAA,TAACCCTAAA" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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235 <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tPASS"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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236 </assert_contents>
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iuc
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237 </output>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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238 </test>
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239
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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240 <test>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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241 <param name="input_file" ftype="vcf" value="norm.setref.vcf" />
8
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
242 <expand macro="test_using_reference" ref="norm.fa" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
243 <param name="check_ref" value="ws" />
0
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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244 <param name="output_type" value="v" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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245 <output name="output_file">
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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246 <assert_contents>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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247 <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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248 <has_text_matching expression="2\t105\t.\tT\t&lt;DEL&gt;\t999\tPASS"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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249 </assert_contents>
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250 </output>
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iuc
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251 </test>
17
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252
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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253 <!-- Test atomize option -->
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254 <test>
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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diff changeset
255 <param name="input_file" ftype="vcf" value="norm.split.vcf" />
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 15
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256 <expand macro="test_using_reference" ref="norm.fa" />
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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257 <param name="normalize_indels" value="true" />
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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258 <conditional name="multiallelics">
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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diff changeset
259 <param name="mode" value="-" />
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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260 </conditional>
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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diff changeset
261 <param name="atomize" value="true"/>
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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diff changeset
262 <param name="output_type" value="v" />
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iuc
parents: 15
diff changeset
263 <output name="output_file">
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 15
diff changeset
264 <assert_contents>
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iuc
parents: 15
diff changeset
265 <not_has_text text="TAA,TAACCCTAAA" />
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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diff changeset
266 <has_text_matching expression="1\t105\t.\tTAAACCCTA\tT\t"/>
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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267 <has_text_matching expression="1\t105\t.\tTA\tT\t"/>
48291658fdf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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268 </assert_contents>
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iuc
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diff changeset
269 </output>
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iuc
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270 <assert_command>
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iuc
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271 <has_text text="--atomize" />
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iuc
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272 </assert_command>
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273 </test>
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274 <!-- Test region overlap options -->
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275 <test>
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276 <param name="input_file" ftype="vcf" dbkey="?" value="norm.vcf" />
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277 <expand macro="test_using_reference" select_from="cached" ref="norm" />
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278 <param name="normalize_indels" value="true" />
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279 <param name="output_type" value="v" />
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280 <section name="sec_restrict">
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281 <param name="regions_overlap" value="1"/>
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282 </section>
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283 <output name="output_file">
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284 <assert_contents>
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285 <has_text text="T,TAACCCTA" />
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286 <not_has_text text="TAA,TAACCCTAAA" />
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287 </assert_contents>
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288 </output>
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289 <assert_command>
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290 <has_text text="--regions-overlap" />
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291 </assert_command>
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292 </test>
0
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293 </tests>
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294 <help><![CDATA[
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295 =====================================
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296 bcftools @EXECUTABLE@
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297 =====================================
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298
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299
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300 Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows.
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301
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302 @REGIONS_HELP@
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303 @TARGETS_HELP@
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304
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305 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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306
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307 @BCFTOOLS_WIKI@
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308 ]]>
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309 </help>
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310 <expand macro="citations" />
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311 </tool>