Mercurial > repos > iuc > bcftools_norm

annotate bcftools_norm.xml @ 15:481476814acc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
author iuc
date Sat, 15 Jan 2022 13:37:35 +0000
parents ff9e769ccd6c
children 48291658fdf6
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
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3 <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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4 <macros>
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5 <token name="@EXECUTABLE@">norm</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools" />
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9 <expand macro="requirements">
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10 <expand macro="samtools_requirement"/>
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11 <!-- gawk only required for current bcftools norm bug workaround
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12 Remove once fixed (see command section below -->
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13 <requirement type="package" version="5.0.1">gawk</requirement>
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14 </expand>
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15 <expand macro="version_command" />
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16 <command detect_errors="aggressive"><![CDATA[
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17 @PREPARE_ENV@
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18 @PREPARE_INPUT_FILE@
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19 #set $section = $reference_source
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20 @PREPARE_FASTA_REF@
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22 ## The next two lines are a workaround for a bug in bcftools norm up to version
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23 ## 1.9, which caused indel normalization to be case-sensitive
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24 ## see:
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25 ## https://github.com/samtools/bcftools/commit/65b211da1f5cdbf1c7c11eb610481a736fa88bda
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26 ## https://github.com/samtools/bcftools/commit/77b0a27a156803e382d60651ff94ea0bd95fad0f
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27 ## With the next release of bcftools, this should be fixed and, at that point,
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28 ## the time-consuming on-the-fly uppercasing should be removed again.
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29 awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' '$input_fa_ref' > ref_upper.fa &&
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30 #set $input_fa_ref = 'ref_upper.fa'
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31
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32 #set $section = $sec_restrict
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33 @PREPARE_TARGETS_FILE@
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34 @PREPARE_REGIONS_FILE@
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36 bcftools @EXECUTABLE@
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37
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38 #set $section = $reference_source
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39 @FASTA_REF@
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40 --check-ref $check_ref
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41 $normalize_indels
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42 #if $rm_dup:
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43 --rm-dup "$rm_dup"
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44 #end if
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45 #if $multiallelics.mode:
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46 --multiallelics '${multiallelics.mode}${multiallelics.multiallelic_types}'
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47 #end if
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48 #if $multiallelics.mode == '+':
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49 ${multiallelics.strict_filter}
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50 #end if
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51 #if $sec_default.site_win:
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52 --site-win ${sec_default.site_win}
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53 #end if
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54
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55 #set $section = $sec_restrict
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56 @REGIONS@
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57 @TARGETS@
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59 @OUTPUT_TYPE@
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60 @THREADS@
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61
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62 ## Primary Input/Outputs
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63 @INPUT_FILE@
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64 > '$output_file'
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65 ]]>
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66 </command>
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67 <inputs>
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68 <expand macro="macro_input" />
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69 <expand macro="macro_fasta_ref" />
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70 <param name="check_ref" type="select" display="radio"
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71 label="When any REF allele does not match the reference genome base"
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72 help="Warnings about REF mismatches will be emitted to the standard
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73 error (stderr) stream, and it is recommended to check there for
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74 problems if you choose not to exit with an error immediately upon
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75 encountering a mismatch.">
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76 <option value="w">ignore the problem (-w)</option>
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77 <option value="wx">exclude the variant record from the output (-wx)</option>
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78 <option value="ws">fix the variant record using the reference genome information (-ws)</option>
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79 <option value="e">exit with an error (-e)</option>
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80 </param>
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81 <param argument="--do-not-normalize" name="normalize_indels" type="boolean" truevalue="" falsevalue="--do-not-normalize" checked="false"
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82 label="Left-align and normalize indels?" />
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83 <param name="rm_dup" type="select" display="radio"
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84 label="Perform deduplication for the folowing types of variant records">
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85 <option value="">do not deduplicate any records</option>
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86 <option value="snps">snps</option>
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87 <option value="indels">indels</option>
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88 <option value="both">both</option>
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89 <option value="any">any</option>
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90 </param>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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91 <conditional name="multiallelics">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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92 <param name="mode" type="select" label="~multiallelics">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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93 <option value="">preserve multiallelic/biallelic sites</option>
0
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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94 <option value="-">split multiallelic sites into biallelic records (-)</option>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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95 <option value="+">join biallelic sites into multiallelic records (+)</option>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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96 </param>
8
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97 <when value="" />
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98 <when value="-">
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99 <param name="multiallelic_types" type="select" display="radio"
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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100 label="split the following variant types">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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101 <option value="snps">SNPs</option>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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102 <option value="indels">indels</option>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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103 <option value="both" selected="true">both</option>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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104 </param>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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105 </when>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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106 <when value="+">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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107 <param name="multiallelic_types" type="select" display="radio"
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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108 label="merge the following variant types">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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109 <option value="snps">SNPs</option>
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110 <option value="indels">indels</option>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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111 <option value="both" selected="true">SNPs and indels, but keep variants of the two types separate (both)</option>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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112 <option value="any">SNPs and indels, and merge variant records of different types (any)</option>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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113 </param>
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114 <param name="strict_filter" type="boolean" truevalue="--strict-filter" falsevalue=""
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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115 label="Strict Filter"
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116 help="merged site is PASS only if all sites being merged PASS" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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117 </when>
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118 </conditional>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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119 <section name="sec_restrict" expanded="false" title="Restrict all operations to">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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120 <expand macro="macro_restrict" type="region" label_type="Region" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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121 <expand macro="macro_restrict" type="target" label_type="Target">
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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122 <expand macro="macro_invert_targets" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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123 </expand>
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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124 </section>
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125
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126 <section name="sec_default" expanded="false" title="Other Options">
2
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127 <param name="site_win" type="integer" label="Site Window" value="1000" optional="True"
0
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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128 help="(-w, --site-win) Buffer for sorting lines which changed position during realignment" />
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129 </section>
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130 <expand macro="macro_select_output_type" />
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131 </inputs>
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132 <outputs>
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133 <expand macro="macro_vcf_output"/>
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134 </outputs>
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135 <tests>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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136 <test>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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137 <param name="input_file" ftype="vcf" value="norm.vcf" />
8
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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138 <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
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139 <param name="normalize_indels" value="true" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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140 <param name="output_type" value="v" />
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141 <output name="output_file">
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142 <assert_contents>
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143 <has_text text="T,TAACCCTA" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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144 <not_has_text text="TAA,TAACCCTAAA" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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145 </assert_contents>
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146 </output>
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147 </test>
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148
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149 <test>
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150 <param name="input_file" ftype="vcf" dbkey="?" value="norm.vcf" />
76655fe2c70e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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151 <expand macro="test_using_reference" select_from="cached" ref="norm" />
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152 <param name="normalize_indels" value="true" />
0
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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153 <param name="output_type" value="v" />
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154 <output name="output_file">
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155 <assert_contents>
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156 <has_text text="T,TAACCCTA" />
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157 <not_has_text text="TAA,TAACCCTAAA" />
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158 </assert_contents>
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159 </output>
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160 </test>
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161
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162 <test>
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163 <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
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164 <expand macro="test_using_reference" ref="norm.fa" />
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165 <conditional name="multiallelics">
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166 <param name="mode" value="-" />
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167 </conditional>
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 <not_has_text text="TAA,TAACCCTAAA" />
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172 <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
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173 <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAACCCTAAA\t"/>
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174 </assert_contents>
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175 </output>
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176 </test>
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177
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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178 <test>
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179 <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
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180 <expand macro="test_using_reference" ref="norm.fa" />
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181 <param name="normalize_indels" value="true" />
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182 <conditional name="multiallelics">
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183 <param name="mode" value="-" />
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184 </conditional>
0
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185 <param name="output_type" value="v" />
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186 <output name="output_file">
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187 <assert_contents>
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188 <not_has_text text="TAA,TAACCCTAAA" />
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189 <has_text_matching expression="1\t105\t.\tTAAACCCTA\tT\t"/>
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190 <has_text_matching expression="1\t105\t.\tTA\tT\t"/>
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191 </assert_contents>
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192 </output>
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193 </test>
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194
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195 <test>
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196 <param name="input_file" ftype="vcf" value="norm.merge.vcf" />
8
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197 <expand macro="test_using_reference" ref="norm.fa" />
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198 <conditional name="multiallelics">
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199 <param name="mode" value="+" />
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200 </conditional>
0
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201 <param name="output_type" value="v" />
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202 <output name="output_file">
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203 <assert_contents>
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204 <has_text text="TAA,TAACCCTAAA" />
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205 <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tFAIL"/>
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206 </assert_contents>
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207 </output>
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208 </test>
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209 <test>
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210 <param name="input_file" ftype="vcf" value="norm.merge.vcf" />
8
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211 <expand macro="test_using_reference" ref="norm.fa" />
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212 <conditional name="multiallelics">
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213 <param name="mode" value="+" />
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214 <param name="strict_filter" value="true" />
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215 </conditional>
0
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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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219 <has_text text="TAA,TAACCCTAAA" />
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220 <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tPASS"/>
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221 </assert_contents>
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222 </output>
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223 </test>
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224
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225 <test>
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226 <param name="input_file" ftype="vcf" value="norm.setref.vcf" />
8
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227 <expand macro="test_using_reference" ref="norm.fa" />
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228 <param name="check_ref" value="ws" />
0
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229 <param name="output_type" value="v" />
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230 <output name="output_file">
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231 <assert_contents>
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232 <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/>
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233 <has_text_matching expression="2\t105\t.\tT\t&lt;DEL&gt;\t999\tPASS"/>
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234 </assert_contents>
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235 </output>
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236 </test>
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237
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238 </tests>
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239 <help><![CDATA[
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240 =====================================
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241 bcftools @EXECUTABLE@
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242 =====================================
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243
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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244
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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245 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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246
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247 @REGIONS_HELP@
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248 @TARGETS_HELP@
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249
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250 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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251
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252 @BCFTOOLS_WIKI@
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253 ]]>
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254 </help>
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255 <expand macro="citations" />
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256 </tool>