Mercurial > repos > iuc > bcftools_norm

annotate bcftools_norm.xml @ 4:660f8eec689d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
author iuc
date Sat, 11 Mar 2017 18:00:25 -0500
parents d110fb275304
children e49eeb4059e0
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e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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="@VERSION@.0">
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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="requirements">
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9 <requirement type="package" version="1.3.1">samtools</requirement>
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10 </expand>
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11 <expand macro="version_command" />
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12 <command detect_errors="aggressive"><![CDATA[
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13 @PREPARE_ENV@
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14 @PREPARE_INPUT_FILE@
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15 #set $section = $sec_ref
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16 @PREPARE_FASTA_REF@
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17 #set $section = $sec_restrict
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18 @PREPARE_TARGETS_FILE@
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20 bcftools @EXECUTABLE@
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22 #set $section = $sec_ref
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23 @FASTA_REF@
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24 ${section.do_not_normalize}
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25 #if $section.check_ref:
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26 --check-ref "${section.check_ref}"
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27 #end if
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28
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29 ## Default section
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30 #set $section = $sec_default
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31 #if $section.rm_dup:
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32 --rm-dup "${section.rm_dup}"
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33 #end if
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34 #if $section.multiallelics:
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35 #set $mtype = ''
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36 #if $section.multiallelic_types:
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37 #set $mtype = $section.multiallelic_types
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38 #end if
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39 --multiallelics "${section.multiallelics}${mtype}"
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 #end if
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41 ${section.strict_filter}
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42 #if $section.site_win:
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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43 --site-win "${section.site_win}"
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44 #end if
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45
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46 #set $section = $sec_restrict
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47 @REGIONS@
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48 @TARGETS@
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49
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50 @OUTPUT_TYPE@
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51 @THREADS@
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52
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53 ## Primary Input/Outputs
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54 @INPUT_FILE@
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55 > "$output_file"
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56 ]]>
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57 </command>
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58 <inputs>
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59 <expand macro="macro_input" />
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60 <section name="sec_restrict" expanded="false" title="Restrict to">
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61 <expand macro="macro_regions" />
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62 <expand macro="macro_targets" />
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63 </section>
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64 <section name="sec_ref" expanded="false" title="Reference Options">
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65 <expand macro="macro_fasta_ref" />
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66 <param name="check_ref" type="select" label="Check REF" optional="true"
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67 help="What to do when incorrect or missing REF allele is encountered">
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68 <option value="e">check REF alleles and exit (e)</option>
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69 <option value="w">warn (w)</option>
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70 <option value="x">exclude (x)</option>
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71 <option value="s">set bad sites (s)</option>
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72 <option value="wx">warn and exclude (wx)</option>
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73 <option value="ws">warn and set bad sites (ws)</option>
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74 </param>
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75 <param name="do_not_normalize" type="boolean" truevalue="--do-not-normalize" falsevalue="" label="Skip Normalization, just set REF allele"
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76 help="Do not normalize indels, just fix or set the REF allele from the reference (-N, --do-not-normalize with -m or -c s)" />
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77 </section>
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78
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79 <section name="sec_default" expanded="false" title="Default Options">
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80 <param name="rm_dup" type="select" label="Rm Dup" optional="true"
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81 help="Remove duplicate snps|indels|both|any">
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82 <option value="snps">snps</option>
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83 <option value="indels">indels</option>
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84 <option value="both">both</option>
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85 <option value="any">any</option>
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86 </param>
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87 <param name="multiallelics" type="select" label="~multiallelics" optional="true">
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88 <option value="-">split multiallelic sites into biallelic records (-)</option>
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89 <option value="+">join biallelic sites into multiallelic records (+)</option>
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90 </param>
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91 <param name="multiallelic_types" type="select" label="variant types which should be split or merged" optional="true">
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92 <option value="snps">snps - only SNP records should be split or merged</option>
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93 <option value="indels">indels - only indel records should be split or merged</option>
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94 <option value="both">both - records should be split or merged</option>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff changeset
95 <option value="any">any - SNPs and indels should be merged into a single record</option>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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96 </param>
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97 <param name="strict_filter" type="boolean" truevalue="--strict-filter" falsevalue="" label="Strict Filter"
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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98 help="When merging (-m+), merged site is PASS only if all sites being merged PASS" />
2
d110fb275304 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
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diff changeset
99 <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
iuc
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100 help="(-w, --site-win) Buffer for sorting lines which changed position during realignment" />
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101 </section>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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102
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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103 <expand macro="macro_select_output_type" />
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104 </inputs>
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105 <outputs>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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106 <expand macro="macro_vcf_output"/>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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107 </outputs>
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108 <tests>
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109 <test>
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110 <param name="input_file" ftype="vcf" value="norm.vcf" />
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111 <param name="fasta_ref" ftype="fasta" value="norm.fa" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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112 <param name="output_type" value="v" />
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113 <output name="output_file">
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114 <assert_contents>
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iuc
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115 <has_text text="T,TAACCCTA" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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116 <not_has_text text="TAA,TAACCCTAAA" />
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117 </assert_contents>
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118 </output>
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119 </test>
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120
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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121 <test>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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122 <param name="input_file" ftype="vcf" value="norm.split.vcf" />
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iuc
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123 <param name="multiallelics" value="-" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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124 <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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125 <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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126 <assert_contents>
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iuc
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127 <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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128 <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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129 <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAACCCTAAA\t"/>
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130 </assert_contents>
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iuc
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131 </output>
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132 </test>
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133
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134 <test>
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135 <param name="input_file" ftype="vcf" value="norm.split.vcf" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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136 <param name="fasta_ref" ftype="fasta" value="norm.fa" />
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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137 <param name="multiallelics" value="-" />
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iuc
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138 <param name="output_type" value="v" />
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iuc
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139 <output name="output_file">
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140 <assert_contents>
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iuc
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141 <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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142 <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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143 <has_text_matching expression="1\t105\t.\tTA\tT\t"/>
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144 </assert_contents>
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145 </output>
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146 </test>
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iuc
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147
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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148 <test>
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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149 <param name="input_file" ftype="vcf" value="norm.merge.vcf" />
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iuc
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150 <param name="multiallelics" value="+" />
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iuc
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151 <param name="output_type" value="v" />
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iuc
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152 <output name="output_file">
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153 <assert_contents>
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iuc
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154 <has_text text="TAA,TAACCCTAAA" />
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iuc
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155 <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
iuc
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156 </assert_contents>
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157 </output>
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158 </test>
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159 <test>
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160 <param name="input_file" ftype="vcf" value="norm.merge.vcf" />
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iuc
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161 <param name="multiallelics" value="+" />
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162 <param name="strict_filter" value="true" />
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163 <param name="output_type" value="v" />
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164 <output name="output_file">
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165 <assert_contents>
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iuc
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166 <has_text text="TAA,TAACCCTAAA" />
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167 <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tPASS"/>
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168 </assert_contents>
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169 </output>
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170 </test>
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171
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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172 <test>
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173 <param name="input_file" ftype="vcf" value="norm.setref.vcf" />
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174 <param name="fasta_ref" ftype="fasta" value="norm.fa" />
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iuc
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175 <param name="do_not_normalize" value="true" />
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iuc
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176 <param name="check_ref" value="s" />
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iuc
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177 <param name="output_type" value="v" />
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iuc
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178 <output name="output_file">
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179 <assert_contents>
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180 <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/>
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iuc
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181 <has_text_matching expression="2\t105\t.\tT\t&lt;DEL&gt;\t999\tPASS"/>
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182 </assert_contents>
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183 </output>
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184 </test>
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185
e9555e894608 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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186 </tests>
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187 <help><![CDATA[
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188 =====================================
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189 bcftools @EXECUTABLE@
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190 =====================================
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191
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192
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193 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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194
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195 @REGIONS_HELP@
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196 @TARGETS_HELP@
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197
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198 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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199
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200 @BCFTOOLS_WIKI@
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201 ]]>
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202 </help>
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203 <expand macro="citations" />
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204 </tool>