Mercurial > repos > iuc > bcftools_consensus

annotate bcftools_consensus.xml @ 17:95c6f3f4c77f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:48:09 +0000
parents edc3d484b99a
children 1171446da5db
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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@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>Create consensus sequence by applying VCF variants to a reference fasta file</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">consensus</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 <requirement type="package" version="5.0.1">gawk</requirement>
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12 </expand>
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13 <expand macro="version_command" />
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14 <command detect_errors="aggressive"><![CDATA[
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15 @PREPARE_ENV@
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16 @PREPARE_INPUT_FILE@
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17 #set $section = $reference_source
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18 @PREPARE_FASTA_REF@
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20 bcftools @EXECUTABLE@
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22 @FASTA_REF@
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24 ## Default section
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25 #set $section = $sec_default
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27 ${section.iupac_codes}
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29 #if $section.mask:
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30 --mask '${section.mask}'
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31 #end if
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32
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33 #if $section.mark_del
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34 --mark-del '$section.mark_del'
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35 #end if
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37 #if $section.mark_ins
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38 --mark-ins $section.mark_ins
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39 #end if
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41 #if $section.mark_snv
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42 --mark-snv $section.mark_snv
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43 #end if
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44
0
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45 #if $section.select_haplotype:
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46 --haplotype '${section.select_haplotype}'
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47 #end if
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48 @SAMPLE@
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49
13
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50 #set $section = $sec_restrict
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51 @INCLUDE@
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52 @EXCLUDE@
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53
0
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54 #if $chain:
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55 --chain '$chain_file'
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56 #end if
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58 #if $absent
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59 --absent '$absent'
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60 #end if
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61
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62 ## Primary Input/Outputs
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63 #if str($rename) == "no"
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64 --output '$output_file'
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65 #end if
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66 @INPUT_FILE@
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67 #if str($rename) == "yes":
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68 #set basename=$input_file.element_identifier
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69 | awk 'BEGIN {i=1} {if (match($0, /^>/)) {if (i==1) {name="${basename}"} else {name=sprintf("%s-%d","${basename}",i);} print(gensub(/>[^ ]+( ?.*)/, ">" name "\\1", 1)); i=i+1;} else {print}}' > '$output_file'
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70 #end if
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71 ]]>
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72 </command>
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73 <inputs>
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74 <expand macro="macro_input" />
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75 <expand macro="macro_fasta_ref" />
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76 <section name="sec_default" expanded="true" title="Default Options">
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77 <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
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78 <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes"
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79 help="Output variants in the form of IUPAC ambiguity codes" />
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80 <expand macro="macro_sample" />
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81 <param name="select_haplotype" type="select" optional="true">
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82 <option value="1">1</option>
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83 <option value="2">2</option>
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84 </param>
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85 <param argument="--mark-del" type="text" value="" optional="true" label="Mark deletions" help="Instead of removing sequence, insert CHAR for deletions">
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86 <sanitizer invalid_char="">
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87 <valid initial="string.letters,string.digits">
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88 <add value="_" />
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89 </valid>
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90 </sanitizer>
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91 <validator type="regex">[0-9a-zA-Z_]+</validator>
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92 </param>
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93 <param argument="--mark-ins" type="select" optional="true" label="Mark insertions" help="Highlight insertions in uppercase (uc) or lowercase (lc), leaving the rest as is">
95c6f3f4c77f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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94 <option value="uc">Uppercase</option>
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95 <option value="lc">Lowercase</option>
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96 </param>
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97 <param argument="--mark-snv" type="select" optional="true" label="Mark substitutions" help="Highlight substitutions in uppercase (uc) or lowercase (lc), leaving the rest as is">
95c6f3f4c77f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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98 <option value="uc">Uppercase</option>
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99 <option value="lc">Lowercase</option>
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100 </param>
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101 <conditional name="conditional_mask">
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102 <param name="selector" type="select" label="Mask file option">
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103 <option value="disabled">Disabled</option>
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104 <option value="enabled">Enabled</option>
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105 </param>
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106 <when value="disabled"/>
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107 <when value="enabled">
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108 <param argument="--mask" type="data" format="tabular" label="Mask" help="Replace regions according to the next --mask-with option" />
95c6f3f4c77f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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109 <param argument="--mask-with" type="text" value="N" optional="true" label="Mask with" help="Replace with CHAR (skips overlapping variants); change to uppercase (uc) or lowercase (lc)">
95c6f3f4c77f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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110 <sanitizer invalid_char="">
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111 <valid initial="string.letters,string.digits">
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112 <add value="_" />
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113 </valid>
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114 </sanitizer>
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115 <validator type="regex">[0-9a-zA-Z_]+</validator>
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116 </param>
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117 </when>
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118 </conditional>
0
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119 </section>
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120 <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" />
11
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121 <param name="rename" type="boolean" truevalue="yes" falsevalue="no" label="Set output FASTA ID from name of VCF" />
17
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122 <param argument="--absent" type="text" value="" label="Absent" optional="true" help="It allows to set positions with no supporting evidence to N (or any other character)">
95c6f3f4c77f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
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123 <sanitizer invalid_char="">
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124 <valid initial="string.letters,string.digits,string.punctuation">
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125 <remove value="@" />
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126 <remove value="'" />
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127 </valid>
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128 </sanitizer>
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129 </param>
13
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130 <section name="sec_restrict" expanded="false" title="Restrict to">
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131 <expand macro="macro_include" />
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132 <expand macro="macro_exclude" />
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133 </section>
0
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134 </inputs>
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135 <outputs>
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136 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/>
74b27d899b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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137 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain">
74b27d899b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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138 <filter>chain</filter>
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139 </data>
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140 </outputs>
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141 <tests>
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142 <test>
8
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143 <expand macro="test_using_reference" ref="consensus.fa" />
0
74b27d899b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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144 <param name="input_file" ftype="vcf" value="consensus.vcf" />
74b27d899b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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145 <param name="mask" ftype="tabular" value="consensus.tab" />
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146 <param name="chain" value="True" />
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147 <output name="output_file">
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148 <assert_contents>
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149 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
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150 </assert_contents>
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151 </output>
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152 <output name="chain_file">
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153 <assert_contents>
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154 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
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155 </assert_contents>
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156 </output>
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157 </test>
8
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158 <test>
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159 <expand macro="test_using_reference" select_from="cached" ref="consensus" />
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160 <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
70b8e9908ea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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161 <param name="mask" ftype="tabular" value="consensus.tab" />
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162 <param name="chain" value="True" />
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163 <output name="output_file">
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164 <assert_contents>
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165 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
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166 </assert_contents>
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167 </output>
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168 <output name="chain_file">
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169 <assert_contents>
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170 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
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171 </assert_contents>
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172 </output>
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173 </test>
11
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174 <test>
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175 <expand macro="test_using_reference" ref="consensus.fa" />
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176 <param name="input_file" ftype="vcf" value="consensus.vcf" />
a87ae767b01d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
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diff changeset
177 <param name="mask" ftype="tabular" value="consensus.tab" />
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178 <param name="chain" value="False" />
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179 <param name="rename" value="True" />
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180 <output name="output_file">
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181 <assert_contents>
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182 <has_text text=">consensus.vcf" />
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183 </assert_contents>
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184 <assert_contents>
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185 <has_text text=">consensus.vcf-2" />
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186 </assert_contents>
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187 </output>
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188 </test>
13
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189 <test>
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190 <expand macro="test_using_reference" ref="consensus.fa" />
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191 <param name="input_file" ftype="vcf" value="consensus.vcf" />
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192 <section name="sec_restrict">
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193 <param name="include" value='TYPE="snp"' />
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194 </section>
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195 <output name="output_file">
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196 <assert_contents>
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197 <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA" />
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198 </assert_contents>
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199 </output>
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200 </test>
17
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201 <!--Test absent option-->
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202 <test>
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203 <expand macro="test_using_reference" ref="consensus.fa" />
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204 <param name="input_file" ftype="vcf" value="consensus.vcf" />
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205 <section name="sec_restrict">
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206 <param name="include" value='TYPE="snp"' />
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207 </section>
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208 <param name="absent" value="W"/>
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209 <output name="output_file">
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210 <assert_contents>
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211 <has_text text="WWWAWAWWAWWWWWWWWCWWWWWWWW" />
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212 </assert_contents>
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213 </output>
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214 <assert_command>
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215 <has_text text="--absent" />
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216 </assert_command>
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217 </test>
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218 <!--Test mask options -->
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219 <test>
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220 <expand macro="test_using_reference" ref="consensus.fa" />
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221 <param name="input_file" ftype="vcf" value="consensus.vcf" />
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222 <section name="sec_restrict">
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223 <param name="include" value='TYPE="snp"' />
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224 </section>
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225 <section name="sec_default">
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226 <param name="mark_del" value="DEL"/>
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227 <param name="mark_ins" value="uc"/>
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228 <param name="mark_snv" value="uc"/>
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229 </section>
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230 <output name="output_file">
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231 <assert_contents>
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232 <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA" />
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233 </assert_contents>
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234 </output>
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235 <assert_command>
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236 <has_text text="--mark-del" />
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237 <has_text text="--mark-ins" />
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238 <has_text text="--mark-snv" />
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239 </assert_command>
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240 </test>
0
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241 </tests>
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242 <help><![CDATA[
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243 =====================================
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244 bcftools @EXECUTABLE@ plugin
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245 =====================================
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246
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247
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248 Create consensus sequence by applying VCF variants to a reference fasta file.
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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@
11
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253
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254 The option to set the new consensus' FASTA ID from the name of the VCF is provided by post-processing
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255 the bcftools consensus output. It is primarily intended for use when the VCF is coming from a list
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256 collection where the elements of the list are named meaningfully (e.g. named after sample names). This
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257 is useful when consensus sequences are being prepared for, for example, feeding a multiple sequence
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258 alignment to a phylogeny program.
0
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259 ]]>
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260 </help>
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261 <expand macro="citations" />
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262 </tool>