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1 <tool id="cg_listtestvariants" name="listvariants(beta)-testvariants(beta) 1.5" version="1.0.0">
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2 <!--
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3 This tool creates a GUI for the listvariants and testvariants functions of cgatools from Complete Genomics, Inc.
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4 to be run consecutively with the same input files.
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5 written 6-18-2012 by bcrain@completegenomics.com
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6 -->
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7
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8 <description>performs listsvariants and testvariants consecutively</description> <!--adds description in toolbar-->
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9
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10 <requirements>
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11 <requirement type="binary">cgatools</requirement>
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12 </requirements>
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13
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14 <command> <!--run executable-->
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15 cgatools | head -1;
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16 cgatools listvariants
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17 --beta
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18 --reference ${crr.fields.path}
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19 --output $output1
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20 #if $include_list.listing == "yes" <!--only added when yes-->
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21 --variant-listing $include_list.list
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22 #end if
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23 $longvar
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24 --variants
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25 #if $file_types.data_sources.data_source == "in"
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26 #for $v in $file_types.data_sources.varfiles <!--get each var file-->
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27 ${v.input}
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28 #end for
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29 #else
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30 `cat $file_types.data_sources.varlist`
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31 #end if
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32 ;
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33
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34 cgatools testvariants
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35 --beta
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36 --reference ${crr.fields.path}
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37 --output $output2
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38 --input $output1
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39 --variants
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40 #if $file_types.data_sources.data_source == "in"
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41 #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file-->
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42 ${v.input}
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43 #end for
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44 #else
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45 `cat $file_types.data_sources.varlist`
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46 #end if
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47 </command>
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48
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49 <outputs>
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50 <data format="tabular" name="output1" label="listvariants output"/>
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51 <data format="tabular" name="output2" label="testvariants output"/>
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52 </outputs>
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53
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54 <inputs>
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55 <!--form field to select crr file-->
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56 <param name="crr" type="select" label="Reference genome (.crr file)">
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57 <options from_data_table="cg_crr_files" />
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58 </param>
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59
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60 <!--form field to select long variants option-->
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61 <param name="longvar" type="select" label="List long variants?">
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62 <option value="" selected="true">no</option>
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63 <option value="--list-long-variants">yes</option>
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64 </param>
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65
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66 <!--form fields to include existing variant list-->
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67 <conditional name="include_list">
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68 <param name="listing" type="select" label="Include variant listing?">
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69 <option value="no" selected="true">no</option>
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70 <option value="yes">yes</option>
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71 </param>
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72 <when value="yes">
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73 <param name="list" type="data" format="tabular" label="Variant listing">
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74 <validator type="unspecified_build" />
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75 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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76 metadata_name="dbkey" metadata_column="1"
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77 message="cgatools is not currently available for this build."/>
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78 </param>
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79 </when>
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80 </conditional>
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81
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82 <!--conditional to select input file type-->
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83 <conditional name="file_types">
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84 <param name="file_type" type="select" label="Select the input file type">
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85 <option value="var" selected="true">var files</option>
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86 <option value="mastervar">mastervar files</option>
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87 </param>
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88
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89 <when value="var">
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90 <!--conditional to select variant file input-->
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91 <conditional name="data_sources">
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92 <param name="data_source" type="select" label="Where are the input var files?">
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93 <option value="in" selected="true">imported into Galaxy</option>
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94 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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95 </param>
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96 <when value="in">
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97 <!--form field to select variant files-->
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98 <repeat name="varfiles" title="Variant files">
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99 <param name="input" type="data" format="cg_var" label="Dataset">
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100 <validator type="unspecified_build" />
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101 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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102 metadata_name="dbkey" metadata_column="1"
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103 message="cgatools is not currently available for this build."/>
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104 </param>
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105 </repeat>
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106 </when>
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107 <when value="out">
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108 <!--form field to select crr file-->
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109 <param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="This file should contain a list of var files, one per line in the format /path/varfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/var-GS00000YYYY-ASM.tsv.bz2), var files can be compressed (gz, bz2)."/>
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110 </when>
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111 </conditional>
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112 </when>
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113
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114 <when value="mastervar">
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115 <!--conditional to select variant file input-->
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116 <conditional name="data_sources">
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117 <param name="data_source" type="select" label="Where are the input mastervar files?">
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118 <option value="in" selected="true">imported into Galaxy</option>
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119 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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120 </param>
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121 <when value="in">
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122 <!--form field to select variant files-->
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123 <repeat name="varfiles" title="Variant files">
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124 <param name="input" type="data" format="cg_mastervar" label="Dataset">
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125 <validator type="unspecified_build" />
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126 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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127 metadata_name="dbkey" metadata_column="1"
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128 message="cgatools is not currently available for this build."/>
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129 </param>
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130 </repeat>
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131 </when>
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132 <when value="out">
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133 <!--form field to select crr file-->
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134 <param name="varlist" type="text" label="List of mastervar files (/path/file)" size="200" help="This file should contain a list of mastervar files, one per line in the format /path/varfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/masterVarBeta-GS00000YYYY-ASM.tsv.bz2), mastervar files can be compressed (gz, bz2)."/>
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135 </when>
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136 </conditional>
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137 </when>
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138 </conditional>
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139 </inputs>
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140
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141 <help>
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142
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143 **What it does**
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144
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145 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
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146
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147 **cgatools 1.5.0 Documentation**
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148
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149 Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf
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150
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151 Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf
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152
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153 **Command line reference**::
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154
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155 COMMAND NAME
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156 listvariants - Lists the variants present in a variant file.
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157
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158 DESCRIPTION
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159 Lists all called variants present in the specified variant files, in a
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160 format suitable for processing by the testvariants command. The output is a
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161 tab-delimited file consisting of the following columns:
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162
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163 variantId Sequential id assigned to each variant.
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164 chromosome The chromosome of the variant.
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165 begin 0-based reference offset of the beginning of the variant.
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166 end 0-based reference offset of the end of the variant.
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167 varType The varType as extracted from the variant file.
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168 reference The reference sequence.
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169 alleleSeq The variant allele sequence as extracted from the variant
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170 file.
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171 xRef The xRef as extrated from the variant file.
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172
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173 OPTIONS
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174 -h [ --help ]
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175 Print this help message.
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176
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177 --beta
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178 This is a beta command. To run this command, you must pass the --beta
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179 flag.
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180
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181 --reference arg
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182 The reference crr file.
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183
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184 --output arg (=STDOUT)
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185 The output file (may be omitted for stdout).
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186
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187 --variants arg
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188 The input variant files (may be positional args).
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189
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190 --variant-listing arg
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191 The output of another listvariants run, to be merged in to produce the
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192 output of this run.
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193
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194 --list-long-variants
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195 In addition to listing short variants, list longer variants as well
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196 (10's of bases) by concatenating nearby calls.
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197
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198 SUPPORTED FORMAT_VERSION
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199 0.3 or later
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200
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201
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202
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203 COMMAND NAME
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204 testvariants - Tests variant files for presence of variants.
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205
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206 DESCRIPTION
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207 Tests variant files for presence of variants. The output is a tab-delimited
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208 file consisting of the columns of the input variants file, plus a column
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209 for each assembly results file that contains a character code for each
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210 allele. The character codes have meaning as follows:
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211
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212 0 This allele of this genome is consistent with the reference at this
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213 locus but inconsistent with the variant.
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214 1 This allele of this genome has the input variant at this locus.
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215 N This allele of this genome has no-calls but is consistent with the
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216 input variant.
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217
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218 OPTIONS
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219 -h [ --help ]
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220 Print this help message.
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221
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222 --beta
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223 This is a beta command. To run this command, you must pass the --beta
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224 flag.
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225
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226 --reference arg
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227 The reference crr file.
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228
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229 --input arg (=STDIN)
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230 The input variants to test for.
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231
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232 --output arg (=STDOUT)
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233 The output file (may be omitted for stdout).
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234
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235 --variants arg
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236 The input variant files (may be passed in as arguments at the end of
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237 the command).
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238
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239 SUPPORTED FORMAT_VERSION
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240 0.3 or later
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241 </help>
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242 </tool>
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