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1 <tool id="cg_listvariant" name="listvariants(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 function of cgatools from Complete Genomics, Inc.
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4 written 6-18-2012 by bcrain@completegenomics.com
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5 -->
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6
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7 <description>lists all called variants</description> <!--adds description in toolbar-->
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8
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9 <requirements>
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10 <requirement type="binary">cgatools</requirement>
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11 </requirements>
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12
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13 <command> <!--run executable-->
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14 cgatools | head -1;
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15 cgatools listvariants
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16 --beta
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17 --reference ${crr.fields.path}
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18 --output $output
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19 #if $include_list.listing == "yes" <!--only added when yes-->
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20 --variant-listing $include_list.list
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21 #end if
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22 $longvar
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23 --variants
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24 #if $file_types.data_sources.data_source == "in"
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25 #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file-->
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26 ${v.input}
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27 #end for
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28 #else
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29 `cat $file_types.data_sources.varlist`
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30 #end if
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31 </command>
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32
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33 <inputs>
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34 <!--form field to select crr file-->
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35 <param name="crr" type="select" label="Reference genome (.crr file)">
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36 <options from_data_table="cg_crr_files" />
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37 </param>
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38
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39 <!--form field to select long variants option-->
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40 <param name="longvar" type="select" label="List long variants?">
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41 <option value="" selected="true">no</option>
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42 <option value="--list-long-variants">yes</option>
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43 </param>
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44
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45 <!--form fields to include existing variant list-->
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46 <conditional name="include_list">
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47 <param name="listing" type="select" label="Include variant listing?">
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48 <option value="no" selected="true">no</option>
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49 <option value="yes">yes</option>
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50 </param>
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51 <when value="yes">
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52 <param name="list" type="data" format="tabular" label="Variant listing"/>
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53 </when>
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54 </conditional>
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55
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56 <!--conditional to select input file type-->
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57 <conditional name="file_types">
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58 <param name="file_type" type="select" label="Select the input file type">
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59 <option value="var" selected="true">var files</option>
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60 <option value="mastervar">mastervar files</option>
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61 </param>
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62
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63 <when value="var">
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64 <!--conditional to select variant file input-->
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65 <conditional name="data_sources">
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66 <param name="data_source" type="select" label="Where are the input var files?">
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67 <option value="in" selected="true">imported into Galaxy</option>
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68 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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69 </param>
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70 <when value="in">
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71 <!--form field to select variant files-->
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72 <repeat name="varfiles" title="Variant files">
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73 <param name="input" type="data" format="cg_var" label="Dataset">
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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 <!--<validator type="expression" message="Dataset does not match selected build.">$dbkey == $crr.fields.dbkey</validator>-->
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79 </param>
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80 </repeat>
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81 </when>
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82 <when value="out">
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83 <!--form field to select crr file-->
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84 <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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85 </when>
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86 </conditional>
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87 </when>
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88
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89 <when value="mastervar">
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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 mastervar 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_mastervar" 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 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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110 </when>
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111 </conditional>
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112 </when>
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113 </conditional>
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114 </inputs>
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115
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116 <outputs>
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117 <data format="tabular" name="output"/>
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118 </outputs>
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119
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120 <!-- <tests>
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121 <test>
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122 <param name="reference" value="hg19.crr"/>
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123 <param name="file_type" value="var"/>
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124 <param name="data_source" value="in"/>
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125 <param name="varfiles?input" value="??"/>
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126 <param name="varfiles?input" value="??"/>
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127 <output name="output" file="??"/>
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128 </test>
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129 </tests>-->
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130
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131 <help>
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132
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133 **What it does**
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134
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135 This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files.
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136
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137 **cgatools 1.5.0 Documentation**
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138
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139 Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf
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140
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141 Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf
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142
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143 **Command line reference**::
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144
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145 COMMAND NAME
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146 listvariants - Lists the variants present in a variant file.
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147
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148 DESCRIPTION
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149 Lists all called variants present in the specified variant files, in a
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150 format suitable for processing by the testvariants command. The output is a
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151 tab-delimited file consisting of the following columns:
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152
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153 variantId Sequential id assigned to each variant.
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154 chromosome The chromosome of the variant.
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155 begin 0-based reference offset of the beginning of the variant.
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156 end 0-based reference offset of the end of the variant.
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157 varType The varType as extracted from the variant file.
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158 reference The reference sequence.
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159 alleleSeq The variant allele sequence as extracted from the variant
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160 file.
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161 xRef The xRef as extrated from the variant file.
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162
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163 OPTIONS
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164 -h [ --help ]
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165 Print this help message.
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166
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167 --beta
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168 This is a beta command. To run this command, you must pass the --beta
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169 flag.
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170
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171 --reference arg
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172 The reference crr file.
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173
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174 --output arg (=STDOUT)
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175 The output file (may be omitted for stdout).
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176
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177 --variants arg
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178 The input variant files (may be positional args).
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179
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180 --variant-listing arg
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181 The output of another listvariants run, to be merged in to produce the
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182 output of this run.
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183
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184 --list-long-variants
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185 In addition to listing short variants, list longer variants as well
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186 (10's of bases) by concatenating nearby calls.
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187
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188 SUPPORTED FORMAT_VERSION
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189 0.3 or later
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190 </help>
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191 </tool>
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