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1 <tool id="cga_listvariant" name="listvariants(beta)" version="0.0.1">
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2 <!--
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3 This tool creates a GUI for cgatools listvariants from Complete Genomics, Inc.
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4 written 5-29-2012 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 listvariants
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15 --beta
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16 --reference ${crr.fields.path}
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17 --output $output
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18 #if $include_list.listing == "yes" <!--only added when yes-->
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19 --variant-listing $include_list.list
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20 #end if
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21 $longvar
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22 --variants
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23 #if $file_types.data_sources.data_source == "in"
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24 #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file-->
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25 ${v.input}
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26 #end for
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27 #else
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28 `cat $file_types.data_sources.varlist`
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29 #end if
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30 </command>
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31
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32 <inputs>
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33 <!--form field to select crr file-->
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34 <param name="crr" type="select" label="Genome build">
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35 <options from_data_table="cg_crr_files" />
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36 </param>
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37
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38 <!--form field to select long variants option-->
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39 <param name="longvar" type="select" label="List long variants?">
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40 <option value="" selected="true">no</option>
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41 <option value="--list-long-variants">yes</option>
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42 </param>
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43
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44 <!--form fields to include existing variant list-->
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45 <conditional name="include_list">
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46 <param name="listing" type="select" label="Include variant listing?">
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47 <option value="no" selected="true">no</option>
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48 <option value="yes">yes</option>
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49 </param>
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50 <when value="yes">
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51 <param name="list" type="data" format="tabular" label="Variant listing"/>
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52 </when>
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53 </conditional>
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54
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55 <!--conditional to select input file type-->
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56 <conditional name="file_types">
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57 <param name="file_type" type="select" label="Select the input file type">
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58 <option value="var" selected="true">var files</option>
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59 <option value="mastervar">mastervar files</option>
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60 </param>
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61
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62 <when value="var">
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63 <!--conditional to select variant file input-->
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64 <conditional name="data_sources">
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65 <param name="data_source" type="select" label="Where are the input var files?">
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66 <option value="in" selected="true">imported into Galaxy</option>
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67 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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68 </param>
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69 <when value="in">
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70 <!--form field to select variant files-->
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71 <repeat name="varfiles" title="Variant files">
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72 <param name="input" type="data" format="cg_var" label="Dataset">
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73 <validator type="unspecified_build" />
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74 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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75 metadata_name="dbkey" metadata_column="1"
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76 message="cgatools is not currently available for this build."/>
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77 <!--<validator type="expression" message="Dataset does not match selected build.">$dbkey == $crr.fields.dbkey</validator>-->
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78 </param>
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79 </repeat>
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80 </when>
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81 <when value="out">
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82 <!--form field to select crr file-->
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83 <param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="file with list of var files (/path/varfile), var files can be compressed (gz, bz2)."/>
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84 </when>
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85 </conditional>
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86 </when>
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87
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88 <when value="mastervar">
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89 <!--conditional to select variant file input-->
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90 <conditional name="data_sources">
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91 <param name="data_source" type="select" label="Where are the input mastervar files?">
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92 <option value="in" selected="true">imported into Galaxy</option>
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93 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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94 </param>
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95 <when value="in">
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96 <!--form field to select variant files-->
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97 <repeat name="varfiles" title="Variant files">
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98 <param name="input" type="data" format="cg_mastervar" label="Dataset">
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99 <validator type="unspecified_build" />
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100 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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101 metadata_name="dbkey" metadata_column="1"
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102 message="cgatools is not currently available for this build."/>
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103 </param>
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104 </repeat>
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105 </when>
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106 <when value="out">
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107 <!--form field to select crr file-->
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108 <param name="varlist" type="text" label="List of mastervar files (/path/file)" size="200" help="file with list of mastervar files (/path/varfile), mastervar files can be compressed (gz, bz2)."/>
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109 </when>
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110 </conditional>
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111 </when>
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112 </conditional>
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113 </inputs>
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114
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115 <outputs>
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116 <data format="tabular" name="output"/>
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117 </outputs>
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118
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119 <!-- <tests>
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120 <test>
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121 <param name="reference" value="hg19.crr"/>
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122 <param name="file_type" value="var"/>
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123 <param name="data_source" value="in"/>
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124 <param name="varfiles?input" value="??"/>
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125 <param name="varfiles?input" value="??"/>
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126 <output name="output" file="??"/>
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127 </test>
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128 </tests>-->
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129
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130 <help>
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131
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132 **What it does**
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133
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134 This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files.
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135
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136 cgatools: http://sourceforge.net/projects/cgatools/files/
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137
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138 -----
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139
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140 **cgatools Manual**::
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141
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142 COMMAND NAME
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143 listvariants - Lists the variants present in a variant file.
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144
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145 DESCRIPTION
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146 Lists all called variants present in the specified variant files, in a
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147 format suitable for processing by the testvariants command. The output is a
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148 tab-delimited file consisting of the following columns:
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149
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150 variantId Sequential id assigned to each variant.
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151 chromosome The chromosome of the variant.
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152 begin 0-based reference offset of the beginning of the variant.
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153 end 0-based reference offset of the end of the variant.
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154 varType The varType as extracted from the variant file.
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155 reference The reference sequence.
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156 alleleSeq The variant allele sequence as extracted from the variant
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157 file.
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158 xRef The xRef as extrated from the variant file.
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159
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160 OPTIONS
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161 -h [ --help ]
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162 Print this help message.
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163
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164 --beta
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165 This is a beta command. To run this command, you must pass the --beta
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166 flag.
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167
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168 --reference arg
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169 The reference crr file.
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170
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171 --output arg (=STDOUT)
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172 The output file (may be omitted for stdout).
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173
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174 --variants arg
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175 The input variant files (may be positional args).
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176
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177 --variant-listing arg
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178 The output of another listvariants run, to be merged in to produce the
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179 output of this run.
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180
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181 --list-long-variants
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182 In addition to listing short variants, list longer variants as well
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183 (10's of bases) by concatenating nearby calls.
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184
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185 SUPPORTED FORMAT_VERSION
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186 0.3 or later
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187 </help>
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188 </tool>
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