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1 <tool id="cg_testvariants" name="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 testvariants 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>test for the presence of 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 testvariants
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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 --input $listing
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20 --variants
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21 #if $file_types.data_sources.data_source == "in"
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22 #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file-->
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23 ${v.input}
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24 #end for
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25 #else
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26 `cat $file_types.data_sources.varlist`
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27 #end if
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28 </command>
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29
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30 <outputs>
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31 <data format="tabular" name="output" />
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32 </outputs>
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33
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34 <inputs>
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35 <!--form field to select crr file-->
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36 <param name="crr" type="select" label="Reference genome (.crr file)">
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37 <options from_data_table="cg_crr_files" />
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38 </param>
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39
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40 <!--form fields to select variant list-->
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41 <param name="listing" type="data" format="tabular" label="Select variant list">
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42 <validator type="unspecified_build" />
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43 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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44 metadata_name="dbkey" metadata_column="1"
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45 message="cgatools is not currently available for this build."/>
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46 </param>
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47
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48 <!--conditional to select input file type-->
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49 <conditional name="file_types">
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50 <param name="file_type" type="select" label="Select the input file type">
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51 <option value="var" selected="true">var files</option>
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52 <option value="mastervar">mastervar files</option>
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53 </param>
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54
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55 <when value="var">
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56 <!--conditional to select variant file input-->
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57 <conditional name="data_sources">
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58 <param name="data_source" type="select" label="Where are the input var files?">
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59 <option value="in" selected="true">imported into Galaxy</option>
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60 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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61 </param>
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62 <when value="in">
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63 <!--form field to select variant files-->
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64 <repeat name="varfiles" title="Variant files">
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65 <param name="input" type="data" format="cg_var" label="Dataset">
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66 <validator type="unspecified_build" />
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67 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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68 metadata_name="dbkey" metadata_column="1"
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69 message="cgatools is not currently available for this build."/>
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70 </param>
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71 </repeat>
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72 </when>
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73 <when value="out">
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74 <!--form field to select crr file-->
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75 <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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76 </when>
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77 </conditional>
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78 </when>
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79
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80 <when value="mastervar">
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81 <!--conditional to select variant file input-->
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82 <conditional name="data_sources">
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83 <param name="data_source" type="select" label="Where are the input mastervar files?">
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84 <option value="in" selected="true">imported into Galaxy</option>
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85 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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86 </param>
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87 <when value="in">
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88 <!--form field to select variant files-->
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89 <repeat name="varfiles" title="Variant files">
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90 <param name="input" type="data" format="cg_mastervar" label="Dataset">
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91 <validator type="unspecified_build" />
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92 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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93 metadata_name="dbkey" metadata_column="1"
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94 message="cgatools is not currently available for this build."/>
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95 </param>
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96 </repeat>
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97 </when>
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98 <when value="out">
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99 <!--form field to select crr file-->
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100 <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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101 </when>
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102 </conditional>
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103 </when>
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104 </conditional>
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105 </inputs>
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106
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107 <help>
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108
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109 **What it does**
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110
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111 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
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112
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113 **cgatools 1.5.0 Documentation**
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114
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115 Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf
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116
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117 Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf
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118
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119 **Command line reference**::
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120
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121 COMMAND NAME
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122 testvariants - Tests variant files for presence of variants.
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123
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124 DESCRIPTION
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125 Tests variant files for presence of variants. The output is a tab-delimited
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126 file consisting of the columns of the input variants file, plus a column
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127 for each assembly results file that contains a character code for each
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128 allele. The character codes have meaning as follows:
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129
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130 0 This allele of this genome is consistent with the reference at this
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131 locus but inconsistent with the variant.
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132 1 This allele of this genome has the input variant at this locus.
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133 N This allele of this genome has no-calls but is consistent with the
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134 input variant.
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135
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136 OPTIONS
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137 -h [ --help ]
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138 Print this help message.
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139
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140 --beta
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141 This is a beta command. To run this command, you must pass the --beta
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142 flag.
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143
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144 --reference arg
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145 The reference crr file.
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146
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147 --input arg (=STDIN)
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148 The input variants to test for.
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149
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150 --output arg (=STDOUT)
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151 The output file (may be omitted for stdout).
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152
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153 --variants arg
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154 The input variant files (may be passed in as arguments at the end of
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155 the command).
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156
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157 SUPPORTED FORMAT_VERSION
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158 0.3 or later
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159 </help>
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160 </tool>
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