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1 <tool id="cga_testvariants" name="testvariants(beta)" version="0.0.1">
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2 <!--
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3 This tool creates a GUI for cgatools testvariants 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>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 testvariants
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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 --input $listing
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19 --variants
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20 #if $file_types.data_sources.data_source == "in"
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21 #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file-->
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22 ${v.input}
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23 #end for
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24 #else
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25 `cat $file_types.data_sources.varlist`
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26 #end if
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27 </command>
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28
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29 <outputs>
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30 <data format="tabular" name="output" />
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31 </outputs>
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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="Genome build">
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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 fields to select variant list-->
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40 <param name="listing" type="data" format="tabular" label="Select variant list">
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41 <validator type="unspecified_build" />
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42 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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43 metadata_name="dbkey" metadata_column="1"
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44 message="cgatools is not currently available for this build."/>
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45 </param>
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46
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47 <!--conditional to select input file type-->
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48 <conditional name="file_types">
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49 <param name="file_type" type="select" label="Select the input file type">
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50 <option value="var" selected="true">var files</option>
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51 <option value="mastervar">mastervar files</option>
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52 </param>
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53
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54 <when value="var">
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55 <!--conditional to select variant file input-->
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56 <conditional name="data_sources">
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57 <param name="data_source" type="select" label="Where are the input var files?">
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58 <option value="in" selected="true">imported into Galaxy</option>
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59 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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60 </param>
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61 <when value="in">
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62 <!--form field to select variant files-->
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63 <repeat name="varfiles" title="Variant files">
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64 <param name="input" type="data" format="cg_var" label="Dataset">
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65 <validator type="unspecified_build" />
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66 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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67 metadata_name="dbkey" metadata_column="1"
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68 message="cgatools is not currently available for this build."/>
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69 </param>
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70 </repeat>
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71 </when>
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72 <when value="out">
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73 <!--form field to select crr file-->
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74 <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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75 </when>
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76 </conditional>
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77 </when>
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78
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79 <when value="mastervar">
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80 <!--conditional to select variant file input-->
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81 <conditional name="data_sources">
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82 <param name="data_source" type="select" label="Where are the input mastervar files?">
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83 <option value="in" selected="true">imported into Galaxy</option>
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84 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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85 </param>
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86 <when value="in">
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87 <!--form field to select variant files-->
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88 <repeat name="varfiles" title="Variant files">
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89 <param name="input" type="data" format="cg_mastervar" label="Dataset">
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90 <validator type="unspecified_build" />
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91 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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92 metadata_name="dbkey" metadata_column="1"
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93 message="cgatools is not currently available for this build."/>
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94 </param>
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95 </repeat>
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96 </when>
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97 <when value="out">
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98 <!--form field to select crr file-->
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99 <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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100 </when>
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101 </conditional>
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102 </when>
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103 </conditional>
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104 </inputs>
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105
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106 <help>
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107
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108 **What it does**
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109
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110 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
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111
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112 cgatools: http://sourceforge.net/projects/cgatools/files/
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113
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114 -----
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115
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116 **cgatools Manual**::
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117
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118 COMMAND NAME
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119 testvariants - Tests variant files for presence of variants.
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120
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121 DESCRIPTION
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122 Tests variant files for presence of variants. The output is a tab-delimited
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123 file consisting of the columns of the input variants file, plus a column
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124 for each assembly results file that contains a character code for each
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125 allele. The character codes have meaning as follows:
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126
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127 0 This allele of this genome is consistent with the reference at this
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128 locus but inconsistent with the variant.
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129 1 This allele of this genome has the input variant at this locus.
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130 N This allele of this genome has no-calls but is consistent with the
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131 input variant.
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132
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133 OPTIONS
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134 -h [ --help ]
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135 Print this help message.
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136
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137 --beta
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138 This is a beta command. To run this command, you must pass the --beta
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139 flag.
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140
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141 --reference arg
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142 The reference crr file.
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143
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144 --input arg (=STDIN)
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145 The input variants to test for.
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146
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147 --output arg (=STDOUT)
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148 The output file (may be omitted for stdout).
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149
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150 --variants arg
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151 The input variant files (may be passed in as arguments at the end of
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152 the command).
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153
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154 SUPPORTED FORMAT_VERSION
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155 0.3 or later
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156 </help>
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157 </tool>
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