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1 <tool id="cg_testvariants" name="testvariants(beta) 1.6" version="1.0.1">
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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 updated 8-14-2012 by bcrain@completegenomics.com
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6 -->
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7
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8 <description>test for the presence of variants</description>
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9
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10 <command>
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11 <!-- print version of cgatools to STDOUT-->
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12 cgatools | head -1;
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13
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14 <!-- print command lines to STDOUT-->
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15 echo "cgatools testvariants --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 $data_sources.data_source == "in" <!--data in galaxy-->
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21 #for $v in $data_sources.file_types.files <!--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 <!--data outside galaxy-->
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25 `cat $data_sources.list`
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26 #end if
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27 ";
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28
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29 <!-- execute cgatools-->
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30 cgatools testvariants
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31 --beta
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32 --reference ${crr.fields.path}
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33 --output $output
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34 --input $listing
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35 --variants
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36 #if $data_sources.data_source == "in" <!--data in galaxy-->
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37 #for $v in $data_sources.file_types.files <!--get each var/mastervar file-->
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38 ${v.input}
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39 #end for
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40 #else <!--data outside galaxy-->
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41 `cat $data_sources.list`
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42 #end if
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43 </command>
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44
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45 <outputs>
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46 <data format="tabular" name="output" label="${tool.name} output"/>
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47 </outputs>
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48
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49 <inputs>
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50 <!--form field to select crr file-->
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51 <param name="crr" type="select" label="Reference genome (.crr file)">
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52 <options from_data_table="cg_crr_files" />
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53 </param>
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54
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55 <!--form fields to select variant list-->
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56 <param name="listing" type="data" format="tabular" label="Select variant list (output of listvariants)">
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57 <validator type="dataset_ok_validator" />
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58 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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59 metadata_name="dbkey" metadata_column="1"
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60 message="cgatools is not currently available for this build."/>
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61 </param>
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62
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63 <!--conditional to select data in/outside galaxy-->
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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 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 (data on server or mounted drive)</option>
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68 </param>
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69
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70 <when value="in">
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71 <!--conditional to select input file type-->
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72 <conditional name="file_types">
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73 <param name="file_type" type="select" label="Select the input file type">
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74 <option value="var" selected="true">var files</option>
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75 <option value="mastervar">masterVar files</option>
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76 </param>
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77
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78 <!--form field to select variant files-->
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79 <when value="var">
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80 <repeat name="files" title="Var file" min="1">
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81 <param name="input" type="data" format="cg_var" label="Dataset">
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82 <validator type="dataset_ok_validator" />
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83 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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84 metadata_name="dbkey" metadata_column="1"
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85 message="cgatools is not currently available for this build."/>
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86 </param>
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87 </repeat>
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88 </when>
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89
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90 <!--form field to select masterVar files-->
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91 <when value="mastervar">
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92 <repeat name="files" title="MasterVar file" min="1">
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93 <param name="input" type="data" format="cg_mastervar" label="Dataset">
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94 <validator type="dataset_ok_validator" />
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95 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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96 metadata_name="dbkey" metadata_column="1"
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97 message="cgatools is not currently available for this build."/>
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98 </param>
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99 </repeat>
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100 </when>
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101 </conditional>
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102 </when>
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103
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104 <!--form field to enter list file-->
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105 <when value="out">
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106 <param name="list" type="text" label="Enter file containing list of var or masterVar files (/path/file)" size="200" help="This file should contain a list of var or masterVar 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), the var or masterVar files can be compressed (gz, bz2).">
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107 <validator type="empty_field" message="You must supply a file containing a list of var or masterVar files"/>
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108 </param>
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109 </when>
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110 </conditional>
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111 </inputs>
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112
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113 <help>
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114
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115 **What it does**
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116
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117 This tool uses the cgatools testvariants to test var or masterVar files for the presence of variants.
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118
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119 **cgatools 1.6.0 Documentation**
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120
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121 Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf
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122
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123 Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf
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124
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125 **Command line reference**::
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126
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127 COMMAND NAME
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128 testvariants - Tests variant files for presence of variants.
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129
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130 DESCRIPTION
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131 Tests variant files for presence of variants. The output is a tab-delimited
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132 file consisting of the columns of the input variants file, plus a column
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133 for each assembly results file that contains a character code for each
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134 allele. The character codes have meaning as follows:
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135
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136 0 This allele of this genome is consistent with the reference at this
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137 locus but inconsistent with the variant.
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138 1 This allele of this genome has the input variant at this locus.
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139 N This allele of this genome has no-calls but is consistent with the
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140 input variant.
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141
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142 OPTIONS
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143 -h [ --help ]
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144 Print this help message.
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145
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146 --beta
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147 This is a beta command. To run this command, you must pass the --beta
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148 flag.
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149
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150 --reference arg
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151 The reference crr file.
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152
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153 --input arg (=STDIN)
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154 The input variants to test for.
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155
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156 --output arg (=STDOUT)
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157 The output file (may be omitted for stdout).
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158
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159 --variants arg
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160 The input variant files (may be passed in as arguments at the end of
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161 the command).
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162
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163 SUPPORTED FORMAT_VERSION
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164 0.3 or later
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165 </help>
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166 </tool>
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