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1 <tool id="cg_snpdiff" name="snpdiff 1.6" version="1.0.1">
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2 <!--
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3 This tool creates a GUI for the snpdiff 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 8-13-2012 by bcrain@completegenomics.com
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6 -->
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7
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8 <description>compares snp calls to var or masterVar file.</description> <!--adds description in toolbar-->
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9
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10 <command> <!--run executable-->
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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 snpdiff
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16 --reference $crr.fields.path
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17 --variants $data_sources.varfile
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18 --genotypes $genotype
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19 --output-prefix cg_
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20 --reports `echo ${report1} ${report2} ${report3} | sed 's/ */,/g'`
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21 ";
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22
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23 <!-- execute cgatools-->
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24 cgatools snpdiff
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25 --reference $crr.fields.path
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26 --variants $data_sources.varfile
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27 --genotypes $genotype
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28 --output-prefix cg_
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29 --reports `echo ${report1} ${report2} ${report3} | sed 's/ */,/g'`
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30
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31 </command>
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32
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33 <outputs>
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34 <data format="tabular" name="output1" from_work_dir="cg_Output.tsv" label="${tool.name} Output">
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35 <filter>(report1 == 'Output')</filter>
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36 </data>
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37 <data format="tabular" name="output2" from_work_dir="cg_Verbose.tsv" label="${tool.name} Verbose">
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38 <filter>(report2 == 'Verbose')</filter>
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39 </data>
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40 <data format="tabular" name="output3" from_work_dir="cg_Stats.tsv" label="${tool.name} Stats">
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41 <filter>(report3 == 'Stats')</filter>
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42 </data>
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43 </outputs>
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44
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45 <inputs>
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46 <!--form field to select crr file-->
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47 <param name="crr" type="select" label="Reference genome (.crr file)">
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48 <options from_data_table="cg_crr_files" />
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49 </param>
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50
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51 <!--conditional to select data in/outside galaxy-->
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52 <conditional name="data_sources">
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53 <param name="data_source" type="select" label="Where is the input var or masterVar file?">
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54 <option value="in" selected="true">imported into Galaxy</option>
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55 <option value="out">located outside Galaxy (data on server or mounted drive)</option>
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56 </param>
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57
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58 <!--form field to select input file-->
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59 <when value="in">
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60 <param name="varfile" type="data" format="cg_var,cg_mastervar" label="Var or masterVar file">
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61 <validator type="dataset_ok_validator" />
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62 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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63 metadata_name="dbkey" metadata_column="1"
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64 message="cgatools is not currently available for this build."/>
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65 </param>
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66 </when>
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67
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68 <!--form field to enter input file-->
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69 <when value="out">
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70 <param name="varfile" type="text" label="Var or masterVar file (/path/file)" size="40" help="Var or masterVar file can be compressed (gz, bz2), e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/var-GS00000YYYY-ASM.tsv.bz2">
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71 <validator type="empty_field" message="You must supply a var or masterVar file"/>
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72 </param>
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73 </when>
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74 </conditional>
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75
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76 <!--param to select genotypes file input-->
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77 <param name="genotype" type="data" format="tabular" label="Genotypes file with SNP calls" help="The genotypes file is a tab-delimited file with at least the following columns: Chromosome, Offset0Based, Genotypes (Optional)">
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78 <validator type="dataset_ok_validator" />
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79 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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80 metadata_name="dbkey" metadata_column="1"
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81 message="cgatools is not currently available for this build."/>
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82 <!--<validator type="expression" message="Dataset does not match selected build.">value.dbkey == $crr.fields.dbkey</validator>-->
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83 </param>
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84
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85 <!--params to select reports-->
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86 <param name="report1" type="select" label="Create report Output">
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87 <option value="">no</option>
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88 <option value="Output" selected="true">yes</option>
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89 </param>
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90 <param name="report2" type="select" label="Create report Verbose">
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91 <option value="">no</option>
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92 <option value="Verbose">yes</option>
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93 </param>
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94 <param name="report3" type="select" label="Create report Stats">
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95 <option value="">no</option>
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96 <option value="Stats">yes</option>
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97 </param>
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98 </inputs>
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99
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100 <help>
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101
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102 **What it does**
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103
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104 This tool ompares snp calls to a Complete Genomics variant file.
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105
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106 **cgatools 1.6.0 Documentation**
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107
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108 Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf
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109
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110 Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf
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111
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112 **Command line reference**::
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113
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114 COMMAND NAME
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115 snpdiff - Compares snp calls to a Complete Genomics variant file.
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116
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117 DESCRIPTION
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118 Compares the snp calls in the "genotypes" file to the calls in a Complete
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119 Genomics variant file. The genotypes file is a tab-delimited file with at
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120 least the following columns (additional columns may be given):
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121
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122 Chromosome (Required) The name of the chromosome.
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123 Offset0Based (Required) The 0-based offset in the chromosome.
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124 GenotypesStrand (Optional) The strand of the calls in the Genotypes
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125 column (+ or -, defaults to +).
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126 Genotypes (Optional) The calls, one per allele. The following
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127 calls are recognized:
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128 A,C,G,T A called base.
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129 N A no-call.
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130 - A deleted base.
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131 . A non-snp variation.
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132
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133 The output is a tab-delimited file consisting of the columns of the
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134 original genotypes file, plus the following additional columns:
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135
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136 Reference The reference base at the given position.
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137 VariantFile The calls made by the variant file, one per allele.
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138 The character codes are the same as is described for
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139 the Genotypes column.
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140 DiscordantAlleles (Only if Genotypes is present) The number of
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141 Genotypes alleles that are discordant with calls in
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142 the VariantFile. If the VariantFile is described as
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143 haploid at the given position but the Genotypes is
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144 diploid, then each genotype allele is compared
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145 against the haploid call of the VariantFile.
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146 NoCallAlleles (Only if Genotypes is present) The number of
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147 Genotypes alleles that were no-called by the
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148 VariantFile. If the VariantFile is described as
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149 haploid at the given position but the Genotypes is
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150 diploid, then a VariantFile no-call is counted twice.
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151
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152 The verbose output is a tab-delimited file consisting of the columns of the
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153 original genotypes file, plus the following additional columns:
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154
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155 Reference The reference base at the given position.
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156 VariantFile The call made by the variant file for one allele (there is
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157 a line in this file for each allele). The character codes
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158 are the same as is described for the Genotypes column.
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159 [CALLS] The rest of the columns are pasted in from the VariantFile,
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160 describing the variant file line used to make the call.
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161
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162 The stats output is a comma-separated file with several tables describing
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163 the results of the snp comparison, for each diploid genotype. The tables
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164 all describe the comparison result (column headers) versus the genotype
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165 classification (row labels) in different ways. The "Locus classification"
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166 tables have the most detailed match classifications, while the "Locus
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167 concordance" tables roll these match classifications up into "discordance"
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168 and "no-call". A locus is considered discordant if it is discordant for
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169 either allele. A locus is considered no-call if it is concordant for both
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170 alleles but has a no-call on either allele. The "Allele concordance"
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171 describes the comparison result on a per-allele basis.
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172
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173 OPTIONS
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174 -h [ --help ]
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175 Print this help message.
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176
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177 --reference arg
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178 The input crr file.
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179
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180 --variants arg
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181 The input variant file.
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182
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183 --genotypes arg
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184 The input genotypes file.
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185
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186 --output-prefix arg
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187 The path prefix for all output reports.
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188
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189 --reports arg (=Output,Verbose,Stats)
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190 Comma-separated list of reports to generate. A report is one of:
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191 Output The output genotypes file.
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192 Verbose The verbose output file.
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193 Stats The stats output file.
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194
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195 SUPPORTED FORMAT_VERSION
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196 0.3 or later
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197 </help>
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198 </tool>
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