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1 <tool id="sniplay_vcftoolsfilter" name="VCF tools filter" version="1.1.1">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> Filter VCF using VCFtools</description>
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5
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <requirement type="binary">perl</requirement>
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9 <requirement type="package" version="0.1.12b">VCFtools</requirement>
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10 </requirements>
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11
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12 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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13 <version_command>
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14 <!--
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15 tool_binary -v
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16 -->
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17 </version_command>
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18
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19 <!-- [REQUIRED] The command to execute -->
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20 <command interpreter="perl">
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21 vcfToolsFilter.sh $filein $fileout_label $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end
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22 #if str( $samples ) == "":
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23 'None'
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24 #else
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25 $samples
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26 #end if
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27 #if str( $chromosomes ) == "":
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28 'None'
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29 #else
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30 $chromosomes
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31 #end if
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32 #if str( $export ) == "plink":
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33 $fileout_map
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34 #else
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35 ''
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36 #end if
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37 </command>
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38
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39 <!-- [REQUIRED] Input files and tool parameters -->
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40 <inputs>
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41 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
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42 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file basename"/>
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43 <param name="samples" type="text" optional="true" label="Samples" help="Samples to be analyzed. Comma separated list">
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44 <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator>
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45 </param>
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46 <param name="chromosomes" type="text" optional="true" label="Chromosomes" help="Chromosomes to be analyzed. Comma separated list">
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47 <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator>
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48 </param>
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49 <param name="export" type="select" label="Output format" >
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50 <option value="VCF" selected="true">VCF</option>
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51 <option value="freq">freq</option>
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52 <option value="plink">plink</option>
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53 </param>
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54 <param name="frequency" type="float" value="0.001" label="Minimum MAF." help="Minimum frequency." />
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55 <param name="max_freq" type="float" value="0.5" label="Maximum MAF." help="Maximum frequency." />
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56 <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." />
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57 <param name="nb_alleles_min" type="integer" value="2" label="Minimum number of alleles" help="Minimum accepted number of alleles." min="2" max="4" />
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58 <param name="nb_alleles_max" type="integer" value="2" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" />
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59 <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." >
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60 <option value="ALL" selected="true">All</option>
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61 <option value="SNP">SNP</option>
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62 <option value="INDEL">Indel</option>
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63 </param>
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64 <param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." />
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65 <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." />
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66 </inputs>
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67
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68 <!-- [REQUIRED] Output files -->
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69 <outputs>
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70 <data name="fileout" format="vcf" label="${fileout_label}.#if str($export)=='plink' then 'ped' else '' # #if str($export)=='freq' then 'frq' else '' # #if str($export)=='VCF' then 'vcf' else '' #" >
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71 <change_format>
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72 <when input="export" value="freq" format="tabular" />
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73 <when input="export" value="plink" format="txt" />
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74 </change_format>
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75 </data>
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76 <data name="fileout_map" format="txt" label="${fileout_label}.map">
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77 <filter>(export == 'plink')</filter>
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78 </data>
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79 <data name="filelog" format="txt" label="${fileout_label}.log" />
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80 </outputs>
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81
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82 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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83 <stdio>
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84 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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85 <exit_code range="1:" level="fatal" />
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86 </stdio>
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87
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88 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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89 <tests>
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90 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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91 <test>
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92 <param name="filein" value="sample.vcf" />
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93 <param name="chromosomes" value="chr1" />
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94 <param name="export" value="VCF" />
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95 <param name="frequency" value="0.001" />
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96 <param name="max_freq" value="0.5" />
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97 <param name="allow_missing" value="0" />
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98 <param name="nb_alleles_min" value="2" />
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99 <param name="nb_alleles_max" value="4" />
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100 <param name="type_p" value="ALL" />
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101 <param name="bound_start" value="1" />
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102 <param name="bound_end" value="100000000" />
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103 <output name="fileout" file="result.vcf" />
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104 <output name="filelog" file="result.log" />
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105 </test>
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106 </tests>
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107
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108 <!-- [OPTIONAL] Help displayed in Galaxy -->
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109 <help>
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110
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111 .. class:: infomark
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112
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113 **Authors**
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114
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115 ---------------------------------------------------
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116
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117 .. class:: infomark
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118
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119 **Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep.
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120
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121 ---------------------------------------------------
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122
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123 ================
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124 VCF tools filter
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125 ================
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126
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127 -----------
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128 Description
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129 -----------
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130
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131 Filter VCF file
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132
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133 -----------------
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134 Workflow position
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135 -----------------
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136
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137 **Upstream tools**
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138
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139 =========== ========================== =======
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140 Name output file(s) format
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141 =========== ========================== =======
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142 =========== ========================== =======
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143
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144
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145 **Downstream tools**
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146
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147 =========== ========================== =======
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148 Name output file(s) format
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149 =========== ========================== =======
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150 =========== ========================== =======
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151
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152
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153 ----------
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154 Input file
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155 ----------
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156
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157 VCF file
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158 VCF file with all SNPs
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159
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160 ----------
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161 Parameters
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162 ----------
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163
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164 Output file basename
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165 Prefix for the output VCF file
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166
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167 Samples
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168 Samples to be analyzed. Comma separated list
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169
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170 Chromosomes
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171 Chromosomes to be analyzed. Comma separated list
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172
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173 Output format
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174 VCF/freq/plink
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175
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176 Minimum MAF
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177 Minimum frequency
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178
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179 Maximum MAF
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180 Maximum frequency
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181
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182 Missing data proportion
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183 Allowed missing data proportion per site. Must be comprised between 0 and 1.
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184
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185 Number of alleles
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186 Accepted number of alleles min and max.
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187
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188 Polymorphisms
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189 Type of polymorphisms to keep (ALL/SNP/INDEL).
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190 Bounds
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191 Lower bound and upper bound for a range of sites to be processed.
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192
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193 ------------
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194 Output files
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195 ------------
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196
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197 VCF file
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198 VCF file filtered
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199
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200 Log file
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201
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202 ---------------------------------------------------
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203
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204 ---------------
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205 Working example
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206 ---------------
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207
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208 Input files
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209 ===========
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210
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211 VCF file
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212 ---------
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213
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214 ::
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215
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216 #fileformat=VCFv4.1
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217 #FILTER=<ID=LowQual,Description="Low quality">
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218 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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219 [...]
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220 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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221 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0
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222
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223
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224 Parameters
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225 ==========
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226
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227 Output name -> filtered_chr1
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228
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229 Chromosomes -> chr1
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230
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231 Output format -> VCF
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232
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233 Minimum MAF -> 0.001
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234
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235 Maximum MAF -> 0.5
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236
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237 Missing data proportion -> 1
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238
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239 Number of alleles min -> 2
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240
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241 Number of alleles max -> 4
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242
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243 Polymorphisms -> All
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244
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245 Lower bound -> 1
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246
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247 Upper bound -> 100000000
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248
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249
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250 Output files
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251 ============
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252
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253 filtered_genelist_intron.vcf
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254 ---------
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255
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256 ::
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257
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258 #fileformat=VCFv4.1
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259 #FILTER=<ID=LowQual,Description="Low quality">
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260 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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261 [...]
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262 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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263 chr1 5059 . C G 146.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:175,18,0
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264
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265
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266 </help>
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267
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268 </tool>
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