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1 <tool id="sniplay_vcftoolsstats" name="VCF tools Stats" version="1.0.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> Various statistics from 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="0.1.13">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 vcfToolsStats.sh $filein $fileout_label $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog
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22 </command>
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23
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24 <!-- [REQUIRED] Input files and tool parameters -->
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25 <inputs>
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26 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
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27 <param name="fileout_label" type="text" value="vcf_stats" optional="false" label="Output file basename"/>
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28 </inputs>
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29
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30 <!-- [REQUIRED] Output files -->
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31 <outputs>
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32 <data name="fileout_annot" format="txt" label="${fileout_label}.annotation" />
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33 <data name="fileout_het" format="txt" label="${fileout_label}.het" />
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34 <data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" />
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35 <data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" />
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36 <data name="filelog" format="txt" label="${fileout_label}.log" />
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37 </outputs>
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38
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39 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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40 <stdio>
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41 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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42 <exit_code range="1:" level="fatal" />
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43 </stdio>
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44
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45 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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46 <tests>
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47 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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48 <test>
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49 <param name="filein" value="sample.vcf" />
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50 <output name="fileout_annot" file="result.annotation" />
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51 <output name="fileout_het" file="result.het" />
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52 <output name="fileout_imiss" file="result.imiss" />
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53 <output name="fileout_sum" file="result.TsTv.summary" />
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54 <output name="filelog" file="result.log" />
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55 </test>
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56 </tests>
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57
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58 <!-- [OPTIONAL] Help displayed in Galaxy -->
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59 <help>
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60
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61 .. class:: infomark
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62
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63 **Authors**
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64
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65 ---------------------------------------------------
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66
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67 .. class:: infomark
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68
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69 **Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep.
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70
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71 ---------------------------------------------------
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72
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73 ================
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74 VCF tools filter
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75 ================
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76
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77 -----------
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78 Description
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79 -----------
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80
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81 Compute statistics on VCF file
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82
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83 -----------------
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84 Workflow position
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85 -----------------
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86
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87 **Upstream tools**
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88
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89 =========== ========================== =======
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90 Name output file(s) format
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91 =========== ========================== =======
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92 =========== ========================== =======
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93
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94
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95 **Downstream tools**
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96
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97 =========== ========================== =======
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98 Name output file(s) format
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99 =========== ========================== =======
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100 =========== ========================== =======
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101
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102
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103 ----------
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104 Input file
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105 ----------
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106
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107 VCF file
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108 VCF file with all SNPs
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109
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110 ----------
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111 Parameters
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112 ----------
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113
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114 Output file basename
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115 Prefix for the output VCF file
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116
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117 ------------
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118 Output files
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119 ------------
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120
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121 .annotation file
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122 Statistics on annotation/location along genome
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123
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124 .het file
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125 Statistics on heterozygosity of the individuals
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126
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127 .imiss
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128 Statistics on missing data of the inidividuals
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129 .TsTv.summary
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130 Statistics on mutation types and transition/transvertion number
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131
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132 .log file
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133
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134 ---------------------------------------------------
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135
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136 ---------------
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137 Working example
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138 ---------------
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139
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140 Input files
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141 ===========
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142
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143 VCF file
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144 ---------
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145
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146 ::
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147
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148 #fileformat=VCFv4.1
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149 #FILTER=<ID=LowQual,Description="Low quality">
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150 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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151 [...]
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152 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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153 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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154
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155
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156 Parameters
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157 ==========
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158
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159 Output name -> vcf_stat
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160
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161
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162 Output files
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163 ============
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164
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165 .annotation file
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166 ----------------
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167
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168 ::
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169
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170 Genic 4489
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171 Intergenic 466
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172 ========
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173 Intron 960
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174 Exon 3248
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175 UTR 281
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176 ========
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177 Non-syn 226
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178 Synonym 3022
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179
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180 .het file
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181 ---------
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182
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183 ::
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184
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185 INDV O(HOM) E(HOM) N_SITES F
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186 CATB1 0 0.0 3616 0.00000
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187
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188 .imiss file
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189 -----------
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190
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191 ::
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192
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193 INDV N_DATA N_GENOTYPES_FILTERED N_MISS F_MISS
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194 CATB1 4813 0 0 0
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195
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196 .TsTv.summary file
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197 ------------------
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198
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199 ::
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200
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201 MODEL COUNT
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202 AC 371
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203 AG 1467
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204 AT 562
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205 CG 330
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206 CT 1659
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207 GT 397
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208 Ts 3126
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209 Tv 1660
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210
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211
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212 </help>
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213
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214 </tool>
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