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1 <tool id="sniplay_filterVCFonAnnotations" name="Filter VCF on Annotations" 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> </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 </requirements>
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10
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11 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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12 <version_command>
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13 <!--
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14 tool_binary -v
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15 -->
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16 </version_command>
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17
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18 <!-- [REQUIRED] The command to execute -->
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19 <command interpreter="perl">
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20 FilterVCFonAnnotations.pl --input $filein --out $fileout
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21 #if str( $genelist ) != "None":
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22 --genelist $genelist
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23 #end if
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24 #if str( $feature ) != "":
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25 --feature $feature
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26 #end if
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27 #if str( $syn ) != "":
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28 --syn $syn
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29 #end if
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30 </command>
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31
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32 <!-- [REQUIRED] Input files and tool parameters -->
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33 <inputs>
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34 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
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35 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/>
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36 <param name="genelist" type="data" format="txt" optional="true" label="Genelist" default="" help="File listing the genes to be filtered, one line per individu/gene"/>
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37 <param name="feature" type="select" label="Genomic feature" optional="true" help="Filter within genomic feature">
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38 <option value="" selected="true">All</option>
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39 <option value="Exon">Exon</option>
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40 <option value="INTRON">Intron</option>
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41 <option value="UTR_5_PRIME">UTR5prime</option>
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42 <option value="UTR_3_PRIME">UTR3prime</option>
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43 <option value="DOWNSTREAM">Downstream</option>
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44 <option value="UPSTREAM">Upstream</option>
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45 <option value="INTERGENIC">Intergenic</option>
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46 </param>
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47 <param name="syn" type="select" label="Synonymous type" optional="true" help="Keep only synonymous, non-synonymous SNP">
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48 <option value="" selected="true">All</option>
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49 <option value="s">Synonymous</option>
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50 <option value="n">Non-synonymous</option>
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51 </param>
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52 </inputs>
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53
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54 <!-- [REQUIRED] Output files -->
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55 <outputs>
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56 <data name="fileout" type="data" format="vcf" label="${fileout_label}.vcf" />
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57 </outputs>
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58
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59 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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60 <stdio>
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61 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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62 <exit_code range="1:" level="fatal" />
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63 </stdio>
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64
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65 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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66 <tests>
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67 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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68 <test>
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69 <param name="filein" value="sample.vcf" />
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70 <param name="genelist" value="accession.txt" />
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71 <param name="feature" value="INTRON" />
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72 <output name="fileout" file="result.vcf" />
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73 </test>
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74 </tests>
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75
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76 <!-- [OPTIONAL] Help displayed in Galaxy -->
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77 <help>
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78
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79 .. class:: infomark
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80
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81 **Authors**
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82
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83 ---------------------------------------------------
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84
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85 .. class:: infomark
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86
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87 **Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep.
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88
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89 ---------------------------------------------------
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90
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91 ======================
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92 Filter And Convert VCF
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93 ======================
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94
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95 -----------
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96 Description
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97 -----------
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98
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99 Filter VCF file and convert in Fasta, Hapmap and PED
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100
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101 -----------------
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102 Workflow position
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103 -----------------
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104
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105 **Upstream tools**
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106
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107 =========== ========================== =======
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108 Name output file(s) format
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109 =========== ========================== =======
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110 =========== ========================== =======
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111
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112
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113 **Downstream tools**
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114
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115 =========== ========================== =======
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116 Name output file(s) format
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117 =========== ========================== =======
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118 =========== ========================== =======
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119
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120
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121 ----------
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122 Input file
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123 ----------
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124
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125 VCF file
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126 VCF file with all SNPs
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127
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128 Genelist
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129 File listing the genes or individuals to be filtered. Gene_id or accesion number can be put in a file, one line per individual
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130
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131
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132 ----------
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133 Parameters
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134 ----------
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135
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136 Output file name
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137 Prefix for the output VCF file
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138
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139 Genomic feature
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140 Filter on genomic feature : Exon,INTRON,UTR_3_PRIME,UTR_5_PRIME,DOWNSTREAM,UPSTREAM or INTERGENIC
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141
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142 Synonymous type
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143 Keep only synonymous, non-synonymous.
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144
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145
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146 ------------
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147 Output files
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148 ------------
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149
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150 VCF file
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151 VCF file filtered
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152
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153 ---------------------------------------------------
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154
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155 ---------------
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156 Working example
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157 ---------------
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158
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159 Input files
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160 ===========
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161
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162 VCF file
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163 ---------
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164
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165 ::
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166
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167 #fileformat=VCFv4.1
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168 #FILTER=<ID=LowQual,Description="Low quality">
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169 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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170 [...]
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171 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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172 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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173
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174 Genelist
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175 ---------
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176
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177 ::
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178
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179 Cc01g00020
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180 Cc01g00010
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181
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182 Parameters
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183 ==========
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184
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185 Output name -> filtered_genelist_intron
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186
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187 Genomic feature -> Intron
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188
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189 Output files
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190 ============
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191
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192 filtered_genelist_intron.vcf
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193 ----------------------------
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194
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195 ::
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196
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197 #fileformat=VCFv4.1
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198 #FILTER=<ID=LowQual,Description="Low quality">
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199 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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200 [...]
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201 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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202 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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203
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204
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205 </help>
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206
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207 </tool>
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