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1 <tool id="snpEff" name="SnpEff" version="1.0">
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2 <description>Variant effect and annotation</description>
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3 <!--
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4 You will need to change the path to wherever your installation is.
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5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
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7 -->
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8 <requirements>
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9 <requirement type="package" version="3.0">snpEff</requirement>
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10 </requirements>
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11 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
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12 <inputs>
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13 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
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14
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15 <param name="inputFormat" type="select" label="Input format">
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16 <option value="vcf">VCF</option>
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17 <option value="txt">Tabular</option>
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18 <option value="pileup">Pileup</option>
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19 <option value="bed">BED</option>
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20 </param>
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21
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22 <param name="outputFormat" type="select" label="Output format">
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23 <option value="txt">Tabular</option>
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24 <option value="vcf">VCF (only if input is VCF)</option>
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25 <option value="bed">BED</option>
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26 <option value="bedAnn">BED Annotations</option>
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27 </param>
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28
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29 <param name="genomeVersion" type="select" label="Genome">
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30 <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option>
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31 <option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option>
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32 <option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option>
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33 <option value="ailMel1.64">Ailuropoda melanoleuca : ailMel1.64</option>
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34 <option value="ailMel1.63">Ailuropoda melanoleuca : ailMel1.63</option>
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35 <option value="anoCar2.0.61">Anolis carolinensis : anoCar2.0.61</option>
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36 <option value="anoCar1.0.60">Anolis carolinensis : anoCar1.0.60</option>
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37 <option value="AnoCar2.0.66">Anolis carolinensis : AnoCar2.0.66</option>
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38 <option value="AnoCar2.0.65">Anolis carolinensis : AnoCar2.0.65</option>
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39 <option value="AnoCar2.0.64">Anolis carolinensis : AnoCar2.0.64</option>
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40 <option value="AnoCar2.0.63">Anolis carolinensis : AnoCar2.0.63</option>
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41 <option value="agam2.6">Anopheles gambiae : agam2.6</option>
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42 <option value="agam">Anopheles gambiae : agam</option>
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43 <option value="aquiCoer">Aquilegia coerulea : aquiCoer</option>
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44 <option value="athalianaTair9">Arabidopsis Thaliana : athalianaTair9</option>
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45 <option value="athalianaTair10">Arabidopsis Thaliana : athalianaTair10</option>
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46 <option value="athaliana130">Arabidopsis Thaliana : athaliana130</option>
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47 <option value="alyrata107">Arabidopsis lyrata : alyrata107</option>
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48 <option value="alyrata1">Arabidopsis lyrata : alyrata1</option>
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49 <option value="amel2">Bee : amel2</option>
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50 <option value="btau4.0.61">Bos taurus : btau4.0.61</option>
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51 <option value="btau4.0.60">Bos taurus : btau4.0.60</option>
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52 <option value="btau4.0.59">Bos taurus : btau4.0.59</option>
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53 <option value="UMD3_1">Bos taurus : UMD3_1</option>
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54 <option value="UMD3.1.66">Bos taurus : UMD3.1.66</option>
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55 <option value="UMD3.1.65">Bos taurus : UMD3.1.65</option>
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56 <option value="UMD3.1.64">Bos taurus : UMD3.1.64</option>
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57 <option value="Btau_4.0.63">Bos taurus : Btau_4.0.63</option>
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58 <option value="c_briggsae_WS230">Caenorhabditis briggsae : c_briggsae_WS230</option>
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59 <option value="ce.WS220.61">Caenorhabditis elegans : ce.WS220.61</option>
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60 <option value="ce.WS210.60">Caenorhabditis elegans : ce.WS210.60</option>
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61 <option value="ce.WS201">Caenorhabditis elegans : ce.WS201</option>
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62 <option value="WS220.66">Caenorhabditis elegans : WS220.66</option>
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63 <option value="WS220.65">Caenorhabditis elegans : WS220.65</option>
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64 <option value="WS220.64">Caenorhabditis elegans : WS220.64</option>
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65 <option value="WS220.63">Caenorhabditis elegans : WS220.63</option>
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66 <option value="calJac3.2.1.61">Callithrix jacchus : calJac3.2.1.61</option>
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67 <option value="calJac3.2.1.60">Callithrix jacchus : calJac3.2.1.60</option>
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68 <option value="C_jacchus3.2.1.66">Callithrix jacchus : C_jacchus3.2.1.66</option>
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69 <option value="C_jacchus3.2.1.65">Callithrix jacchus : C_jacchus3.2.1.65</option>
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70 <option value="C_jacchus3.2.1.64">Callithrix jacchus : C_jacchus3.2.1.64</option>
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71 <option value="C_jacchus3.2.1.63">Callithrix jacchus : C_jacchus3.2.1.63</option>
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72 <option value="cAlbicansv21">Candida albicans SC5314 : cAlbicansv21</option>
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73 <option value="canFam2.61">Canis familiaris : canFam2.61</option>
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74 <option value="canFam2.60">Canis familiaris : canFam2.60</option>
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75 <option value="canFam2.59">Canis familiaris : canFam2.59</option>
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76 <option value="BROADD2.66">Canis familiaris : BROADD2.66</option>
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77 <option value="BROADD2.65">Canis familiaris : BROADD2.65</option>
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78 <option value="BROADD2.64">Canis familiaris : BROADD2.64</option>
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79 <option value="BROADD2.63">Canis familiaris : BROADD2.63</option>
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80 <option value="crubella">Capsella rubella v1.0 : crubella</option>
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81 <option value="cavPor3.66">Cavia porcellus : cavPor3.66</option>
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82 <option value="cavPor3.65">Cavia porcellus : cavPor3.65</option>
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83 <option value="cavPor3.64">Cavia porcellus : cavPor3.64</option>
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84 <option value="cavPor3.63">Cavia porcellus : cavPor3.63</option>
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85 <option value="cavPor3.61">Cavia porcellus : cavPor3.61</option>
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86 <option value="cavPor3.60">Cavia porcellus : cavPor3.60</option>
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87 <option value="choHof1.66">Choloepus hoffmanni : choHof1.66</option>
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88 <option value="choHof1.65">Choloepus hoffmanni : choHof1.65</option>
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89 <option value="choHof1.64">Choloepus hoffmanni : choHof1.64</option>
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90 <option value="choHof1.63">Choloepus hoffmanni : choHof1.63</option>
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91 <option value="choHof1.61">Choloepus hoffmanni : choHof1.61</option>
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92 <option value="choHof1.60">Choloepus hoffmanni : choHof1.60</option>
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93 <option value="cInt2.61">Ciona intestinalis : cInt2.61</option>
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94 <option value="cInt2.60">Ciona intestinalis : cInt2.60</option>
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95 <option value="KH.66">Ciona intestinalis : KH.66</option>
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96 <option value="JGI2.65">Ciona intestinalis : JGI2.65</option>
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97 <option value="JGI2.64">Ciona intestinalis : JGI2.64</option>
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98 <option value="JGI2.63">Ciona intestinalis : JGI2.63</option>
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99 <option value="cSav2.0.61">Ciona savignyi : cSav2.0.61</option>
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100 <option value="cSav2.0.60">Ciona savignyi : cSav2.0.60</option>
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101 <option value="CSAV2.0.66">Ciona savignyi : CSAV2.0.66</option>
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102 <option value="CSAV2.0.65">Ciona savignyi : CSAV2.0.65</option>
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103 <option value="CSAV2.0.64">Ciona savignyi : CSAV2.0.64</option>
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104 <option value="CSAV2.0.63">Ciona savignyi : CSAV2.0.63</option>
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105 <option value="NC_009089.1">Clostridium difficile : NC_009089.1</option>
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106 <option value="c_neoformans">Cryptococcus neoformans : c_neoformans</option>
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107 <option value="danRer9.61">Danio rerio : danRer9.61</option>
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108 <option value="danRer9.60">Danio rerio : danRer9.60</option>
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109 <option value="danRer8.59">Danio rerio : danRer8.59</option>
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110 <option value="Zv9.66">Danio rerio : Zv9.66</option>
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111 <option value="Zv9.65">Danio rerio : Zv9.65</option>
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112 <option value="Zv9.64">Danio rerio : Zv9.64</option>
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113 <option value="Zv9.63">Danio rerio : Zv9.63</option>
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114 <option value="dasNov2.66">Dasypus novemcinctus : dasNov2.66</option>
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115 <option value="dasNov2.65">Dasypus novemcinctus : dasNov2.65</option>
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116 <option value="dasNov2.64">Dasypus novemcinctus : dasNov2.64</option>
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117 <option value="dasNov2.63">Dasypus novemcinctus : dasNov2.63</option>
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118 <option value="dasNov2.61">Dasypus novemcinctus : dasNov2.61</option>
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119 <option value="dasNov2.60">Dasypus novemcinctus : dasNov2.60</option>
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120 <option value="dipOrd1.66">Dipodomys ordii : dipOrd1.66</option>
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121 <option value="dipOrd1.65">Dipodomys ordii : dipOrd1.65</option>
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122 <option value="dipOrd1.64">Dipodomys ordii : dipOrd1.64</option>
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123 <option value="dipOrd1.63">Dipodomys ordii : dipOrd1.63</option>
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124 <option value="dipOrd1.61">Dipodomys ordii : dipOrd1.61</option>
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125 <option value="dipOrd1.60">Dipodomys ordii : dipOrd1.60</option>
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126 <option value="dm5.42">Drosophila melanogaster : dm5.42</option>
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127 <option value="dm5.40">Drosophila melanogaster : dm5.40</option>
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128 <option value="dm5.34">Drosophila melanogaster : dm5.34</option>
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129 <option value="dm5.32">Drosophila melanogaster : dm5.32</option>
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130 <option value="dm5.31">Drosophila melanogaster : dm5.31</option>
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131 <option value="dm5.30">Drosophila melanogaster : dm5.30</option>
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132 <option value="dm5.25.63">Drosophila melanogaster : dm5.25.63</option>
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133 <option value="dm5.25.61">Drosophila melanogaster : dm5.25.61</option>
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134 <option value="dm5.25.60">Drosophila melanogaster : dm5.25.60</option>
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135 <option value="dm5.25.59">Drosophila melanogaster : dm5.25.59</option>
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136 <option value="dm5.22">Drosophila melanogaster : dm5.22</option>
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137 <option value="dm5.12">Drosophila melanogaster : dm5.12</option>
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138 <option value="BDGP5.66">Drosophila melanogaster : BDGP5.66</option>
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139 <option value="BDGP5.25.65">Drosophila melanogaster : BDGP5.25.65</option>
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140 <option value="BDGP5.25.64">Drosophila melanogaster : BDGP5.25.64</option>
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141 <option value="BDGP5.25.63">Drosophila melanogaster : BDGP5.25.63</option>
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142 <option value="tenrec1.61">Echinops telfairi : tenrec1.61</option>
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143 <option value="tenrec1.60">Echinops telfairi : tenrec1.60</option>
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144 <option value="TENREC.66">Echinops telfairi : TENREC.66</option>
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145 <option value="TENREC.65">Echinops telfairi : TENREC.65</option>
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146 <option value="TENREC.64">Echinops telfairi : TENREC.64</option>
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147 <option value="TENREC.63">Echinops telfairi : TENREC.63</option>
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148 <option value="equCab2.61">Equus caballus : equCab2.61</option>
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149 <option value="equCab2.60">Equus caballus : equCab2.60</option>
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150 <option value="EquCab2.66">Equus caballus : EquCab2.66</option>
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151 <option value="EquCab2.65">Equus caballus : EquCab2.65</option>
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152 <option value="EquCab2.64">Equus caballus : EquCab2.64</option>
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153 <option value="EquCab2.63">Equus caballus : EquCab2.63</option>
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154 <option value="eriEur1.61">Erinaceus europaeus : eriEur1.61</option>
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155 <option value="eriEur1.60">Erinaceus europaeus : eriEur1.60</option>
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156 <option value="HEDGEHOG.66">Erinaceus europaeus : HEDGEHOG.66</option>
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157 <option value="HEDGEHOG.65">Erinaceus europaeus : HEDGEHOG.65</option>
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158 <option value="HEDGEHOG.64">Erinaceus europaeus : HEDGEHOG.64</option>
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159 <option value="HEDGEHOG.63">Erinaceus europaeus : HEDGEHOG.63</option>
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160 <option value="NC_000913">Escherichia coli : NC_000913</option>
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161 <option value="cat1.61">Felis catus : cat1.61</option>
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162 <option value="cat1.60">Felis catus : cat1.60</option>
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163 <option value="CAT.66">Felis catus : CAT.66</option>
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164 <option value="CAT.65">Felis catus : CAT.65</option>
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165 <option value="CAT.64">Felis catus : CAT.64</option>
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166 <option value="CAT.63">Felis catus : CAT.63</option>
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167 <option value="gadMor1.66">Gadus morhua : gadMor1.66</option>
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168 <option value="ggallus2.61">Gallus gallus : ggallus2.61</option>
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169 <option value="ggallus2.60">Gallus gallus : ggallus2.60</option>
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170 <option value="ggallus2.59">Gallus gallus : ggallus2.59</option>
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171 <option value="WASHUC2.66">Gallus gallus : WASHUC2.66</option>
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172 <option value="WASHUC2.65">Gallus gallus : WASHUC2.65</option>
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173 <option value="WASHUC2.64">Gallus gallus : WASHUC2.64</option>
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174 <option value="WASHUC2.63">Gallus gallus : WASHUC2.63</option>
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175 <option value="gacu1.61">Gasterosteus aculeatus : gacu1.61</option>
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176 <option value="gacu1.60">Gasterosteus aculeatus : gacu1.60</option>
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177 <option value="BROADS1.66">Gasterosteus aculeatus : BROADS1.66</option>
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178 <option value="BROADS1.65">Gasterosteus aculeatus : BROADS1.65</option>
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179 <option value="BROADS1.64">Gasterosteus aculeatus : BROADS1.64</option>
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180 <option value="BROADS1.63">Gasterosteus aculeatus : BROADS1.63</option>
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181 <option value="gmax1.09v8">Glycine Max : gmax1.09v8</option>
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182 <option value="gmax1.09">Glycine Max : gmax1.09</option>
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183 <option value="gorGor3.63">Gorilla gorilla : gorGor3.63</option>
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184 <option value="gorGor3.61">Gorilla gorilla : gorGor3.61</option>
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185 <option value="gorGor3.60">Gorilla gorilla : gorGor3.60</option>
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186 <option value="gorGor3.1.66">Gorilla gorilla : gorGor3.1.66</option>
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187 <option value="gorGor3.1.65">Gorilla gorilla : gorGor3.1.65</option>
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188 <option value="gorGor3.1.64">Gorilla gorilla : gorGor3.1.64</option>
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189 <option value="kw1407.2012">Grosmannia clavigera : kw1407.2012</option>
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190 <option value="hiv">HIV : hiv</option>
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191 <option value="SIVmac239">HIV : SIVmac239</option>
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192 <option value="herpesvirus1">Herpesvirus : herpesvirus1</option>
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193 <option value="hg37.63">Homo sapiens : hg37.63</option>
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194 <option value="hg37.61">Homo sapiens : hg37.61</option>
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195 <option value="hg37.60">Homo sapiens : hg37.60</option>
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196 <option value="hg37.59">Homo sapiens : hg37.59</option>
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197 <option value="hg36.54">Homo sapiens : hg36.54</option>
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198 <option value="hg19">Homo sapiens : hg19</option>
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199 <option value="GRCh37.66">Homo sapiens : GRCh37.66</option>
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200 <option value="GRCh37.65">Homo sapiens : GRCh37.65</option>
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201 <option value="GRCh37.64">Homo sapiens : GRCh37.64</option>
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202 <option value="GRCh37.63">Homo sapiens : GRCh37.63</option>
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203 <option value="LatCha1.66">Latimeria chalumnae : LatCha1.66</option>
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204 <option value="lmjf4">LmajorFriedlin : lmjf4</option>
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205 <option value="loxAfr3.66">Loxodonta africana : loxAfr3.66</option>
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206 <option value="loxAfr3.65">Loxodonta africana : loxAfr3.65</option>
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207 <option value="loxAfr3.64">Loxodonta africana : loxAfr3.64</option>
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208 <option value="loxAfr3.63">Loxodonta africana : loxAfr3.63</option>
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209 <option value="loxAfr3.61">Loxodonta africana : loxAfr3.61</option>
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210 <option value="loxAfr3.60">Loxodonta africana : loxAfr3.60</option>
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211 <option value="mmul1.61">Macaca mulatta : mmul1.61</option>
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212 <option value="mmul1.60">Macaca mulatta : mmul1.60</option>
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213 <option value="MMUL_1.66">Macaca mulatta : MMUL_1.66</option>
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214 <option value="MMUL_1.65">Macaca mulatta : MMUL_1.65</option>
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215 <option value="MMUL_1.64">Macaca mulatta : MMUL_1.64</option>
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216 <option value="MMUL_1.63">Macaca mulatta : MMUL_1.63</option>
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217 <option value="meug1.0.61">Macropus eugenii : meug1.0.61</option>
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218 <option value="meug1.0.60">Macropus eugenii : meug1.0.60</option>
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219 <option value="Meug_1.0.66">Macropus eugenii : Meug_1.0.66</option>
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220 <option value="Meug_1.0.65">Macropus eugenii : Meug_1.0.65</option>
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221 <option value="Meug_1.0.64">Macropus eugenii : Meug_1.0.64</option>
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222 <option value="Meug_1.0.63">Macropus eugenii : Meug_1.0.63</option>
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223 <option value="maizeZmB73">Maize ZmB73 : maizeZmB73</option>
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224 <option value="turkey.UMD2.61">Meleagris gallopavo : turkey.UMD2.61</option>
|
|
|
225 <option value="UMD2.66">Meleagris gallopavo : UMD2.66</option>
|
|
|
226 <option value="UMD2.65">Meleagris gallopavo : UMD2.65</option>
|
|
|
227 <option value="UMD2.64">Meleagris gallopavo : UMD2.64</option>
|
|
|
228 <option value="UMD2.63">Meleagris gallopavo : UMD2.63</option>
|
|
|
229 <option value="micMur1.66">Microcebus murinus : micMur1.66</option>
|
|
|
230 <option value="micMur1.65">Microcebus murinus : micMur1.65</option>
|
|
|
231 <option value="micMur1.64">Microcebus murinus : micMur1.64</option>
|
|
|
232 <option value="micMur1.63">Microcebus murinus : micMur1.63</option>
|
|
|
233 <option value="micMur1.61">Microcebus murinus : micMur1.61</option>
|
|
|
234 <option value="micMur1.60">Microcebus murinus : micMur1.60</option>
|
|
|
235 <option value="monDom5.61">Monodelphis domestica : monDom5.61</option>
|
|
|
236 <option value="monDom5.60">Monodelphis domestica : monDom5.60</option>
|
|
|
237 <option value="BROADO5.66">Monodelphis domestica : BROADO5.66</option>
|
|
|
238 <option value="BROADO5.65">Monodelphis domestica : BROADO5.65</option>
|
|
|
239 <option value="BROADO5.64">Monodelphis domestica : BROADO5.64</option>
|
|
|
240 <option value="BROADO5.63">Monodelphis domestica : BROADO5.63</option>
|
|
|
241 <option value="mm37.61">Mus musculus : mm37.61</option>
|
|
|
242 <option value="mm37.60">Mus musculus : mm37.60</option>
|
|
|
243 <option value="mm37.59">Mus musculus : mm37.59</option>
|
|
|
244 <option value="mm37">Mus musculus : mm37</option>
|
|
|
245 <option value="NCBIM37.66">Mus musculus : NCBIM37.66</option>
|
|
|
246 <option value="NCBIM37.65">Mus musculus : NCBIM37.65</option>
|
|
|
247 <option value="NCBIM37.64">Mus musculus : NCBIM37.64</option>
|
|
|
248 <option value="NCBIM37.63">Mus musculus : NCBIM37.63</option>
|
|
|
249 <option value="mmm.2012">Mycobacterium marinum M : mmm.2012</option>
|
|
|
250 <option value="m_tuberculosis">Mycobacterium tuberculosis : m_tuberculosis</option>
|
|
|
251 <option value="myco_fh">Mycoplasma pneumoninae FH : myco_fh</option>
|
|
|
252 <option value="myco_m129">Mycoplasma pneumoninae M129 : myco_m129</option>
|
|
|
253 <option value="myoLuc1.61">Myotis lucifugus : myoLuc1.61</option>
|
|
|
254 <option value="myoLuc1.60">Myotis lucifugus : myoLuc1.60</option>
|
|
|
255 <option value="Myoluc2.0.66">Myotis lucifugus : Myoluc2.0.66</option>
|
|
|
256 <option value="Myoluc2.0.65">Myotis lucifugus : Myoluc2.0.65</option>
|
|
|
257 <option value="Myoluc2.0.64">Myotis lucifugus : Myoluc2.0.64</option>
|
|
|
258 <option value="Myoluc2.0.63">Myotis lucifugus : Myoluc2.0.63</option>
|
|
|
259 <option value="ncrassa">Neurospora Crassa : ncrassa</option>
|
|
|
260 <option value="Nleu1.0.66">Nomascus leucogenys : Nleu1.0.66</option>
|
|
|
261 <option value="Nleu1.0.65">Nomascus leucogenys : Nleu1.0.65</option>
|
|
|
262 <option value="Nleu1.0.64">Nomascus leucogenys : Nleu1.0.64</option>
|
|
|
263 <option value="Nleu1.0.63">Nomascus leucogenys : Nleu1.0.63</option>
|
|
|
264 <option value="pika.66">Ochotona princeps : pika.66</option>
|
|
|
265 <option value="pika.65">Ochotona princeps : pika.65</option>
|
|
|
266 <option value="pika.64">Ochotona princeps : pika.64</option>
|
|
|
267 <option value="pika.63">Ochotona princeps : pika.63</option>
|
|
|
268 <option value="ochPri2.61">Ochotona princeps : ochPri2.61</option>
|
|
|
269 <option value="ochPri2.60">Ochotona princeps : ochPri2.60</option>
|
|
|
270 <option value="oana5.61">Ornithorhynchus anatinus : oana5.61</option>
|
|
|
271 <option value="oana5.60">Ornithorhynchus anatinus : oana5.60</option>
|
|
|
272 <option value="OANA5.66">Ornithorhynchus anatinus : OANA5.66</option>
|
|
|
273 <option value="OANA5.65">Ornithorhynchus anatinus : OANA5.65</option>
|
|
|
274 <option value="OANA5.64">Ornithorhynchus anatinus : OANA5.64</option>
|
|
|
275 <option value="OANA5.63">Ornithorhynchus anatinus : OANA5.63</option>
|
|
|
276 <option value="oryCun2.66">Oryctolagus cuniculus : oryCun2.66</option>
|
|
|
277 <option value="oryCun2.65">Oryctolagus cuniculus : oryCun2.65</option>
|
|
|
278 <option value="oryCun2.64">Oryctolagus cuniculus : oryCun2.64</option>
|
|
|
279 <option value="oryCun2.63">Oryctolagus cuniculus : oryCun2.63</option>
|
|
|
280 <option value="oryCun2.61">Oryctolagus cuniculus : oryCun2.61</option>
|
|
|
281 <option value="oryCun2.60">Oryctolagus cuniculus : oryCun2.60</option>
|
|
|
282 <option value="medaka1.61">Oryzias latipes : medaka1.61</option>
|
|
|
283 <option value="medaka1.60">Oryzias latipes : medaka1.60</option>
|
|
|
284 <option value="MEDAKA1.66">Oryzias latipes : MEDAKA1.66</option>
|
|
|
285 <option value="MEDAKA1.65">Oryzias latipes : MEDAKA1.65</option>
|
|
|
286 <option value="MEDAKA1.64">Oryzias latipes : MEDAKA1.64</option>
|
|
|
287 <option value="MEDAKA1.63">Oryzias latipes : MEDAKA1.63</option>
|
|
|
288 <option value="bushBaby1.61">Otolemur garnettii : bushBaby1.61</option>
|
|
|
289 <option value="bushBaby1.60">Otolemur garnettii : bushBaby1.60</option>
|
|
|
290 <option value="OtoGar3.66">Otolemur garnettii : OtoGar3.66</option>
|
|
|
291 <option value="BUSHBABY1.65">Otolemur garnettii : BUSHBABY1.65</option>
|
|
|
292 <option value="BUSHBABY1.64">Otolemur garnettii : BUSHBABY1.64</option>
|
|
|
293 <option value="BUSHBABY1.63">Otolemur garnettii : BUSHBABY1.63</option>
|
|
|
294 <option value="chimp2.1.61">Pan troglodytes : chimp2.1.61</option>
|
|
|
295 <option value="chimp2.1.60">Pan troglodytes : chimp2.1.60</option>
|
|
|
296 <option value="chimp2.1.59">Pan troglodytes : chimp2.1.59</option>
|
|
|
297 <option value="CHIMP2.1.65">Pan troglodytes : CHIMP2.1.65</option>
|
|
|
298 <option value="CHIMP2.1.64">Pan troglodytes : CHIMP2.1.64</option>
|
|
|
299 <option value="CHIMP2.1.63">Pan troglodytes : CHIMP2.1.63</option>
|
|
|
300 <option value="CHIMP2.1.4.66">Pan troglodytes : CHIMP2.1.4.66</option>
|
|
|
301 <option value="ppersica139">Peach : ppersica139</option>
|
|
|
302 <option value="peromyscus">Peromyscus leucopus : peromyscus</option>
|
|
|
303 <option value="Pmarinus_7.0.66">Petromyzon marinus : Pmarinus_7.0.66</option>
|
|
|
304 <option value="Petromyzon_marinus_7.0.65">Petromyzon marinus : Petromyzon_marinus_7.0.65</option>
|
|
|
305 <option value="Petromyzon_marinus_7.0.64">Petromyzon marinus : Petromyzon_marinus_7.0.64</option>
|
|
|
306 <option value="plasmo72">Plasmodium falciparum : plasmo72</option>
|
|
|
307 <option value="PPYG2.66">Pongo abelii : PPYG2.66</option>
|
|
|
308 <option value="PPYG2.65">Pongo abelii : PPYG2.65</option>
|
|
|
309 <option value="PPYG2.64">Pongo abelii : PPYG2.64</option>
|
|
|
310 <option value="PPYG2.63">Pongo abelii : PPYG2.63</option>
|
|
|
311 <option value="ppyg2.61">Pongo pygmaeus : ppyg2.61</option>
|
|
|
312 <option value="ppyg2.60">Pongo pygmaeus : ppyg2.60</option>
|
|
|
313 <option value="proCap1.66">Procavia capensis : proCap1.66</option>
|
|
|
314 <option value="proCap1.65">Procavia capensis : proCap1.65</option>
|
|
|
315 <option value="proCap1.64">Procavia capensis : proCap1.64</option>
|
|
|
316 <option value="proCap1.63">Procavia capensis : proCap1.63</option>
|
|
|
317 <option value="proCap1.61">Procavia capensis : proCap1.61</option>
|
|
|
318 <option value="proCap1.60">Procavia capensis : proCap1.60</option>
|
|
|
319 <option value="paeru.PA14">Pseudomonas aeruginosa : paeru.PA14</option>
|
|
|
320 <option value="paeru.PA01">Pseudomonas aeruginosa : paeru.PA01</option>
|
|
|
321 <option value="pfluo.SBW25.NC_012660">Pseudomonas fluorescens : pfluo.SBW25.NC_012660</option>
|
|
|
322 <option value="pfluo.SBW25.NC_009444">Pseudomonas fluorescens : pfluo.SBW25.NC_009444</option>
|
|
|
323 <option value="pteVam1.66">Pteropus vampyrus : pteVam1.66</option>
|
|
|
324 <option value="pteVam1.65">Pteropus vampyrus : pteVam1.65</option>
|
|
|
325 <option value="pteVam1.64">Pteropus vampyrus : pteVam1.64</option>
|
|
|
326 <option value="pteVam1.63">Pteropus vampyrus : pteVam1.63</option>
|
|
|
327 <option value="pteVam1.61">Pteropus vampyrus : pteVam1.61</option>
|
|
|
328 <option value="pteVam1.60">Pteropus vampyrus : pteVam1.60</option>
|
|
|
329 <option value="rat3.4.61">Rattus norvegicus : rat3.4.61</option>
|
|
|
330 <option value="rat3.4.60">Rattus norvegicus : rat3.4.60</option>
|
|
|
331 <option value="rat3.4.59">Rattus norvegicus : rat3.4.59</option>
|
|
|
332 <option value="RGSC3.4.66">Rattus norvegicus : RGSC3.4.66</option>
|
|
|
333 <option value="RGSC3.4.65">Rattus norvegicus : RGSC3.4.65</option>
|
|
|
334 <option value="RGSC3.4.64">Rattus norvegicus : RGSC3.4.64</option>
|
|
|
335 <option value="RGSC3.4.63">Rattus norvegicus : RGSC3.4.63</option>
|
|
|
336 <option value="rice6.1">Rice : rice6.1</option>
|
|
|
337 <option value="rice5">Rice : rice5</option>
|
|
|
338 <option value="SCU49845">SCU49845 : SCU49845</option>
|
|
|
339 <option value="sacCer2.61">Saccharomyces cerevisiae : sacCer2.61</option>
|
|
|
340 <option value="sacCer2.60">Saccharomyces cerevisiae : sacCer2.60</option>
|
|
|
341 <option value="sacCer2.59">Saccharomyces cerevisiae : sacCer2.59</option>
|
|
|
342 <option value="sacCer2">Saccharomyces cerevisiae : sacCer2</option>
|
|
|
343 <option value="EF4.66">Saccharomyces cerevisiae : EF4.66</option>
|
|
|
344 <option value="EF4.65">Saccharomyces cerevisiae : EF4.65</option>
|
|
|
345 <option value="EF3.64">Saccharomyces cerevisiae : EF3.64</option>
|
|
|
346 <option value="EF3.63">Saccharomyces cerevisiae : EF3.63</option>
|
|
|
347 <option value="DEVIL7.0.66">Sarcophilus harrisii : DEVIL7.0.66</option>
|
|
|
348 <option value="DEVIL7.0.65">Sarcophilus harrisii : DEVIL7.0.65</option>
|
|
|
349 <option value="DEVIL7.0.64">Sarcophilus harrisii : DEVIL7.0.64</option>
|
|
|
350 <option value="spombe">Schizosaccharomyces pombe : spombe</option>
|
|
|
351 <option value="sorAra1.61">Sorex araneus : sorAra1.61</option>
|
|
|
352 <option value="sorAra1.60">Sorex araneus : sorAra1.60</option>
|
|
|
353 <option value="COMMON_SHREW1.66">Sorex araneus : COMMON_SHREW1.66</option>
|
|
|
354 <option value="COMMON_SHREW1.65">Sorex araneus : COMMON_SHREW1.65</option>
|
|
|
355 <option value="COMMON_SHREW1.64">Sorex araneus : COMMON_SHREW1.64</option>
|
|
|
356 <option value="COMMON_SHREW1.63">Sorex araneus : COMMON_SHREW1.63</option>
|
|
|
357 <option value="speTri1.61">Spermophilus tridecemlineatus : speTri1.61</option>
|
|
|
358 <option value="speTri1.60">Spermophilus tridecemlineatus : speTri1.60</option>
|
|
|
359 <option value="SQUIRREL.66">Spermophilus tridecemlineatus : SQUIRREL.66</option>
|
|
|
360 <option value="SQUIRREL.65">Spermophilus tridecemlineatus : SQUIRREL.65</option>
|
|
|
361 <option value="SQUIRREL.64">Spermophilus tridecemlineatus : SQUIRREL.64</option>
|
|
|
362 <option value="SQUIRREL.63">Spermophilus tridecemlineatus : SQUIRREL.63</option>
|
|
|
363 <option value="CP000730">Staphylococcus aureus : CP000730</option>
|
|
|
364 <option value="sScrofa9.61">Sus scrofa : sScrofa9.61</option>
|
|
|
365 <option value="sScrofa9.60">Sus scrofa : sScrofa9.60</option>
|
|
|
366 <option value="Sscrofa9.66">Sus scrofa : Sscrofa9.66</option>
|
|
|
367 <option value="Sscrofa9.65">Sus scrofa : Sscrofa9.65</option>
|
|
|
368 <option value="Sscrofa9.64">Sus scrofa : Sscrofa9.64</option>
|
|
|
369 <option value="Sscrofa9.63">Sus scrofa : Sscrofa9.63</option>
|
|
|
370 <option value="taeGut3.2.4.66">Taeniopygia guttata : taeGut3.2.4.66</option>
|
|
|
371 <option value="taeGut3.2.4.65">Taeniopygia guttata : taeGut3.2.4.65</option>
|
|
|
372 <option value="taeGut3.2.4.64">Taeniopygia guttata : taeGut3.2.4.64</option>
|
|
|
373 <option value="taeGut3.2.4.63">Taeniopygia guttata : taeGut3.2.4.63</option>
|
|
|
374 <option value="taeGut3.2.4.61">Taeniopygia guttata : taeGut3.2.4.61</option>
|
|
|
375 <option value="taeGut3.2.4.60">Taeniopygia guttata : taeGut3.2.4.60</option>
|
|
|
376 <option value="fugu4.61">Takifugu rubripes : fugu4.61</option>
|
|
|
377 <option value="fugu4.60">Takifugu rubripes : fugu4.60</option>
|
|
|
378 <option value="FUGU4.66">Takifugu rubripes : FUGU4.66</option>
|
|
|
379 <option value="FUGU4.65">Takifugu rubripes : FUGU4.65</option>
|
|
|
380 <option value="FUGU4.64">Takifugu rubripes : FUGU4.64</option>
|
|
|
381 <option value="FUGU4.63">Takifugu rubripes : FUGU4.63</option>
|
|
|
382 <option value="tarSyr1.66">Tarsius syrichta : tarSyr1.66</option>
|
|
|
383 <option value="tarSyr1.65">Tarsius syrichta : tarSyr1.65</option>
|
|
|
384 <option value="tarSyr1.64">Tarsius syrichta : tarSyr1.64</option>
|
|
|
385 <option value="tarSyr1.63">Tarsius syrichta : tarSyr1.63</option>
|
|
|
386 <option value="tarSyr1.61">Tarsius syrichta : tarSyr1.61</option>
|
|
|
387 <option value="tarSyr1.60">Tarsius syrichta : tarSyr1.60</option>
|
|
|
388 <option value="test_ENSG00000158062">TestCase : test_ENSG00000158062</option>
|
|
|
389 <option value="testHg3765Chr22">TestCase : testHg3765Chr22</option>
|
|
|
390 <option value="testHg3763ChrY">TestCase : testHg3763ChrY</option>
|
|
|
391 <option value="testHg3763Chr20">TestCase : testHg3763Chr20</option>
|
|
|
392 <option value="testHg3763Chr1">TestCase : testHg3763Chr1</option>
|
|
|
393 <option value="testHg3761Chr16">TestCase : testHg3761Chr16</option>
|
|
|
394 <option value="testHg3761Chr15">TestCase : testHg3761Chr15</option>
|
|
|
395 <option value="testCase">TestCase : testCase</option>
|
|
|
396 <option value="test">TestCase : test</option>
|
|
|
397 <option value="tetraodon8.61">Tetraodon nigroviridis : tetraodon8.61</option>
|
|
|
398 <option value="tetraodon8.60">Tetraodon nigroviridis : tetraodon8.60</option>
|
|
|
399 <option value="TETRAODON8.66">Tetraodon nigroviridis : TETRAODON8.66</option>
|
|
|
400 <option value="TETRAODON8.65">Tetraodon nigroviridis : TETRAODON8.65</option>
|
|
|
401 <option value="TETRAODON8.64">Tetraodon nigroviridis : TETRAODON8.64</option>
|
|
|
402 <option value="TETRAODON8.63">Tetraodon nigroviridis : TETRAODON8.63</option>
|
|
|
403 <option value="SL2.40">Tomato : SL2.40</option>
|
|
|
404 <option value="tupBel1.61">Tupaia belangeri : tupBel1.61</option>
|
|
|
405 <option value="tupBel1.60">Tupaia belangeri : tupBel1.60</option>
|
|
|
406 <option value="TREESHREW.66">Tupaia belangeri : TREESHREW.66</option>
|
|
|
407 <option value="TREESHREW.65">Tupaia belangeri : TREESHREW.65</option>
|
|
|
408 <option value="TREESHREW.64">Tupaia belangeri : TREESHREW.64</option>
|
|
|
409 <option value="TREESHREW.63">Tupaia belangeri : TREESHREW.63</option>
|
|
|
410 <option value="turTru1.66">Tursiops truncatus : turTru1.66</option>
|
|
|
411 <option value="turTru1.65">Tursiops truncatus : turTru1.65</option>
|
|
|
412 <option value="turTru1.64">Tursiops truncatus : turTru1.64</option>
|
|
|
413 <option value="turTru1.63">Tursiops truncatus : turTru1.63</option>
|
|
|
414 <option value="turTru1.61">Tursiops truncatus : turTru1.61</option>
|
|
|
415 <option value="turTru1.60">Tursiops truncatus : turTru1.60</option>
|
|
|
416 <option value="vacwr">Vaccinia Western Reserve : vacwr</option>
|
|
|
417 <option value="vibrio">Vibrio Cholerae : vibrio</option>
|
|
|
418 <option value="vicPac1.66">Vicugna pacos : vicPac1.66</option>
|
|
|
419 <option value="vicPac1.65">Vicugna pacos : vicPac1.65</option>
|
|
|
420 <option value="vicPac1.64">Vicugna pacos : vicPac1.64</option>
|
|
|
421 <option value="vicPac1.63">Vicugna pacos : vicPac1.63</option>
|
|
|
422 <option value="vicPac1.61">Vicugna pacos : vicPac1.61</option>
|
|
|
423 <option value="vicPac1.60">Vicugna pacos : vicPac1.60</option>
|
|
|
424 <option value="xtrop7.1">Xenopus tropicalis : xtrop7.1</option>
|
|
|
425 <option value="xtrop4.1.61">Xenopus tropicalis : xtrop4.1.61</option>
|
|
|
426 <option value="xtrop4.1.60">Xenopus tropicalis : xtrop4.1.60</option>
|
|
|
427 <option value="JGI_4.2.66">Xenopus tropicalis : JGI_4.2.66</option>
|
|
|
428 <option value="JGI_4.2.64">Xenopus tropicalis : JGI_4.2.64</option>
|
|
|
429 <option value="JGI_4.2.63">Xenopus tropicalis : JGI_4.2.63</option>
|
|
|
430 </param>
|
|
|
431
|
|
|
432 <param name="udLength" type="select" label="Upstream / Downstream length">
|
|
|
433 <option value="0">No upstream / downstream intervals (0 bases)</option>
|
|
|
434 <option value="200">200 bases</option>
|
|
|
435 <option value="500">500 bases</option>
|
|
|
436 <option value="1000">1000 bases</option>
|
|
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437 <option value="2000">2000 bases</option>
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438 <option value="5000" selected="true">5000 bases</option>
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439 <option value="10000">10000 bases</option>
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440 <option value="20000">20000 bases</option>
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441 </param>
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442
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443 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
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444 <option value="">No filter (analyze everything)</option>
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445 <option value="-hom">Analyze homozygous sequence changes only </option>
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446 <option value="-het">Analyze heterozygous sequence changes only </option>
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447 </param>
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448
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449 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
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450 <option value="">No filter (analyze everything)</option>
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451 <option value="-del">Analyze deletions only </option>
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452 <option value="-ins">Analyze insertions only </option>
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453 <option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option>
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454 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
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455 </param>
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456
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457 <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output">
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458 <option value="None" selected="true">None</option>
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459 <option value="downstream">Do not show DOWNSTREAM changes </option>
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460 <option value="intergenic">Do not show INTERGENIC changes </option>
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461 <option value="intron">Do not show INTRON changes </option>
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462 <option value="upstream">Do not show UPSTREAM changes </option>
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463 <option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
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464 </param>
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465
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466 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
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467 <option value="">Use default (based on input type)</option>
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468 <option value="-0">Force zero-based positions (both input and output)</option>
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469 <option value="-1">Force one-based positions (both input and output)</option>
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470 </param>
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471 </inputs>
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472 <outputs>
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473 <data format="tabular" name="output" >
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474 <change_format>
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475 <when input="outputFormat" value="txt" format="tabular" />
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476 <when input="outputFormat" value="vcf" format="vcf" />
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477 <when input="outputFormat" value="bed" format="bed" />
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478 <when input="outputFormat" value="bedAnn" format="bed" />
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479 </change_format>
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480 </data>
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481 <data format="html" name="statsFile" />
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482 </outputs>
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483 <stdio>
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484 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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485 <exit_code range="1:" level="fatal" description="Error" />
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486 </stdio>
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487 <help>
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488
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489 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
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490
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491 For details about this tool, please go to http://snpEff.sourceforge.net
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492
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493 </help>
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494 </tool>
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495
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