Mercurial > repos > jjohnson > snpeff_with_dep
view snpEff.xml @ 16:24c77a318a0f
Fix SnpSift dependency
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 21 Sep 2012 16:20:13 -0500 |
| parents | ef4598ea7179 |
| children | aab5e0adb26d |
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<tool id="snpEff" name="SnpEff" version="1.0"> <description>Variant effect and annotation</description> <!-- You will need to change the path to wherever your installation is. You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) <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> --> <requirements> <requirement type="package" version="3.0">snpEff</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> <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> <inputs> <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> <param name="inputFormat" type="select" label="Input format"> <option value="vcf">VCF</option> <option value="txt">Tabular</option> <option value="pileup">Pileup</option> <option value="bed">BED</option> </param> <param name="outputFormat" type="select" label="Output format"> <option value="txt">Tabular</option> <option value="vcf">VCF (only if input is VCF)</option> <option value="bed">BED</option> <option value="bedAnn">BED Annotations</option> </param> <param name="genomeVersion" type="select" label="Genome"> <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option> <option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option> <option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option> <option value="ailMel1.64">Ailuropoda melanoleuca : ailMel1.64</option> <option value="ailMel1.63">Ailuropoda melanoleuca : ailMel1.63</option> <option value="anoCar2.0.61">Anolis carolinensis : anoCar2.0.61</option> <option value="anoCar1.0.60">Anolis carolinensis : anoCar1.0.60</option> <option value="AnoCar2.0.66">Anolis carolinensis : AnoCar2.0.66</option> <option value="AnoCar2.0.65">Anolis carolinensis : AnoCar2.0.65</option> <option value="AnoCar2.0.64">Anolis carolinensis : AnoCar2.0.64</option> <option value="AnoCar2.0.63">Anolis carolinensis : AnoCar2.0.63</option> <option value="agam2.6">Anopheles gambiae : agam2.6</option> <option value="agam">Anopheles gambiae : agam</option> <option value="aquiCoer">Aquilegia coerulea : aquiCoer</option> <option value="athalianaTair9">Arabidopsis Thaliana : athalianaTair9</option> <option value="athalianaTair10">Arabidopsis Thaliana : athalianaTair10</option> <option value="athaliana130">Arabidopsis Thaliana : athaliana130</option> <option value="alyrata107">Arabidopsis lyrata : alyrata107</option> <option value="alyrata1">Arabidopsis lyrata : alyrata1</option> <option value="amel2">Bee : amel2</option> <option value="btau4.0.61">Bos taurus : btau4.0.61</option> <option value="btau4.0.60">Bos taurus : btau4.0.60</option> <option value="btau4.0.59">Bos taurus : btau4.0.59</option> <option value="UMD3_1">Bos taurus : UMD3_1</option> <option value="UMD3.1.66">Bos taurus : UMD3.1.66</option> <option value="UMD3.1.65">Bos taurus : UMD3.1.65</option> <option value="UMD3.1.64">Bos taurus : UMD3.1.64</option> <option value="Btau_4.0.63">Bos taurus : Btau_4.0.63</option> <option value="c_briggsae_WS230">Caenorhabditis briggsae : c_briggsae_WS230</option> <option value="ce.WS220.61">Caenorhabditis elegans : ce.WS220.61</option> <option value="ce.WS210.60">Caenorhabditis elegans : ce.WS210.60</option> <option value="ce.WS201">Caenorhabditis elegans : ce.WS201</option> <option value="WS220.66">Caenorhabditis elegans : WS220.66</option> <option value="WS220.65">Caenorhabditis elegans : WS220.65</option> <option value="WS220.64">Caenorhabditis elegans : WS220.64</option> <option value="WS220.63">Caenorhabditis elegans : WS220.63</option> <option value="calJac3.2.1.61">Callithrix jacchus : calJac3.2.1.61</option> <option value="calJac3.2.1.60">Callithrix jacchus : calJac3.2.1.60</option> <option value="C_jacchus3.2.1.66">Callithrix jacchus : C_jacchus3.2.1.66</option> <option value="C_jacchus3.2.1.65">Callithrix jacchus : C_jacchus3.2.1.65</option> <option value="C_jacchus3.2.1.64">Callithrix jacchus : C_jacchus3.2.1.64</option> <option value="C_jacchus3.2.1.63">Callithrix jacchus : C_jacchus3.2.1.63</option> <option value="cAlbicansv21">Candida albicans SC5314 : cAlbicansv21</option> <option value="canFam2.61">Canis familiaris : canFam2.61</option> <option value="canFam2.60">Canis familiaris : canFam2.60</option> <option value="canFam2.59">Canis familiaris : canFam2.59</option> <option value="BROADD2.66">Canis familiaris : BROADD2.66</option> <option value="BROADD2.65">Canis familiaris : BROADD2.65</option> <option value="BROADD2.64">Canis familiaris : BROADD2.64</option> <option value="BROADD2.63">Canis familiaris : BROADD2.63</option> <option value="crubella">Capsella rubella v1.0 : crubella</option> <option value="cavPor3.66">Cavia porcellus : cavPor3.66</option> <option value="cavPor3.65">Cavia porcellus : cavPor3.65</option> <option value="cavPor3.64">Cavia porcellus : cavPor3.64</option> <option value="cavPor3.63">Cavia porcellus : cavPor3.63</option> <option value="cavPor3.61">Cavia porcellus : cavPor3.61</option> <option value="cavPor3.60">Cavia porcellus : cavPor3.60</option> <option value="choHof1.66">Choloepus hoffmanni : choHof1.66</option> <option value="choHof1.65">Choloepus hoffmanni : choHof1.65</option> <option value="choHof1.64">Choloepus hoffmanni : choHof1.64</option> <option value="choHof1.63">Choloepus hoffmanni : choHof1.63</option> <option value="choHof1.61">Choloepus hoffmanni : choHof1.61</option> <option value="choHof1.60">Choloepus hoffmanni : choHof1.60</option> <option value="cInt2.61">Ciona intestinalis : cInt2.61</option> <option value="cInt2.60">Ciona intestinalis : cInt2.60</option> <option value="KH.66">Ciona intestinalis : KH.66</option> <option value="JGI2.65">Ciona intestinalis : JGI2.65</option> <option value="JGI2.64">Ciona intestinalis : JGI2.64</option> <option value="JGI2.63">Ciona intestinalis : JGI2.63</option> <option value="cSav2.0.61">Ciona savignyi : cSav2.0.61</option> <option value="cSav2.0.60">Ciona savignyi : cSav2.0.60</option> <option value="CSAV2.0.66">Ciona savignyi : CSAV2.0.66</option> <option value="CSAV2.0.65">Ciona savignyi : CSAV2.0.65</option> <option value="CSAV2.0.64">Ciona savignyi : CSAV2.0.64</option> <option value="CSAV2.0.63">Ciona savignyi : CSAV2.0.63</option> <option value="NC_009089.1">Clostridium difficile : NC_009089.1</option> <option value="c_neoformans">Cryptococcus neoformans : c_neoformans</option> <option value="danRer9.61">Danio rerio : danRer9.61</option> <option value="danRer9.60">Danio rerio : danRer9.60</option> <option value="danRer8.59">Danio rerio : danRer8.59</option> <option value="Zv9.66">Danio rerio : Zv9.66</option> <option value="Zv9.65">Danio rerio : Zv9.65</option> <option value="Zv9.64">Danio rerio : Zv9.64</option> <option value="Zv9.63">Danio rerio : Zv9.63</option> <option value="dasNov2.66">Dasypus novemcinctus : dasNov2.66</option> <option value="dasNov2.65">Dasypus novemcinctus : dasNov2.65</option> <option value="dasNov2.64">Dasypus novemcinctus : dasNov2.64</option> <option value="dasNov2.63">Dasypus novemcinctus : dasNov2.63</option> <option value="dasNov2.61">Dasypus novemcinctus : dasNov2.61</option> <option value="dasNov2.60">Dasypus novemcinctus : dasNov2.60</option> <option value="dipOrd1.66">Dipodomys ordii : dipOrd1.66</option> <option value="dipOrd1.65">Dipodomys ordii : dipOrd1.65</option> <option value="dipOrd1.64">Dipodomys ordii : dipOrd1.64</option> <option value="dipOrd1.63">Dipodomys ordii : dipOrd1.63</option> <option value="dipOrd1.61">Dipodomys ordii : dipOrd1.61</option> <option value="dipOrd1.60">Dipodomys ordii : dipOrd1.60</option> <option value="dm5.42">Drosophila melanogaster : dm5.42</option> <option value="dm5.40">Drosophila melanogaster : dm5.40</option> <option value="dm5.34">Drosophila melanogaster : dm5.34</option> <option value="dm5.32">Drosophila melanogaster : dm5.32</option> <option value="dm5.31">Drosophila melanogaster : dm5.31</option> <option value="dm5.30">Drosophila melanogaster : dm5.30</option> <option value="dm5.25.63">Drosophila melanogaster : dm5.25.63</option> <option value="dm5.25.61">Drosophila melanogaster : dm5.25.61</option> <option value="dm5.25.60">Drosophila melanogaster : dm5.25.60</option> <option value="dm5.25.59">Drosophila melanogaster : dm5.25.59</option> <option value="dm5.22">Drosophila melanogaster : dm5.22</option> <option value="dm5.12">Drosophila melanogaster : dm5.12</option> <option value="BDGP5.66">Drosophila melanogaster : BDGP5.66</option> <option value="BDGP5.25.65">Drosophila melanogaster : BDGP5.25.65</option> <option value="BDGP5.25.64">Drosophila melanogaster : BDGP5.25.64</option> <option value="BDGP5.25.63">Drosophila melanogaster : BDGP5.25.63</option> <option value="tenrec1.61">Echinops telfairi : tenrec1.61</option> <option value="tenrec1.60">Echinops telfairi : tenrec1.60</option> <option value="TENREC.66">Echinops telfairi : TENREC.66</option> <option value="TENREC.65">Echinops telfairi : TENREC.65</option> <option value="TENREC.64">Echinops telfairi : TENREC.64</option> <option value="TENREC.63">Echinops telfairi : TENREC.63</option> <option value="equCab2.61">Equus caballus : equCab2.61</option> <option value="equCab2.60">Equus caballus : equCab2.60</option> <option value="EquCab2.66">Equus caballus : EquCab2.66</option> <option value="EquCab2.65">Equus caballus : EquCab2.65</option> <option value="EquCab2.64">Equus caballus : EquCab2.64</option> <option value="EquCab2.63">Equus caballus : EquCab2.63</option> <option value="eriEur1.61">Erinaceus europaeus : eriEur1.61</option> <option value="eriEur1.60">Erinaceus europaeus : eriEur1.60</option> <option value="HEDGEHOG.66">Erinaceus europaeus : HEDGEHOG.66</option> <option value="HEDGEHOG.65">Erinaceus europaeus : HEDGEHOG.65</option> <option value="HEDGEHOG.64">Erinaceus europaeus : HEDGEHOG.64</option> <option value="HEDGEHOG.63">Erinaceus europaeus : HEDGEHOG.63</option> <option value="NC_000913">Escherichia coli : NC_000913</option> <option value="cat1.61">Felis catus : cat1.61</option> <option value="cat1.60">Felis catus : cat1.60</option> <option value="CAT.66">Felis catus : CAT.66</option> <option value="CAT.65">Felis catus : CAT.65</option> <option value="CAT.64">Felis catus : CAT.64</option> <option value="CAT.63">Felis catus : CAT.63</option> <option value="gadMor1.66">Gadus morhua : gadMor1.66</option> <option value="ggallus2.61">Gallus gallus : ggallus2.61</option> <option value="ggallus2.60">Gallus gallus : ggallus2.60</option> <option value="ggallus2.59">Gallus gallus : ggallus2.59</option> <option value="WASHUC2.66">Gallus gallus : WASHUC2.66</option> <option value="WASHUC2.65">Gallus gallus : WASHUC2.65</option> <option value="WASHUC2.64">Gallus gallus : WASHUC2.64</option> <option value="WASHUC2.63">Gallus gallus : WASHUC2.63</option> <option value="gacu1.61">Gasterosteus aculeatus : gacu1.61</option> <option value="gacu1.60">Gasterosteus aculeatus : gacu1.60</option> <option value="BROADS1.66">Gasterosteus aculeatus : BROADS1.66</option> <option value="BROADS1.65">Gasterosteus aculeatus : BROADS1.65</option> <option value="BROADS1.64">Gasterosteus aculeatus : BROADS1.64</option> <option value="BROADS1.63">Gasterosteus aculeatus : BROADS1.63</option> <option value="gmax1.09v8">Glycine Max : gmax1.09v8</option> <option value="gmax1.09">Glycine Max : gmax1.09</option> <option value="gorGor3.63">Gorilla gorilla : gorGor3.63</option> <option value="gorGor3.61">Gorilla gorilla : gorGor3.61</option> <option value="gorGor3.60">Gorilla gorilla : gorGor3.60</option> <option value="gorGor3.1.66">Gorilla gorilla : gorGor3.1.66</option> <option value="gorGor3.1.65">Gorilla gorilla : gorGor3.1.65</option> <option value="gorGor3.1.64">Gorilla gorilla : gorGor3.1.64</option> <option value="kw1407.2012">Grosmannia clavigera : kw1407.2012</option> <option value="hiv">HIV : hiv</option> <option value="SIVmac239">HIV : SIVmac239</option> <option value="herpesvirus1">Herpesvirus : herpesvirus1</option> <option value="hg37.63">Homo sapiens : hg37.63</option> <option value="hg37.61">Homo sapiens : hg37.61</option> <option value="hg37.60">Homo sapiens : hg37.60</option> <option value="hg37.59">Homo sapiens : hg37.59</option> <option value="hg36.54">Homo sapiens : hg36.54</option> <option value="hg19">Homo sapiens : hg19</option> <option value="GRCh37.66">Homo sapiens : GRCh37.66</option> <option value="GRCh37.65">Homo sapiens : GRCh37.65</option> <option value="GRCh37.64">Homo sapiens : GRCh37.64</option> <option value="GRCh37.63">Homo sapiens : GRCh37.63</option> <option value="LatCha1.66">Latimeria chalumnae : LatCha1.66</option> <option value="lmjf4">LmajorFriedlin : lmjf4</option> <option value="loxAfr3.66">Loxodonta africana : loxAfr3.66</option> <option value="loxAfr3.65">Loxodonta africana : loxAfr3.65</option> <option value="loxAfr3.64">Loxodonta africana : loxAfr3.64</option> <option value="loxAfr3.63">Loxodonta africana : loxAfr3.63</option> <option value="loxAfr3.61">Loxodonta africana : loxAfr3.61</option> <option value="loxAfr3.60">Loxodonta africana : loxAfr3.60</option> <option value="mmul1.61">Macaca mulatta : mmul1.61</option> <option value="mmul1.60">Macaca mulatta : mmul1.60</option> <option value="MMUL_1.66">Macaca mulatta : MMUL_1.66</option> <option value="MMUL_1.65">Macaca mulatta : MMUL_1.65</option> <option value="MMUL_1.64">Macaca mulatta : MMUL_1.64</option> <option value="MMUL_1.63">Macaca mulatta : MMUL_1.63</option> <option value="meug1.0.61">Macropus eugenii : meug1.0.61</option> <option value="meug1.0.60">Macropus eugenii : meug1.0.60</option> <option value="Meug_1.0.66">Macropus eugenii : Meug_1.0.66</option> <option value="Meug_1.0.65">Macropus eugenii : Meug_1.0.65</option> <option value="Meug_1.0.64">Macropus eugenii : Meug_1.0.64</option> <option value="Meug_1.0.63">Macropus eugenii : Meug_1.0.63</option> <option value="maizeZmB73">Maize ZmB73 : maizeZmB73</option> <option value="turkey.UMD2.61">Meleagris gallopavo : turkey.UMD2.61</option> <option value="UMD2.66">Meleagris gallopavo : UMD2.66</option> <option value="UMD2.65">Meleagris gallopavo : UMD2.65</option> <option value="UMD2.64">Meleagris gallopavo : UMD2.64</option> <option value="UMD2.63">Meleagris gallopavo : UMD2.63</option> <option value="micMur1.66">Microcebus murinus : micMur1.66</option> <option value="micMur1.65">Microcebus murinus : micMur1.65</option> <option value="micMur1.64">Microcebus murinus : micMur1.64</option> <option value="micMur1.63">Microcebus murinus : micMur1.63</option> <option value="micMur1.61">Microcebus murinus : micMur1.61</option> <option value="micMur1.60">Microcebus murinus : micMur1.60</option> <option value="monDom5.61">Monodelphis domestica : monDom5.61</option> <option value="monDom5.60">Monodelphis domestica : monDom5.60</option> <option value="BROADO5.66">Monodelphis domestica : BROADO5.66</option> <option value="BROADO5.65">Monodelphis domestica : BROADO5.65</option> <option value="BROADO5.64">Monodelphis domestica : BROADO5.64</option> <option value="BROADO5.63">Monodelphis domestica : BROADO5.63</option> <option value="mm37.61">Mus musculus : mm37.61</option> <option value="mm37.60">Mus musculus : mm37.60</option> <option value="mm37.59">Mus musculus : mm37.59</option> <option value="mm37">Mus musculus : mm37</option> <option value="NCBIM37.66">Mus musculus : NCBIM37.66</option> <option value="NCBIM37.65">Mus musculus : NCBIM37.65</option> <option value="NCBIM37.64">Mus musculus : NCBIM37.64</option> <option value="NCBIM37.63">Mus musculus : NCBIM37.63</option> <option value="mmm.2012">Mycobacterium marinum M : mmm.2012</option> <option value="m_tuberculosis">Mycobacterium tuberculosis : m_tuberculosis</option> <option value="myco_fh">Mycoplasma pneumoninae FH : myco_fh</option> <option value="myco_m129">Mycoplasma pneumoninae M129 : myco_m129</option> <option value="myoLuc1.61">Myotis lucifugus : myoLuc1.61</option> <option value="myoLuc1.60">Myotis lucifugus : myoLuc1.60</option> <option value="Myoluc2.0.66">Myotis lucifugus : Myoluc2.0.66</option> <option value="Myoluc2.0.65">Myotis lucifugus : Myoluc2.0.65</option> <option value="Myoluc2.0.64">Myotis lucifugus : Myoluc2.0.64</option> <option value="Myoluc2.0.63">Myotis lucifugus : Myoluc2.0.63</option> <option value="ncrassa">Neurospora Crassa : ncrassa</option> <option value="Nleu1.0.66">Nomascus leucogenys : Nleu1.0.66</option> <option value="Nleu1.0.65">Nomascus leucogenys : Nleu1.0.65</option> <option value="Nleu1.0.64">Nomascus leucogenys : Nleu1.0.64</option> <option value="Nleu1.0.63">Nomascus leucogenys : Nleu1.0.63</option> <option value="pika.66">Ochotona princeps : pika.66</option> <option value="pika.65">Ochotona princeps : pika.65</option> <option value="pika.64">Ochotona princeps : pika.64</option> <option value="pika.63">Ochotona princeps : pika.63</option> <option value="ochPri2.61">Ochotona princeps : ochPri2.61</option> <option value="ochPri2.60">Ochotona princeps : ochPri2.60</option> <option value="oana5.61">Ornithorhynchus anatinus : oana5.61</option> <option value="oana5.60">Ornithorhynchus anatinus : oana5.60</option> <option value="OANA5.66">Ornithorhynchus anatinus : OANA5.66</option> <option value="OANA5.65">Ornithorhynchus anatinus : OANA5.65</option> <option value="OANA5.64">Ornithorhynchus anatinus : OANA5.64</option> <option value="OANA5.63">Ornithorhynchus anatinus : OANA5.63</option> <option value="oryCun2.66">Oryctolagus cuniculus : oryCun2.66</option> <option value="oryCun2.65">Oryctolagus cuniculus : oryCun2.65</option> <option value="oryCun2.64">Oryctolagus cuniculus : oryCun2.64</option> <option value="oryCun2.63">Oryctolagus cuniculus : oryCun2.63</option> <option value="oryCun2.61">Oryctolagus cuniculus : oryCun2.61</option> <option value="oryCun2.60">Oryctolagus cuniculus : oryCun2.60</option> <option value="medaka1.61">Oryzias latipes : medaka1.61</option> <option value="medaka1.60">Oryzias latipes : medaka1.60</option> <option value="MEDAKA1.66">Oryzias latipes : MEDAKA1.66</option> <option value="MEDAKA1.65">Oryzias latipes : MEDAKA1.65</option> <option value="MEDAKA1.64">Oryzias latipes : MEDAKA1.64</option> <option value="MEDAKA1.63">Oryzias latipes : MEDAKA1.63</option> <option value="bushBaby1.61">Otolemur garnettii : bushBaby1.61</option> <option value="bushBaby1.60">Otolemur garnettii : bushBaby1.60</option> <option value="OtoGar3.66">Otolemur garnettii : OtoGar3.66</option> <option value="BUSHBABY1.65">Otolemur garnettii : BUSHBABY1.65</option> <option value="BUSHBABY1.64">Otolemur garnettii : BUSHBABY1.64</option> <option value="BUSHBABY1.63">Otolemur garnettii : BUSHBABY1.63</option> <option value="chimp2.1.61">Pan troglodytes : chimp2.1.61</option> <option value="chimp2.1.60">Pan troglodytes : chimp2.1.60</option> <option value="chimp2.1.59">Pan troglodytes : chimp2.1.59</option> <option value="CHIMP2.1.65">Pan troglodytes : CHIMP2.1.65</option> <option value="CHIMP2.1.64">Pan troglodytes : CHIMP2.1.64</option> <option value="CHIMP2.1.63">Pan troglodytes : CHIMP2.1.63</option> <option value="CHIMP2.1.4.66">Pan troglodytes : CHIMP2.1.4.66</option> <option value="ppersica139">Peach : ppersica139</option> <option value="peromyscus">Peromyscus leucopus : peromyscus</option> <option value="Pmarinus_7.0.66">Petromyzon marinus : Pmarinus_7.0.66</option> <option value="Petromyzon_marinus_7.0.65">Petromyzon marinus : Petromyzon_marinus_7.0.65</option> <option value="Petromyzon_marinus_7.0.64">Petromyzon marinus : Petromyzon_marinus_7.0.64</option> <option value="plasmo72">Plasmodium falciparum : plasmo72</option> <option value="PPYG2.66">Pongo abelii : PPYG2.66</option> <option value="PPYG2.65">Pongo abelii : PPYG2.65</option> <option value="PPYG2.64">Pongo abelii : PPYG2.64</option> <option value="PPYG2.63">Pongo abelii : PPYG2.63</option> <option value="ppyg2.61">Pongo pygmaeus : ppyg2.61</option> <option value="ppyg2.60">Pongo pygmaeus : ppyg2.60</option> <option value="proCap1.66">Procavia capensis : proCap1.66</option> <option value="proCap1.65">Procavia capensis : proCap1.65</option> <option value="proCap1.64">Procavia capensis : proCap1.64</option> <option value="proCap1.63">Procavia capensis : proCap1.63</option> <option value="proCap1.61">Procavia capensis : proCap1.61</option> <option value="proCap1.60">Procavia capensis : proCap1.60</option> <option value="paeru.PA14">Pseudomonas aeruginosa : paeru.PA14</option> <option value="paeru.PA01">Pseudomonas aeruginosa : paeru.PA01</option> <option value="pfluo.SBW25.NC_012660">Pseudomonas fluorescens : pfluo.SBW25.NC_012660</option> <option value="pfluo.SBW25.NC_009444">Pseudomonas fluorescens : pfluo.SBW25.NC_009444</option> <option value="pteVam1.66">Pteropus vampyrus : pteVam1.66</option> <option value="pteVam1.65">Pteropus vampyrus : pteVam1.65</option> <option value="pteVam1.64">Pteropus vampyrus : pteVam1.64</option> <option value="pteVam1.63">Pteropus vampyrus : pteVam1.63</option> <option value="pteVam1.61">Pteropus vampyrus : pteVam1.61</option> <option value="pteVam1.60">Pteropus vampyrus : pteVam1.60</option> <option value="rat3.4.61">Rattus norvegicus : rat3.4.61</option> <option value="rat3.4.60">Rattus norvegicus : rat3.4.60</option> <option value="rat3.4.59">Rattus norvegicus : rat3.4.59</option> <option value="RGSC3.4.66">Rattus norvegicus : RGSC3.4.66</option> <option value="RGSC3.4.65">Rattus norvegicus : RGSC3.4.65</option> <option value="RGSC3.4.64">Rattus norvegicus : RGSC3.4.64</option> <option value="RGSC3.4.63">Rattus norvegicus : RGSC3.4.63</option> <option value="rice6.1">Rice : rice6.1</option> <option value="rice5">Rice : rice5</option> <option value="SCU49845">SCU49845 : SCU49845</option> <option value="sacCer2.61">Saccharomyces cerevisiae : sacCer2.61</option> <option value="sacCer2.60">Saccharomyces cerevisiae : sacCer2.60</option> <option value="sacCer2.59">Saccharomyces cerevisiae : sacCer2.59</option> <option value="sacCer2">Saccharomyces cerevisiae : sacCer2</option> <option value="EF4.66">Saccharomyces cerevisiae : EF4.66</option> <option value="EF4.65">Saccharomyces cerevisiae : EF4.65</option> <option value="EF3.64">Saccharomyces cerevisiae : EF3.64</option> <option value="EF3.63">Saccharomyces cerevisiae : EF3.63</option> <option value="DEVIL7.0.66">Sarcophilus harrisii : DEVIL7.0.66</option> <option value="DEVIL7.0.65">Sarcophilus harrisii : DEVIL7.0.65</option> <option value="DEVIL7.0.64">Sarcophilus harrisii : DEVIL7.0.64</option> <option value="spombe">Schizosaccharomyces pombe : spombe</option> <option value="sorAra1.61">Sorex araneus : sorAra1.61</option> <option value="sorAra1.60">Sorex araneus : sorAra1.60</option> <option value="COMMON_SHREW1.66">Sorex araneus : COMMON_SHREW1.66</option> <option value="COMMON_SHREW1.65">Sorex araneus : COMMON_SHREW1.65</option> <option value="COMMON_SHREW1.64">Sorex araneus : COMMON_SHREW1.64</option> <option value="COMMON_SHREW1.63">Sorex araneus : COMMON_SHREW1.63</option> <option value="speTri1.61">Spermophilus tridecemlineatus : speTri1.61</option> <option value="speTri1.60">Spermophilus tridecemlineatus : speTri1.60</option> <option value="SQUIRREL.66">Spermophilus tridecemlineatus : SQUIRREL.66</option> <option value="SQUIRREL.65">Spermophilus tridecemlineatus : SQUIRREL.65</option> <option value="SQUIRREL.64">Spermophilus tridecemlineatus : SQUIRREL.64</option> <option value="SQUIRREL.63">Spermophilus tridecemlineatus : SQUIRREL.63</option> <option value="CP000730">Staphylococcus aureus : CP000730</option> <option value="sScrofa9.61">Sus scrofa : sScrofa9.61</option> <option value="sScrofa9.60">Sus scrofa : sScrofa9.60</option> <option value="Sscrofa9.66">Sus scrofa : Sscrofa9.66</option> <option value="Sscrofa9.65">Sus scrofa : Sscrofa9.65</option> <option value="Sscrofa9.64">Sus scrofa : Sscrofa9.64</option> <option value="Sscrofa9.63">Sus scrofa : Sscrofa9.63</option> <option value="taeGut3.2.4.66">Taeniopygia guttata : taeGut3.2.4.66</option> <option value="taeGut3.2.4.65">Taeniopygia guttata : taeGut3.2.4.65</option> <option value="taeGut3.2.4.64">Taeniopygia guttata : taeGut3.2.4.64</option> <option value="taeGut3.2.4.63">Taeniopygia guttata : taeGut3.2.4.63</option> <option value="taeGut3.2.4.61">Taeniopygia guttata : taeGut3.2.4.61</option> <option value="taeGut3.2.4.60">Taeniopygia guttata : taeGut3.2.4.60</option> <option value="fugu4.61">Takifugu rubripes : fugu4.61</option> <option value="fugu4.60">Takifugu rubripes : fugu4.60</option> <option value="FUGU4.66">Takifugu rubripes : FUGU4.66</option> <option value="FUGU4.65">Takifugu rubripes : FUGU4.65</option> <option value="FUGU4.64">Takifugu rubripes : FUGU4.64</option> <option value="FUGU4.63">Takifugu rubripes : FUGU4.63</option> <option value="tarSyr1.66">Tarsius syrichta : tarSyr1.66</option> <option value="tarSyr1.65">Tarsius syrichta : tarSyr1.65</option> <option value="tarSyr1.64">Tarsius syrichta : tarSyr1.64</option> <option value="tarSyr1.63">Tarsius syrichta : tarSyr1.63</option> <option value="tarSyr1.61">Tarsius syrichta : tarSyr1.61</option> <option value="tarSyr1.60">Tarsius syrichta : tarSyr1.60</option> <option value="test_ENSG00000158062">TestCase : test_ENSG00000158062</option> <option value="testHg3765Chr22">TestCase : testHg3765Chr22</option> <option value="testHg3763ChrY">TestCase : testHg3763ChrY</option> <option value="testHg3763Chr20">TestCase : testHg3763Chr20</option> <option value="testHg3763Chr1">TestCase : testHg3763Chr1</option> <option value="testHg3761Chr16">TestCase : testHg3761Chr16</option> <option value="testHg3761Chr15">TestCase : testHg3761Chr15</option> <option value="testCase">TestCase : testCase</option> <option value="test">TestCase : test</option> <option value="tetraodon8.61">Tetraodon nigroviridis : tetraodon8.61</option> <option value="tetraodon8.60">Tetraodon nigroviridis : tetraodon8.60</option> <option value="TETRAODON8.66">Tetraodon nigroviridis : TETRAODON8.66</option> <option value="TETRAODON8.65">Tetraodon nigroviridis : TETRAODON8.65</option> <option value="TETRAODON8.64">Tetraodon nigroviridis : TETRAODON8.64</option> <option value="TETRAODON8.63">Tetraodon nigroviridis : TETRAODON8.63</option> <option value="SL2.40">Tomato : SL2.40</option> <option value="tupBel1.61">Tupaia belangeri : tupBel1.61</option> <option value="tupBel1.60">Tupaia belangeri : tupBel1.60</option> <option value="TREESHREW.66">Tupaia belangeri : TREESHREW.66</option> <option value="TREESHREW.65">Tupaia belangeri : TREESHREW.65</option> <option value="TREESHREW.64">Tupaia belangeri : TREESHREW.64</option> <option value="TREESHREW.63">Tupaia belangeri : TREESHREW.63</option> <option value="turTru1.66">Tursiops truncatus : turTru1.66</option> <option value="turTru1.65">Tursiops truncatus : turTru1.65</option> <option value="turTru1.64">Tursiops truncatus : turTru1.64</option> <option value="turTru1.63">Tursiops truncatus : turTru1.63</option> <option value="turTru1.61">Tursiops truncatus : turTru1.61</option> <option value="turTru1.60">Tursiops truncatus : turTru1.60</option> <option value="vacwr">Vaccinia Western Reserve : vacwr</option> <option value="vibrio">Vibrio Cholerae : vibrio</option> <option value="vicPac1.66">Vicugna pacos : vicPac1.66</option> <option value="vicPac1.65">Vicugna pacos : vicPac1.65</option> <option value="vicPac1.64">Vicugna pacos : vicPac1.64</option> <option value="vicPac1.63">Vicugna pacos : vicPac1.63</option> <option value="vicPac1.61">Vicugna pacos : vicPac1.61</option> <option value="vicPac1.60">Vicugna pacos : vicPac1.60</option> <option value="xtrop7.1">Xenopus tropicalis : xtrop7.1</option> <option value="xtrop4.1.61">Xenopus tropicalis : xtrop4.1.61</option> <option value="xtrop4.1.60">Xenopus tropicalis : xtrop4.1.60</option> <option value="JGI_4.2.66">Xenopus tropicalis : JGI_4.2.66</option> <option value="JGI_4.2.64">Xenopus tropicalis : JGI_4.2.64</option> <option value="JGI_4.2.63">Xenopus tropicalis : JGI_4.2.63</option> </param> <param name="udLength" type="select" label="Upstream / Downstream length"> <option value="0">No upstream / downstream intervals (0 bases)</option> <option value="200">200 bases</option> <option value="500">500 bases</option> <option value="1000">1000 bases</option> <option value="2000">2000 bases</option> <option value="5000" selected="true">5000 bases</option> <option value="10000">10000 bases</option> <option value="20000">20000 bases</option> </param> <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> <option value="">No filter (analyze everything)</option> <option value="-hom">Analyze homozygous sequence changes only </option> <option value="-het">Analyze heterozygous sequence changes only </option> </param> <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> <option value="">No filter (analyze everything)</option> <option value="-del">Analyze deletions only </option> <option value="-ins">Analyze insertions only </option> <option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option> <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> </param> <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output"> <option value="None" selected="true">None</option> <option value="downstream">Do not show DOWNSTREAM changes </option> <option value="intergenic">Do not show INTERGENIC changes </option> <option value="intron">Do not show INTRON changes </option> <option value="upstream">Do not show UPSTREAM changes </option> <option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option> </param> <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> <option value="">Use default (based on input type)</option> <option value="-0">Force zero-based positions (both input and output)</option> <option value="-1">Force one-based positions (both input and output)</option> </param> </inputs> <outputs> <data format="tabular" name="output" > <change_format> <when input="outputFormat" value="txt" format="tabular" /> <when input="outputFormat" value="vcf" format="vcf" /> <when input="outputFormat" value="bed" format="bed" /> <when input="outputFormat" value="bedAnn" format="bed" /> </change_format> </data> <data format="html" name="statsFile" /> </outputs> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" /> </stdio> <help> This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. For details about this tool, please go to http://snpEff.sourceforge.net </help> </tool>