| Previous changeset 4:916846f73e25 (2016-04-29) Next changeset 6:46a10309dfe2 (2016-06-28) |
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Commit message:
Uploaded |
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modified:
R/compareSignature_Galaxy.r hg19_listAVDB.txt mutspecAnnot.pl mutspecAnnot.xml mutspecCompare.xml mutspecFilter.pl mutspecNmf_wrapper.sh mutspecStat_wrapper.sh tool_dependencies.xml |
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removed:
Frequency-COSMICv72-Hupki-Others.txt hg18_listAVDB.txt hg38_listAVDB.txt mm10_listAVDB.txt rn6_listAVDB.txt |
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| diff -r 916846f73e25 -r 097ae310ced0 Frequency-COSMICv72-Hupki-Others.txt --- a/Frequency-COSMICv72-Hupki-Others.txt Fri Apr 29 05:11:28 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,97 +0,0 @@\n-Substitution Type\tTrinucleotide\tSomatic Mutation Type\tSignature 1\tSignature 2\tSignature 3\tSignature 4\tSignature 5\tSignature 6\tSignature 7\tSignature 8\tSignature 9\tSignature 10\tSignature 11\tSignature 12\tSignature 13\tSignature 14\tSignature 15\tSignature 16\tSignature 17\tSignature 18\tSignature 19\tSignature 20\tSignature 21\tSignature 22\tSignature 23\tSignature 24\tSignature 25\tSignature 26\tSignature 27\tSignature 28\tSignature 29\tSignature 30\tSignature 1 MEF\tSignature 2 MEF\tSignature 3 MEF\tSignature 5 MEF\tSignature DMBA\tSignature MNU\tSignature Urethane\n-C>A\tACA\tA[C>A]A\t0.0110983262\t0.0006827082\t0.0221723068\t0.0365\t0.0149415477\t0.0017\t0.0004\t0.0367180038\t0.012\t0.0007\t0.0002\t0.0077\t0.0003347572\t0.0001\t0.0013\t0.0161\t0.0018320192\t0.0505364186\t0.0107\t0.0011799616\t0.0001\t0.0015040704\t0.0004533607\t0.0286459925\t0.009896768\t0.0020397729\t0.0052056269\t0.0013974388\t0.0699819873\t0\t0.000781083\t0.0037229109\t0.0283533537\t0.0003710632\t0.0121138158\t0.0010972115\t0.0044388346\n-C>A\tACC\tA[C>A]C\t0.0091493407\t0.0006191072\t0.0178716754\t0.0309\t0.008960918\t0.0028\t0.0005\t0.0332457222\t0.0067\t0.001\t0.001\t0.0047\t0.0006487361\t0.0042\t0.004\t0.0097\t0.0003422356\t0.0109398248\t0.0074\t0.0022115051\t0.0007\t0.002451011\t0.0003668005\t0.0202146384\t0.0069989288\t0.0014871623\t0.0047382274\t0.0009171877\t0.0551523572\t0\t0.0022972224\t0.0070460466\t0.015676074\t0.001672691\t0.0046539767\t0.0009508214\t0.0004001609\n-C>A\tACG\tA[C>A]G\t0.0014900705\t0.000099279\t0.0021383396\t0.0183\t0.002207846\t0.0005\t0\t0.0025253113\t0.0005\t0.0003\t0\t0.0017\t3.8144594E-005\t0.0005\t0\t0.0022\t1.576225E-006\t0.0022880727\t0.0005\t1.61691E-007\t0\t0\t0\t0.0204789965\t0.001448443\t0.0002839456\t0.0007826979\t0\t0.017846984\t0.0019673\t0.0031701397\t0.0025537924\t0.0272331284\t0.0007812591\t0.0071227909\t0.0003972991\t1.63618104265282E-020\n-C>A\tACT\tA[C>A]T\t0.0062338852\t0.0003238914\t0.0162651456\t0.0243\t0.0092069053\t0.0019\t0.0004\t0.0335985495\t0.0068\t0.0092\t0.0002\t0.0046\t0.0008466585\t0.0296\t0.0057\t0.0088\t0.0031796648\t0.0194240914\t0.0074\t0.00300801\t0.0006\t0.0009224525\t0\t0.0246001454\t0.004966565\t0.0005978656\t0.0027182425\t0.00051341\t0.026804716\t0\t0.0015620621\t0.0104484061\t0.0079498813\t0.0004287024\t0.0083172408\t0.0002539234\t0.0015287933\n-C>A\tCCA\tC[C>A]A\t0.0065958701\t0.000677445\t0.0187817256\t0.0461\t0.0096749043\t0.0101\t0.0012\t0.0317237566\t0.0098\t0.0031\t0.0007\t0.0135\t0.0017100896\t0.0056\t0.0106\t0.0159\t0.0010324302\t0.0887681088\t0.0112\t0.0173771106\t0.002\t0.0045496929\t0.0001647394\t0.0635592838\t0.0148329479\t0.0037058501\t0.0050650733\t0.0011685156\t0.0514102117\t0\t0.0094052338\t0.0035222831\t0.0414403498\t0.0050521059\t0.0224513894\t0.0008540231\t0.0031599431\n-C>A\tCCC\tC[C>A]C\t0.0073423678\t0.000213681\t0.0157604578\t0.0614\t0.0049523006\t0.0241\t0.0006\t0.0255054071\t0.0057\t0.0009\t0.0017\t0.0112\t0.0011592566\t0.0102\t0.0084\t0.01\t0.0004218801\t0.0206413906\t0.0159\t0.036502463\t0.0014\t0.0037644739\t0.0007368748\t0.0337570047\t0.0078221753\t0.0039807234\t0.0022341533\t0.0003342918\t0.0258256508\t0\t0.0031118726\t0.0059886212\t0.0390237536\t0.0007556355\t0.0096511373\t0.0007989301\t0.0042099735\n-C>A\tCCG\tC[C>A]G\t0.0008928404\t6.77046E-006\t0.0019633898\t0.0088\t0.0028006273\t0.0091\t0\t0.0011596243\t0\t0.0007\t0.001\t0.0028\t0.0002441665\t0.0009\t0.0015\t0.0022\t0.0002974628\t0.0171784025\t0.0018\t0.0124825875\t0.0027\t0.0009001633\t0.0001639537\t0.0224289858\t0.0012769767\t0.000811742\t0.0002663122\t0.000053652\t0.0144961833\t0.0022624\t0.0031056722\t0.0027351313\t0.0444175322\t0.000426758\t0.0104292165\t0.0004936949\t0.001053447\n-C>A\tCCT\tC[C>A]T\t0.0071865816\t0.0004163329\t0.0147228611\t0.0432\t0.0110134658\t0.0571\t0.0013\t0.028791173\t0.0091\t0.016\t0.0014\t0.0071\t0.0012567682\t0.1257\t0.0228\t0.0084\t3.1479429E-005\t0.0376769589\t0.0096\t0.1034012262\t0.0056\t0.0044398462\t0.0007227318\t0.0200865154\t0.0125636547\t0.0190384313\t0.00310057\t0.0001866719\t0.0403550741\t0\t0.0069708534\t0.0135089174\t0.0262144919\t0.0012449334\t0.0241632334\t0.0004829446\t0.0011918687\n-C>A\tGCA\tG[C>A]A\t0.008232604\t0.0003520134\t0.0096965397\t0.0376\t0.011892169\t0.0024\t0.0003\t0.0236823289\t0.0118\t0.0014\t0.0004\t0.0062\t0.0001321096\t0.0018\t0.0024\t0.0096\t0.0065354049\t0.1287241581\t0.00'..b'376549\t0.0060513622\t2.28346914246428E-020\t0.0088482202\t0.0009775125\t0.0090219017\n-T>G\tCTG\tC[T>G]G\t0.0015995485\t0.0002282459\t0.0104646545\t0.0046\t0.0071474562\t0.005\t0.0009\t0.0066040463\t0.0126\t0.0037\t0.0011\t0.0045\t4.59873E-005\t0.0005\t0.0007\t0.0067\t0.0134498376\t0.0053119673\t0.0013\t0.0153837761\t0.0004\t0.0041885681\t0\t0.0001139097\t0.0117694925\t0.0054973573\t0.0004032572\t0.0185164816\t0.0021696933\t0.0073775\t0.0039200627\t0.0028967736\t0.007564699\t0.0003827374\t0.0207298099\t1.06168434038267E-020\t0.003023422\n-T>G\tCTT\tC[T>G]T\t0.0027585376\t6.711134E-005\t0.0087243873\t0.0012\t0.0114868115\t0.0086\t0.0013\t0.0048667139\t0.0509\t0.0182\t0.0009\t0.0063\t0.0004637147\t0.0063\t0.0045\t0.0186\t0.2614566141\t0.0023416292\t0.0019\t0.0021853947\t0.0032\t0.0016294096\t0.000210835\t0.0025337183\t0.0085508075\t0.0067887187\t0.0014390961\t0.118967103\t0.0011436633\t0.0091481\t0.0157841091\t0.012870271\t0.0262293556\t0.0019670653\t0.0047092177\t0.0002687511\t0.003570495\n-T>G\tGTA\tG[T>G]A\t0.000099045\t9.5552392E-005\t0.004144488\t0\t0.0016276645\t0\t0\t0.0009745787\t0.0072\t0\t0\t0\t1.8489857E-005\t0\t0\t0\t3.9193821E-005\t0.0013415325\t0\t3.579149E-006\t0\t0\t0\t0\t0.0055462269\t3.7393232E-005\t0\t0\t0\t0.0032461\t0.0015356557\t0.0019915953\t0.0015778632\t0.0008546281\t0.0021439553\t0.0003157141\t0.0037470482\n-T>G\tGTC\tG[T>G]C\t0.0002023656\t4.7002381E-005\t0.0045019853\t0\t0.0003277349\t0.0016\t0\t0.0005248216\t0.0006\t0.002\t0\t0.0004\t9.3373513E-005\t0.0019\t0.0022\t0.0032\t0.0090784615\t9.20431E-007\t0\t0.0028305751\t0.0006\t0\t0\t0.0010736323\t0\t0.002460705\t5.0790565E-005\t0\t0\t0.001869\t0.0007606153\t0.0041116159\t0.0032012845\t0.0008454968\t0.0013465618\t0.0003570074\t0.0027277577\n-T>G\tGTG\tG[T>G]G\t0.0011883532\t0.0001099257\t0.0163914526\t0.0018\t0.0059488798\t0.001\t0.0017\t0.0060877535\t0.005\t0.0009\t0.001\t0.0011\t1.0579194E-005\t0.0012\t0.0037\t0.0008\t0.0047827755\t0.009695\t0.0043\t0.0027332194\t0.0004\t0.0018775892\t0.0001871324\t0.002924697\t0.0086852444\t0.0008172016\t0.0047429186\t0.0042178083\t0.0036405938\t0.0033445\t0.0054079152\t3.70860800590008E-020\t0.002512037\t0.0012687784\t0.0077472793\t0.0015192874\t0.0082395121\n-T>G\tGTT\tG[T>G]T\t0.0008007233\t8.647718E-005\t0.0070672366\t0.0002\t0.0033074666\t0.0035\t0.0009\t0.0054274338\t0.0185\t0.003\t0\t0.0032\t5.3741207E-005\t0.0038\t0.019\t0.0044\t0.0634977566\t0.0028905535\t0.0025\t0.0035585586\t0.0008\t0\t0\t0.0008250983\t0.0027685717\t0.0078335613\t0.002298476\t0.0316489973\t0.0061810238\t0.0056069\t0.0101885638\t0.0066566288\t0.0079578565\t0.0029254388\t0.0018168896\t0.0004726412\t0.0032734591\n-T>G\tTTA\tT[T>G]A\t0.0013975537\t0.000071737\t0.0054271842\t0\t0.0052028744\t0.0009\t0\t0.0017432214\t0.0502\t0.005\t0\t0.0019\t0.0005465818\t0\t0\t0.0068\t0.0001334106\t3.6318404E-005\t0.0032\t2.69147E-007\t0\t0.0016516988\t0\t0\t0.0020814799\t8.534935E-006\t0.0011890225\t0.0093896587\t0\t0.0086563\t0.0008187477\t0.000948451\t0.0005293442\t2.28346914246428E-020\t0.0002407249\t7.25392033429029E-005\t0.0017254818\n-T>G\tTTC\tT[T>G]C\t0.001291737\t1.4281456E-005\t0.0061602504\t0.0003\t0.0051316079\t0.0019\t0.001\t0.0025498383\t0.0081\t0.0092\t0\t0.0027\t0.0002353471\t0.0015\t0.0004\t0.0069\t0.0096133452\t0.003233838\t0.0018\t0.0003772344\t0.0018\t0\t0\t0\t0.0005789788\t0.0027185098\t0.0002802954\t0.030117077\t0\t0.0043282\t0.0015336834\t0.0010831046\t0.0010211012\t2.28346914246428E-020\t0.0013929045\t0.0003332825\t0.0037135711\n-T>G\tTTG\tT[T>G]G\t0.0020310769\t0.0002066152\t0.0110765263\t0.003\t0.0060552541\t0.0011\t0.001\t0.0060303952\t0.0088\t0.0022\t0.0003\t0.0011\t0.000000479\t0.0002\t0.0009\t0.0049\t0.0045224623\t0.0007546018\t0.0011\t0.0005154216\t0.0003\t0.002572752\t0.0002475019\t0.0013605049\t0.0094291959\t0.0013691612\t0.0023530556\t0.0126987508\t0.000353696\t0.0082628\t0.0015835907\t3.70860800590008E-020\t0.003717572\t2.28346914246428E-020\t0.0039677318\t0.0002233266\t0.0022664664\n-T>G\tTTT\tT[T>G]T\t0.0040301282\t2.3598204E-005\t0.0130009842\t0.0011\t0.0133699358\t0.0072\t0.0014\t0.0072239989\t0.0545\t0.0633\t0.0003\t0.0032\t0.0006705883\t0.0025\t0.0033\t0.0163\t0.0580404078\t0.0021264415\t0.0013\t0.0006156567\t0.0003\t0\t0\t6.9515778E-005\t0.0078696716\t0.0025680767\t0.0001395613\t0.2336597833\t0.0061048341\t0\t0.0031734006\t0.001871395\t0.0032018465\t2.28346914246428E-020\t0.0014171235\t0.0003757336\t0.0024231362\n' |
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| diff -r 916846f73e25 -r 097ae310ced0 R/compareSignature_Galaxy.r --- a/R/compareSignature_Galaxy.r Fri Apr 29 05:11:28 2016 -0400 +++ b/R/compareSignature_Galaxy.r Fri Apr 29 05:14:23 2016 -0400 |
| b |
| @@ -8,7 +8,7 @@ ######################################################################################################################################### -# Compare new sigantures with published one using the cosine similarity method # +# Compare new signatures with published one using the cosine similarity method # ######################################################################################################################################### |
| b |
| diff -r 916846f73e25 -r 097ae310ced0 hg18_listAVDB.txt --- a/hg18_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,32 +0,0 @@ -#This is a sample file distributed with Galaxy that is used by the -#MutSpec-Annot tools. The hg18_listAVDB.txt has this format (white space -#characters are TAB characters): -# -#<RefGenome_DatabaseName> <operation> -# -# -# -#hg18_refGene.txt g -#hg18_genomicSuperDups.txt r -#hg18_snp138.txt f -hg18_refGene.txt g -hg18_knownGene.txt g -hg18_ensGene.txt g -hg18_cytoBand.txt r -hg18_gwasCatalog.txt r -hg18_genomicSuperDups.txt r -hg18_snp138.txt f -hg18_ALL.sites.2014_10.txt f -hg18_AFR.sites.2014_10.txt f -hg18_AMR.sites.2014_10.txt f -hg18_EAS.sites.2014_10.txt f -hg18_EUR.sites.2014_10.txt f -hg18_SAS.sites.2014_10.txt f -hg18_esp6500siv2_all.txt f -hg18_esp6500siv2_aa.txt f -hg18_esp6500siv2_ea.txt f -hg18_ljb26_sift.txt f -hg18_ljb26_pp2hdiv.txt f -hg18_ljb26_pp2hvar.txt f -hg18_cosmic70.txt f -hg18_exac03.txt f |
| b |
| diff -r 916846f73e25 -r 097ae310ced0 hg19_listAVDB.txt --- a/hg19_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 +++ b/hg19_listAVDB.txt Fri Apr 29 05:14:23 2016 -0400 |
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| @@ -29,11 +29,9 @@ hg19_ljb26_sift.txt f hg19_ljb26_pp2hdiv.txt f hg19_ljb26_pp2hvar.txt f -hg19_ljb26_mt.txt f hg19_cosmic70.txt f hg19_exac03.txt f hg19_exac03nontcga.txt f hg19_exac03nonpsych.txt f hg19_kaviar20150923.txt f hg19_hrcr1.txt f -hg19_dbscsnv11.txt f |
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| diff -r 916846f73e25 -r 097ae310ced0 hg38_listAVDB.txt --- a/hg38_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,36 +0,0 @@ -#This is a sample file distributed with Galaxy that is used by the -#MutSpec-Annot tools. The hg38_listAVDB.txt has this format (white space -#characters are TAB characters): -# -#<RefGenome_DatabaseName> <operation> -# -# -# -#hg38_refGene.txt g -#hg38_genomicSuperDups.txt r -#hg38_snp142.txt f -hg38_refGene.txt g -hg38_knownGene.txt g -hg38_cytoBand.txt r -hg38_gwasCatalog.txt r -hg38_genomicSuperDups.txt r -hg38_snp142.txt f -hg38_ALL.sites.2015_08.txt f -hg38_AFR.sites.2015_08.txt f -hg38_AMR.sites.2015_08.txt f -hg38_EAS.sites.2015_08.txt f -hg38_EUR.sites.2015_08.txt f -hg38_SAS.sites.2015_08.txt f -hg38_esp6500siv2_all.txt f -hg38_esp6500siv2_aa.txt f -hg38_esp6500siv2_ea.txt f -hg38_ljb26_sift.txt f -hg38_ljb26_pp2hdiv.txt f -hg38_ljb26_pp2hvar.txt f -hg38_cosmic70.txt f -hg38_exac03.txt f -hg38_exac03nontcga.txt f -hg38_exac03nonpsych.txt f -hg38_kaviar20150923.txt f -hg38_hrcr1.txt f -hg38_dbscsnv11.txt f \ No newline at end of file |
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| diff -r 916846f73e25 -r 097ae310ced0 mm10_listAVDB.txt --- a/mm10_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,17 +0,0 @@ -#This is a sample file distributed with Galaxy that is used by the -#MutSpec-Annot tools. The mm10_listAVDB.txt has this format (white space -#characters are TAB characters): -# -#<RefGenome_DatabaseName> <operation> -# -# -# -#mm10_refGene.txt g -#mm10_genomicSuperDups.txt r -#mm10_snp137.txt f -mm10_refGene.txt g -mm10_knownGene.txt g -mm10_ensGene.txt g -mm10_cytoBand.txt r -mm10_genomicSuperDups.txt r -mm10_snp142.txt f |
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| diff -r 916846f73e25 -r 097ae310ced0 mutspecAnnot.pl --- a/mutspecAnnot.pl Fri Apr 29 05:11:28 2016 -0400 +++ b/mutspecAnnot.pl Fri Apr 29 05:14:23 2016 -0400 |
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| @@ -38,7 +38,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -our $max_cpu = 12; # Max number of CPU to use for the annotation +our $max_cpu = 1; # Max number of CPU to use for the annotation # Recover the current path |
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| diff -r 916846f73e25 -r 097ae310ced0 mutspecAnnot.xml --- a/mutspecAnnot.xml Fri Apr 29 05:11:28 2016 -0400 +++ b/mutspecAnnot.xml Fri Apr 29 05:14:23 2016 -0400 |
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| @@ -33,6 +33,7 @@ <data name="output" type="data" format="tabular" label="${input.name} annotated" /> </outputs> + <stdio> <regex match="ANNOVAR LOG FILE" source="stdout" @@ -117,9 +118,7 @@ **ANNOVAR annotations** -An example of annotations retrieved by the tool (for the full list please visit the Galaxy pages `Annovar databases`__) - -.. __: http://galaxy.iarc.fr/galaxy/u/ardinm/p/annovar-databases +An example of annotations retrieved by the tool. Gene-based: RefSeqGene, UCSC Known Gene and Ensembl Gene @@ -170,7 +169,6 @@ </help> - <citations> <citation type="bibtex"> @article{ardin_mutspec:_2016, |
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| diff -r 916846f73e25 -r 097ae310ced0 mutspecCompare.xml --- a/mutspecCompare.xml Fri Apr 29 05:11:28 2016 -0400 +++ b/mutspecCompare.xml Fri Apr 29 05:14:23 2016 -0400 |
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| @@ -106,7 +106,6 @@ </help> - <citations> <citation type="bibtex"> @article{ardin_mutspec:_2016, |
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| diff -r 916846f73e25 -r 097ae310ced0 mutspecFilter.pl --- a/mutspecFilter.pl Fri Apr 29 05:11:28 2016 -0400 +++ b/mutspecFilter.pl Fri Apr 29 05:14:23 2016 -0400 |
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| @@ -45,7 +45,7 @@ # Zero databases is specified if( ($dbSNP == 0) && ($segDup == 0) && ($esp == 0) && ($thG == 0) ) { - print STDERR "There is no databases selected for filtering against!!!\nPlease chose at least one between dbSNP, SegDup, ESP (only for human genome) or 1000 genome (only for human genome)\n"; + print STDERR "There is no databases selected for filtering against!!!\nPlease choose at least one between dbSNP, SegDup, ESP (only for human genome) or 1000 genome (only for human genome)\n"; exit; } |
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| diff -r 916846f73e25 -r 097ae310ced0 mutspecNmf_wrapper.sh --- a/mutspecNmf_wrapper.sh Fri Apr 29 05:11:28 2016 -0400 +++ b/mutspecNmf_wrapper.sh Fri Apr 29 05:14:23 2016 -0400 |
| [ |
| @@ -3,7 +3,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -cpu=8 +cpu=1 @@ -13,7 +13,7 @@ source=$1;shift input=$1 -if [[ $source == "html" ]] +if [[ $source == "html" ]] then input=${input%%.*}_files/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt fi @@ -44,7 +44,7 @@ else echo "<td> <center> <a href="NMF/Figures/Heatmap_MixtureCoeff.png">" >> $html echo "<img src="NMF/Figures/Heatmap_MixtureCoeff.png" /></a> <center> </td>" >> $html -fi +fi echo "</tr>" >> $html echo "</table>" >> $html |
| b |
| diff -r 916846f73e25 -r 097ae310ced0 mutspecStat_wrapper.sh --- a/mutspecStat_wrapper.sh Fri Apr 29 05:11:28 2016 -0400 +++ b/mutspecStat_wrapper.sh Fri Apr 29 05:14:23 2016 -0400 |
| b |
| @@ -3,7 +3,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -cpu=8 +cpu=1 @@ -119,9 +119,9 @@ touch $outEstimateSign echo "<a href='Mutational_Analysis/EstimatingSignatures.html'>Estimating the number of signatures</a><br/>" >> $html echo "<br/> <center> <h2>Computed statistics for estimating the number of signatures</h2> </center> <br/>" >> $outEstimateSign - echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF. <br/> + echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF. <br/> Brunet et al. 2004, proposed to take the first number of signature for which the cophenetic coefficient starts decreasing, <br/> - Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point. <br/> + Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point. <br/> Frigyesi et al. 2008, considered the smallest value at which the decrease in the RSS is lower than the decrease of the RSS obtained from random data. <br/><br/> The estimation are based on Brunet’s algorithm computed from 50 runs for each value of signature to estimate. <br/> <br/> The original data are shuffled for comparing the quality measures obtained with our data (Data x) and from randomized data (Data y). The curves for the actual data are in solid line, those for the randomized data are in dashed line. <br/> <br/>" >> $outEstimateSign |
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| diff -r 916846f73e25 -r 097ae310ced0 rn6_listAVDB.txt --- a/rn6_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,14 +0,0 @@ -#This is a sample file distributed with Galaxy that is used by the -#MutSpec-Annot tools. The hg18_listAVDB.txt has this format (white space -#characters are TAB characters): -# -#<RefGenome_DatabaseName> <operation> -# -# -# -#rn6_refGene.txt g -#rn6_genomicSuperDups.txt r -#rn6_snp138.txt f -rn6_refGene.txt g -rn6_ensGene.txt g -rn6_snp146.txt f \ No newline at end of file |
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| diff -r 916846f73e25 -r 097ae310ced0 tool_dependencies.xml --- a/tool_dependencies.xml Fri Apr 29 05:11:28 2016 -0400 +++ b/tool_dependencies.xml Fri Apr 29 05:14:23 2016 -0400 |
| b |
| @@ -3,8 +3,8 @@ <set_environment version="1.0"> <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> - - <package name="perl" version="5.18.1"> + + <package name="perl" version="5.18.1"> <install version="1.0"> <actions> <action type="setup_perl_environment"> @@ -43,7 +43,7 @@ <repository changeset_revision="57b37f63cb84" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="R" version="3.1.2"> + <package name="R" version="3.1.2"> <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> |