# HG changeset patch
# User galaxyp
# Date 1484327912 18000
# Node ID 982fb2cde6c520235f7f5c9b88bee81a8e60f6c9
# Parent ed65d110c1b5487d7809f682b53c9649d7050b2f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
diff -r ed65d110c1b5 -r 982fb2cde6c5 COPYING
diff -r ed65d110c1b5 -r 982fb2cde6c5 README.md
diff -r ed65d110c1b5 -r 982fb2cde6c5 customProDB.R
--- a/customProDB.R Wed Jun 08 15:02:58 2016 -0400
+++ b/customProDB.R Fri Jan 13 12:18:32 2017 -0500
@@ -1,113 +1,113 @@
-#!/usr/bin/env Rscript
-
-initial.options <- commandArgs(trailingOnly = FALSE)
-script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
-
-## begin warning handler
-withCallingHandlers({
-
-library(methods) # Because Rscript does not always do this
-
-options('useFancyQuotes' = FALSE)
-
-suppressPackageStartupMessages(library("optparse"))
-suppressPackageStartupMessages(library("RGalaxy"))
-
-
-option_list <- list()
-
-option_list$bam <- make_option('--bam', type='character')
-option_list$bai <- make_option('--bai', type='character')
-option_list$vcf <- make_option('--vcf', type='character')
-option_list$exon_anno <- make_option('--exon_anno', type='character')
-option_list$proteinseq <- make_option('--proteinseq', type='character')
-option_list$procodingseq <- make_option('--procodingseq', type='character')
-option_list$ids <- make_option('--ids', type='character')
-option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
-option_list$cosmic <- make_option('--cosmic', type='character')
-option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE)
-option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
-#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE)
-#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
-option_list$outputFile <- make_option('--outputFile', type='character')
-
-
-opt <- parse_args(OptionParser(option_list=option_list))
-
-
-customProDB <- function(
- bam_file = GalaxyInputFile(required=TRUE),
- bai_file = GalaxyInputFile(required=TRUE),
- vcf_file = GalaxyInputFile(required=TRUE),
- exon_anno_file = GalaxyInputFile(required=TRUE),
- proteinseq_file = GalaxyInputFile(required=TRUE),
- procodingseq_file = GalaxyInputFile(required=TRUE),
- ids_file = GalaxyInputFile(required=TRUE),
- dbsnpinCoding_file = GalaxyInputFile(required=FALSE),
- cosmic_file = GalaxyInputFile(required=FALSE),
- annotationFromHistory = GalaxyLogicalParam(required=FALSE),
- rpkmCutoff = GalaxyNumericParam(required=TRUE),
- #outputIndels = GalaxyLogicalParam(required=FALSE),
- #outputNovelJunctions = GalaxyLogicalParam(required=FALSE),
- outputFile = GalaxyOutput("FASTA","fasta"))
-{
- file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))
- file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))
- file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))
- file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))
-
- if (length(dbsnpinCoding_file) > 0)
- {
- file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
- labelrsid = T
- }
- else
- {
- labelrsid = F
- }
-
- if (length(cosmic_file) > 0)
- {
- file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
- cosmic = T
- }
- else
- {
- cosmic = F
- }
-
- bamLink = "input.bam"
- file.symlink(bam_file, bamLink)
- file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
-
- suppressPackageStartupMessages(library(customProDB))
-
- easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
- rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
- nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic)
-}
-
-
-params <- list()
-for(param in names(opt))
-{
- if (!param == "help")
- params[param] <- opt[param]
-}
-
-setClass("GalaxyRemoteError", contains="character")
-wrappedFunction <- function(f)
-{
- tryCatch(do.call(f, params),
- error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
-}
-
-
-suppressPackageStartupMessages(library(RGalaxy))
-do.call(customProDB, params)
-
-## end warning handler
-}, warning = function(w) {
- cat(paste("Warning:", conditionMessage(w), "\n"))
- invokeRestart("muffleWarning")
-})
+#!/usr/bin/env Rscript
+
+initial.options <- commandArgs(trailingOnly = FALSE)
+script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
+
+## begin warning handler
+withCallingHandlers({
+
+library(methods) # Because Rscript does not always do this
+
+options('useFancyQuotes' = FALSE)
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("RGalaxy"))
+
+
+option_list <- list()
+
+option_list$bam <- make_option('--bam', type='character')
+option_list$bai <- make_option('--bai', type='character')
+option_list$vcf <- make_option('--vcf', type='character')
+option_list$exon_anno <- make_option('--exon_anno', type='character')
+option_list$proteinseq <- make_option('--proteinseq', type='character')
+option_list$procodingseq <- make_option('--procodingseq', type='character')
+option_list$ids <- make_option('--ids', type='character')
+option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
+option_list$cosmic <- make_option('--cosmic', type='character')
+option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE)
+option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
+#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE)
+#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
+option_list$outputFile <- make_option('--outputFile', type='character')
+
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+
+customProDB <- function(
+ bam_file = GalaxyInputFile(required=TRUE),
+ bai_file = GalaxyInputFile(required=TRUE),
+ vcf_file = GalaxyInputFile(required=TRUE),
+ exon_anno_file = GalaxyInputFile(required=TRUE),
+ proteinseq_file = GalaxyInputFile(required=TRUE),
+ procodingseq_file = GalaxyInputFile(required=TRUE),
+ ids_file = GalaxyInputFile(required=TRUE),
+ dbsnpinCoding_file = GalaxyInputFile(required=FALSE),
+ cosmic_file = GalaxyInputFile(required=FALSE),
+ annotationFromHistory = GalaxyLogicalParam(required=FALSE),
+ rpkmCutoff = GalaxyNumericParam(required=TRUE),
+ #outputIndels = GalaxyLogicalParam(required=FALSE),
+ #outputNovelJunctions = GalaxyLogicalParam(required=FALSE),
+ outputFile = GalaxyOutput("FASTA","fasta"))
+{
+ file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))
+ file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))
+ file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))
+ file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))
+
+ if (length(dbsnpinCoding_file) > 0)
+ {
+ file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
+ labelrsid = T
+ }
+ else
+ {
+ labelrsid = F
+ }
+
+ if (length(cosmic_file) > 0)
+ {
+ file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
+ cosmic = T
+ }
+ else
+ {
+ cosmic = F
+ }
+
+ bamLink = "input.bam"
+ file.symlink(bam_file, bamLink)
+ file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
+
+ suppressPackageStartupMessages(library(customProDB))
+
+ easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
+ rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
+ nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic)
+}
+
+
+params <- list()
+for(param in names(opt))
+{
+ if (!param == "help")
+ params[param] <- opt[param]
+}
+
+setClass("GalaxyRemoteError", contains="character")
+wrappedFunction <- function(f)
+{
+ tryCatch(do.call(f, params),
+ error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
+}
+
+
+suppressPackageStartupMessages(library(RGalaxy))
+do.call(customProDB, params)
+
+## end warning handler
+}, warning = function(w) {
+ cat(paste("Warning:", conditionMessage(w), "\n"))
+ invokeRestart("muffleWarning")
+})
diff -r ed65d110c1b5 -r 982fb2cde6c5 customProDB.xml
--- a/customProDB.xml Wed Jun 08 15:02:58 2016 -0400
+++ b/customProDB.xml Fri Jan 13 12:18:32 2017 -0500
@@ -1,110 +1,116 @@
-
- Generate protein FASTAs from exosome or transcriptome data
-
-
-
- customProDB.R
-
- --bam="$genome_annotation.bamInput"
- --bai="${genome_annotation.bamInput.metadata.bam_index}"
- --vcf="$genome_annotation.vcfInput"
- --rpkmCutoff=$rpkmCutoff
- --outputFile="${output_rpkm}"
-
- #if str($genome_annotation.source) == "history":
- --exon_anno="$genome_annotation.exonAnno"
- --proteinseq="$genome_annotation.proteinSeq"
- --procodingseq="$genome_annotation.proCodingSeq"
- --ids="$genome_annotation.ids"
- #if str($genome_annotation.dbsnpInCoding) != "None":
- --dbsnpinCoding="$genome_annotation.dbsnpInCoding"
- #end if
- #if str($genome_annotation.cosmic) != "None":
- --cosmic="$genome_annotation.cosmic"
- #end if
- #else:
- #set index_path = $genome_annotation.builtin.fields.path
- --exon_anno="$index_path/exon_anno.RData"
- --proteinseq="$index_path/proseq.RData"
- --procodingseq="$index_path/procodingseq.RData"
- --ids="$index_path/ids.RData"
- #if $genome_annotation.dbsnpInCoding:
- --dbsnpinCoding="$index_path/dbsnpinCoding.RData"
- #end if
- #if $genome_annotation.cosmic:
- --cosmic="$index_path/cosmic.RData"
- #end if
- #end if
-
-2>&1
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-**Description**
-
-Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files).
-
-
\ No newline at end of file
+
+ Generate protein FASTAs from exosome or transcriptome data
+
+
+
+ customProDB.R
+
+ --bam="$genome_annotation.bamInput"
+ --bai="${genome_annotation.bamInput.metadata.bam_index}"
+ --vcf="$genome_annotation.vcfInput"
+ --rpkmCutoff=$rpkmCutoff
+ --outputFile="${output_rpkm}"
+
+ #if str($genome_annotation.source) == "history":
+ --exon_anno="$genome_annotation.exonAnno"
+ --proteinseq="$genome_annotation.proteinSeq"
+ --procodingseq="$genome_annotation.proCodingSeq"
+ --ids="$genome_annotation.ids"
+ #if str($genome_annotation.dbsnpInCoding) != "None":
+ --dbsnpinCoding="$genome_annotation.dbsnpInCoding"
+ #end if
+ #if str($genome_annotation.cosmic) != "None":
+ --cosmic="$genome_annotation.cosmic"
+ #end if
+ #else:
+ #set index_path = $genome_annotation.builtin.fields.path
+ --exon_anno="$index_path/exon_anno.RData"
+ --proteinseq="$index_path/proseq.RData"
+ --procodingseq="$index_path/procodingseq.RData"
+ --ids="$index_path/ids.RData"
+ #if $genome_annotation.dbsnpInCoding:
+ --dbsnpinCoding="$index_path/dbsnpinCoding.RData"
+ #end if
+ #if $genome_annotation.cosmic:
+ --cosmic="$index_path/cosmic.RData"
+ #end if
+ #end if
+
+2>&1
+
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+
+
+**Description**
+
+Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files).
+
+ 10.1093/bioinformatics/btt543
+ @misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub
+repository},
+ year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}
+
+
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/exon_anno.RData
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/ids.RData
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/procodingseq.RData
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/proseq.RData
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/test1.vcf
--- a/test-data/test1.vcf Wed Jun 08 15:02:58 2016 -0400
+++ b/test-data/test1.vcf Fri Jan 13 12:18:32 2017 -0500
@@ -1,87 +1,87 @@
-##fileformat=VCFv4.1
-##samtoolsVersion=0.1.17 (r973:277)
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
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-##INFO=
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-##INFO=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test
-chr1 32386425 . T C 24 . DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:56,9,0:15
-chr1 32507666 . G T 6.2 . DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36 GT:PL:GQ 0/1:35,0,78:36
-chr1 32524459 . A C 3.54 . DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1 GT:PL:GQ 0/1:31,0,98:30
-chr1 32622505 . G A 101 . DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075 GT:PL:GQ 0/1:131,0,162:99
-chr12 25357574 . CAA C 109 . INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5 GT:PL:GQ 1/1:149,12,0:21
-chr12 25357628 . TA T 53.4 . INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16
-chr12 25358650 . A T 73 . DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72 GT:PL:GQ 1/1:106,45,0:87
-chr12 25358662 . CTTTTTTTT CTTTTTT,CTTTTTTT 31.6 . INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5 GT:PL:GQ 1/1:96,42,24,91,0,64:33
-chr12 25358943 . T C 67.1 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:100,21,0:39
-chr12 25358969 . T G 36.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:69,12,0:21
-chr12 25359352 . G A 172 . DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:205,42,0:81
-chr12 25359464 . TAA TA 123 . INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113 GT:PL:GQ 1/1:164,78,0:99
-chr12 25360138 . T C 169 . DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84 GT:PL:GQ 1/1:202,57,0:99
-chr12 25361091 . T C 93 . DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:126,42,0:81
-chr12 25362217 . A G 179 . DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87 GT:PL:GQ 1/1:212,60,0:99
-chr12 25362465 . G A 38.3 . DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42 GT:PL:GQ 1/1:71,15,0:27
-chr12 25362552 . A C 156 . DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57 GT:PL:GQ 1/1:189,30,0:57
-chr12 25364387 . T C 21 . DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1 GT:PL:GQ 0/1:51,0,112:54
-chr12 25368462 . C T 112 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:145,21,0:39
-chr17 37866082 . G A 141 . DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1 GT:PL:GQ 0/1:171,0,180:99
-chr17 37870047 . A G 30 . DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1 GT:PL:GQ 0/1:60,0,25:28
-chr17 37879466 . G A 7.8 . DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1 GT:PL:GQ 0/1:37,0,31:34
-chr17 37885332 . G A 83.5 . DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39 GT:PL:GQ 1/1:116,12,0:21
-chr17 37898543 . T C 165 . DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90 GT:PL:GQ 1/1:198,63,0:99
-chr17 7530271 . C T 143 . DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1 GT:PL:GQ 0/1:173,0,238:99
-chr17 7572657 . G T 225 . DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27 GT:PL:GQ 0/1:255,0,190:99
-chr17 7591866 . G T 45 . DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01 GT:PL:GQ 0/1:75,0,162:78
-chr17 7606153 . C T 74 . DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1 GT:PL:GQ 0/1:104,0,165:99
-chr2 48010558 . C A 12.3 . DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1 GT:PL:GQ 0/1:42,0,31:34
-chr2 48016554 . T C 32 . DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21 GT:PL:GQ 0/1:62,0,48:51
-chr2 48018081 . A G 77 . DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34 GT:PL:GQ 0/1:107,0,24:27
-chr2 48018221 . C T 22 . DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1 GT:PL:GQ 0/1:52,0,116:55
-chr2 48027990 . G T 122 . DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039 GT:PL:GQ 0/1:152,0,131:99
-chr2 48030458 . G C 105 . DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39 GT:PL:GQ 1/1:137,12,0:21
-chr5 112154737 . CT C 29 . INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012 GT:PL:GQ 0/1:59,0,85:62
-chr5 112162854 . T C 60 . DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36 GT:PL:GQ 1/1:92,9,0:16
-chr5 112164561 . G A 87.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:120,12,0:21
-chr5 112175639 . C T 31 . DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1 GT:PL:GQ 0/1:61,0,62:61
-chr5 112175897 . GAA GA 7.8 . INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33 GT:PL:GQ 0/1:37,0,97:39
-chr5 112176559 . T G 72 . DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51 GT:PL:GQ 1/1:105,24,0:45
-chr5 112176756 . T A 143 . DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54 GT:PL:GQ 1/1:176,27,0:51
-chr5 112180015 . C A 123 . DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1 GT:PL:GQ 0/1:153,0,67:70
-chr5 112204170 . G A 112 . DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:144,12,0:21
-chr7 140043303 . C T 88 . DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42 GT:PL:GQ 0/1:118,0,167:99
-chr7 140065806 . T C 38.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:71,12,0:21
-chr7 140065845 . C A 44.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:77,12,0:21
-chr7 140152904 . CAAAA CAAAAA 41.5 . INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1 GT:PL:GQ 0/1:79,0,91:82
-chr7 140153495 . G T 140 . DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038 GT:PL:GQ 0/1:170,0,184:99
-chr7 140158851 . C G 153 . DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1 GT:PL:GQ 1/1:186,75,0:99
-chr7 140244560 . C T 78 . DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1 GT:PL:GQ 0/1:108,0,23:26
-chr7 140406430 . T A 8.64 . DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021 GT:PL:GQ 0/1:38,0,167:40
-chr7 140406436 . A G 4.77 . DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08 GT:PL:GQ 0/1:33,0,170:33
-chr7 140424582 . G C 18.1 . DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1 GT:PL:GQ 0/1:48,0,56:50
-chr7 140426098 . G A 10.2 . DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
-chr7 140702871 . G A 77.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:110,12,0:21
-chr7 140706061 . G T 119 . DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1 GT:PL:GQ 0/1:149,0,178:99
-chr7 140706157 . G T 42 . DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013 GT:PL:GQ 0/1:72,0,170:75
-chr9 86583076 . C T 64 . DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1 GT:PL:GQ 0/1:94,0,100:96
-chr9 86593314 . G C 186 . DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072 GT:PL:GQ 0/1:216,0,216:99
-chr9 86595070 . C T 140 . DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1 GT:PL:GQ 0/1:170,0,188:99
-chr9 86595498 . G A 66 . DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1 GT:PL:GQ 0/1:96,0,225:99
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+chr1 32386425 . T C 24 . DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:56,9,0:15
+chr1 32507666 . G T 6.2 . DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36 GT:PL:GQ 0/1:35,0,78:36
+chr1 32524459 . A C 3.54 . DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1 GT:PL:GQ 0/1:31,0,98:30
+chr1 32622505 . G A 101 . DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075 GT:PL:GQ 0/1:131,0,162:99
+chr12 25357574 . CAA C 109 . INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5 GT:PL:GQ 1/1:149,12,0:21
+chr12 25357628 . TA T 53.4 . INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16
+chr12 25358650 . A T 73 . DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72 GT:PL:GQ 1/1:106,45,0:87
+chr12 25358662 . CTTTTTTTT CTTTTTT,CTTTTTTT 31.6 . INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5 GT:PL:GQ 1/1:96,42,24,91,0,64:33
+chr12 25358943 . T C 67.1 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:100,21,0:39
+chr12 25358969 . T G 36.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:69,12,0:21
+chr12 25359352 . G A 172 . DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:205,42,0:81
+chr12 25359464 . TAA TA 123 . INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113 GT:PL:GQ 1/1:164,78,0:99
+chr12 25360138 . T C 169 . DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84 GT:PL:GQ 1/1:202,57,0:99
+chr12 25361091 . T C 93 . DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:126,42,0:81
+chr12 25362217 . A G 179 . DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87 GT:PL:GQ 1/1:212,60,0:99
+chr12 25362465 . G A 38.3 . DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42 GT:PL:GQ 1/1:71,15,0:27
+chr12 25362552 . A C 156 . DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57 GT:PL:GQ 1/1:189,30,0:57
+chr12 25364387 . T C 21 . DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1 GT:PL:GQ 0/1:51,0,112:54
+chr12 25368462 . C T 112 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:145,21,0:39
+chr17 37866082 . G A 141 . DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1 GT:PL:GQ 0/1:171,0,180:99
+chr17 37870047 . A G 30 . DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1 GT:PL:GQ 0/1:60,0,25:28
+chr17 37879466 . G A 7.8 . DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1 GT:PL:GQ 0/1:37,0,31:34
+chr17 37885332 . G A 83.5 . DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39 GT:PL:GQ 1/1:116,12,0:21
+chr17 37898543 . T C 165 . DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90 GT:PL:GQ 1/1:198,63,0:99
+chr17 7530271 . C T 143 . DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1 GT:PL:GQ 0/1:173,0,238:99
+chr17 7572657 . G T 225 . DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27 GT:PL:GQ 0/1:255,0,190:99
+chr17 7591866 . G T 45 . DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01 GT:PL:GQ 0/1:75,0,162:78
+chr17 7606153 . C T 74 . DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1 GT:PL:GQ 0/1:104,0,165:99
+chr2 48010558 . C A 12.3 . DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1 GT:PL:GQ 0/1:42,0,31:34
+chr2 48016554 . T C 32 . DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21 GT:PL:GQ 0/1:62,0,48:51
+chr2 48018081 . A G 77 . DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34 GT:PL:GQ 0/1:107,0,24:27
+chr2 48018221 . C T 22 . DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1 GT:PL:GQ 0/1:52,0,116:55
+chr2 48027990 . G T 122 . DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039 GT:PL:GQ 0/1:152,0,131:99
+chr2 48030458 . G C 105 . DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39 GT:PL:GQ 1/1:137,12,0:21
+chr5 112154737 . CT C 29 . INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012 GT:PL:GQ 0/1:59,0,85:62
+chr5 112162854 . T C 60 . DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36 GT:PL:GQ 1/1:92,9,0:16
+chr5 112164561 . G A 87.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:120,12,0:21
+chr5 112175639 . C T 31 . DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1 GT:PL:GQ 0/1:61,0,62:61
+chr5 112175897 . GAA GA 7.8 . INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33 GT:PL:GQ 0/1:37,0,97:39
+chr5 112176559 . T G 72 . DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51 GT:PL:GQ 1/1:105,24,0:45
+chr5 112176756 . T A 143 . DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54 GT:PL:GQ 1/1:176,27,0:51
+chr5 112180015 . C A 123 . DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1 GT:PL:GQ 0/1:153,0,67:70
+chr5 112204170 . G A 112 . DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:144,12,0:21
+chr7 140043303 . C T 88 . DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42 GT:PL:GQ 0/1:118,0,167:99
+chr7 140065806 . T C 38.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:71,12,0:21
+chr7 140065845 . C A 44.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:77,12,0:21
+chr7 140152904 . CAAAA CAAAAA 41.5 . INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1 GT:PL:GQ 0/1:79,0,91:82
+chr7 140153495 . G T 140 . DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038 GT:PL:GQ 0/1:170,0,184:99
+chr7 140158851 . C G 153 . DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1 GT:PL:GQ 1/1:186,75,0:99
+chr7 140244560 . C T 78 . DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1 GT:PL:GQ 0/1:108,0,23:26
+chr7 140406430 . T A 8.64 . DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021 GT:PL:GQ 0/1:38,0,167:40
+chr7 140406436 . A G 4.77 . DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08 GT:PL:GQ 0/1:33,0,170:33
+chr7 140424582 . G C 18.1 . DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1 GT:PL:GQ 0/1:48,0,56:50
+chr7 140426098 . G A 10.2 . DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
+chr7 140702871 . G A 77.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:110,12,0:21
+chr7 140706061 . G T 119 . DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1 GT:PL:GQ 0/1:149,0,178:99
+chr7 140706157 . G T 42 . DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013 GT:PL:GQ 0/1:72,0,170:75
+chr9 86583076 . C T 64 . DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1 GT:PL:GQ 0/1:94,0,100:96
+chr9 86593314 . G C 186 . DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072 GT:PL:GQ 0/1:216,0,216:99
+chr9 86595070 . C T 140 . DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1 GT:PL:GQ 0/1:170,0,188:99
+chr9 86595498 . G A 66 . DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1 GT:PL:GQ 0/1:96,0,225:99
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/test1_sort.bam
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/test1_sort.bam.bai
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/test_indel.fasta
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/test_rpkm.fasta
diff -r ed65d110c1b5 -r 982fb2cde6c5 test-data/test_snv.fasta
diff -r ed65d110c1b5 -r 982fb2cde6c5 tool-data/customProDB.loc.sample
diff -r ed65d110c1b5 -r 982fb2cde6c5 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Wed Jun 08 15:02:58 2016 -0400
+++ b/tool_data_table_conf.xml.sample Fri Jan 13 12:18:32 2017 -0500
@@ -1,7 +1,7 @@
-
-
-
- value, dbkey, name, path
-
-
-
+
+
+
+ value, dbkey, name, path
+
+
+