Mercurial > repos > crs4 > exomedepth

comparison exomedepth.R @ 7:45af4a9748cf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth commit 91a0182476a7fc26be7bef1677790518c4e88348"
author iuc
date Fri, 08 Nov 2019 13:25:44 -0500
parents 9ccde1867fbb
children 5d60331757d3
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6:165732ee5a48 7:45af4a9748cf
1 # Load ExomeDepth library (without warnings) 1 # Load ExomeDepth library (without warnings)
2 suppressMessages(library(ExomeDepth)) 2 suppressMessages(library(ExomeDepth))
3 3
4 # Import parameters from xml wrapper (args_file) 4 # Import parameters from xml wrapper (args_file)
5 args <- commandArgs(trailingOnly=TRUE) 5 args <- commandArgs(trailingOnly=TRUE)
6 eval(parse(text=args[[1]])) 6 param <- read.table(args[1],sep="=", as.is=TRUE)
7 param <- read.table(mypars,sep="=", as.is=TRUE)
8 7
9 # Set common parameters 8 # Set common parameters
10 target <- param[match("target",param[,1]),2] 9 target <- param[match("target",param[,1]),2]
11 trans_prob <- as.numeric(param[match("trans_prob",param[,1]),2]) 10 trans_prob <- as.numeric(param[match("trans_prob",param[,1]),2])
12 output <- param[match("output",param[,1]),2] 11 output <- param[match("output",param[,1]),2]