Mercurial > repos > morinlab > correct_read_counter
changeset 0:75c4a4c32bae draft default tip
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
| author | morinlab |
|---|---|
| date | Tue, 11 Oct 2016 14:18:25 -0400 |
| parents | |
| children | |
| files | correctReads.R correctReads.xml tool_dependencies.xml |
| diffstat | 3 files changed, 59 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/correctReads.R Tue Oct 11 14:18:25 2016 -0400 @@ -0,0 +1,21 @@ +library(TitanCNA) +version <- "0.1.1" +args <- commandArgs(TRUE) + +tumWig <- args[1] +normWig <- args[2] +gc <- args[3] +map <- args[4] +target_list <- args[5] +outfile <- args[6] + +message('titan: Correcting GC content and mappability biases...') + +if( !is.null(target_list) ){ + target_list_data <- read.table(target_list, sep="\t", header=F, stringsAsFactors=F) + cnData <- correctReadDepth(tumWig, normWig, gc, map, targetedSequence = target_list_data) +} else { + cnData <- correctReadDepth(tumWig, normWig, gc, map) +} + +write.table(cnData, file = outfile, col.names = TRUE, row.names = FALSE, quote = FALSE, sep ="\t")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/correctReads.xml Tue Oct 11 14:18:25 2016 -0400 @@ -0,0 +1,32 @@ +<tool id="correct_read_counter" name="correctReadCounter" version="1.8.0"> + <description> + Correct Read Counter for GC content and mappability biases + </description> + <requirements> + <requirement type="binary">Rscript</requirement> + <requirement type="R-module">TitanCNA</requirement> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.8.0">titancna</requirement> + </requirements> + <command> + + Rscript $__tool_directory__/correctReads.R $tumour $normal $gc $map + #if $target: + $target + #else: + NULL + #end if + $output 2>&1 + + </command> + <inputs> + <param type="data" format="wig" name="normal" label="Normal Read Counts"/> + <param type="data" format="wig" name="tumour" label="Tumour Read Counts"/> + <param type="data" format="wig" name="gc" label="GC Wig"/> + <param type="data" format="wig" name="map" label="MAP Wig"/> + <param type="data" format="txt,bed" name="target" label="Target File" help="Specify Targets if using Exome Data" optional="True"/> + </inputs> + <outputs> + <data format="wig" name="output"/> + </outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 11 14:18:25 2016 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="titancna" version="1.8.0"> + <repository changeset_revision="5991e428f9d8" name="package_titancna_1_8_0" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>