MAplotFile<-paste(snakemake@output[["plot_FDR_5_perc_MA"]],"/",snakemake@params[["antibody"]],".",CompPrefix,".MA-plot_FDR_0.05.pdf",sep="")# AVI: added to create separate pdf files
VolcanoPlotFile<-paste(snakemake@output[["plot_FDR_5_perc_volcano"]],"/",snakemake@params[["antibody"]],".",CompPrefix,".volcano_FDR_0.05.pdf",sep="")# AVI: added to create separate pdf files
Description='Create IGV session file from a list of files and associated colours - ".bed", ".bw", ".bigwig", ".tdf", ".gtf" files currently supported.'
argParser.add_argument('LIST_FILE',help="Tab-delimited file containing two columns i.e. file_name\tcolour. Header isnt required.")
argParser.add_argument('GENOME',help="Full path to genome fasta file or shorthand for genome available in IGV e.g. hg19.")
## OPTIONAL PARAMETERS
argParser.add_argument('-pp','--path_prefix',type=str,dest="PATH_PREFIX",default='',help="Path prefix to be added at beginning of all files in input list file.")