From 4297c61aed222b49c344a8581b080bacbc990b97 Mon Sep 17 00:00:00 2001 From: Annika Fust Date: Tue, 5 Sep 2017 08:54:32 +0200 Subject: [PATCH] added help message --- reformat_output.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/reformat_output.R b/reformat_output.R index eec906e..6859c4d 100755 --- a/reformat_output.R +++ b/reformat_output.R @@ -2,7 +2,7 @@ ## author afust ## reformat BestperQuery_Hits table to table with all information about one peak in one row -library(getopt) +library(getopt, quietly=TRUE) ## columns given with $3 should be unique and not be seprated by the delimiter ## with the aggregate function the same entries are sepereated by it, so this has to be adjusted @@ -18,8 +18,8 @@ library(getopt) # 2 optional parameter options <- matrix(c( 'input', 'i', 1, 'character', 'file which should be reformatted', - 'key', 'k', 1, 'character', 'key columns seperated by "," without spaces', - 'cols', 'c', 1, 'character', 'columns that should be kept ', + 'key', 'k', 1, 'character', 'key column', + 'cols', 'c', 1, 'character', 'columns that should be kept, e.g 1,2,5 or 1:5', 'delimiter', 'd', 2, 'character', 'delimiter [,]', 'threads', 't', 2, 'integer', 'cores to be used for reformatting', 'help', 'h', 0, 'logical','Provides command line help.'