Mercurial > repos > proteore > proteore_ms_observation_pepatlas
changeset 10:ef723082fc54 draft default tip
"planemo upload commit b061341e1157cccd90e33b945bc17705880b3e57"
| author | proteore |
|---|---|
| date | Mon, 04 May 2020 03:29:36 -0400 |
| parents | 14c890ff105a |
| children | |
| files | Get_ms-ms_observations.R Get_ms-ms_observations.xml |
| diffstat | 2 files changed, 5 insertions(+), 11 deletions(-) [+] |
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--- a/Get_ms-ms_observations.R Mon May 04 03:18:37 2020 -0400 +++ b/Get_ms-ms_observations.R Mon May 04 03:29:36 2020 -0400 @@ -77,12 +77,9 @@ } clean_ids <- function(ids){ - - ids = gsub(" ","",ids) - ids = ids[which(ids!="")] - ids = ids[which(ids!="NA")] - ids = ids[!is.na(ids)] - + ids = gsub(" ",NA,ids) + ids = gsub("^$|^ $", NA, ids) + ids = gsub("NA",NA,ids) return(ids) } @@ -109,9 +106,6 @@ args <- as.list(as.character(argsDF$V2)) names(args) <- argsDF$V1 - #save(args,file="/Users/David/work/ProteoRE/tools/Get_ms-ms_observations/args.Rda") - load("/Users/David/work/ProteoRE/tools/Get_ms-ms_observations/args.Rda") - # Extract input input_type = args$input_type if (input_type == "list") {
--- a/Get_ms-ms_observations.xml Mon May 04 03:18:37 2020 -0400 +++ b/Get_ms-ms_observations.xml Mon May 04 03:29:36 2020 -0400 @@ -1,7 +1,7 @@ -<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2020.01.23"> +<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2020.04.30"> <description>[Human Peptide Atlas]</description> <requirements> - <requirement type="package" version="3.4.1">R</requirement> + <requirement type="package" version="3.6.1">r-base</requirement> </requirements> <stdio> <exit_code range="1:" />