Mercurial > repos > proteore > proteore_ms_observation_pepatlas
changeset 16:03f3d7d3acfc draft default tip
"planemo upload commit 9a871575622a1318adc64dad63fa5e3a9d2a19fd-dirty"
| author | proteore |
|---|---|
| date | Thu, 30 Apr 2020 14:06:22 +0000 |
| parents | 82cec53a3123 |
| children | |
| files | Get_ms-ms_observations.R Get_ms-ms_observations.xml |
| diffstat | 2 files changed, 6 insertions(+), 12 deletions(-) [+] |
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--- a/Get_ms-ms_observations.R Thu Jun 27 04:16:06 2019 -0400 +++ b/Get_ms-ms_observations.R Thu Apr 30 14:06:22 2020 +0000 @@ -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$V1 - #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/Get_ms-ms_observations/args.Rda") - #load("/home/dchristiany/proteore_project/ProteoRE/tools/Get_ms-ms_observations/args.Rda") - # Extract input input_type = args$input_type if (input_type == "list") {
--- a/Get_ms-ms_observations.xml Thu Jun 27 04:16:06 2019 -0400 +++ b/Get_ms-ms_observations.xml Thu Apr 30 14:06:22 2020 +0000 @@ -1,7 +1,7 @@ -<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.06.27"> - <description>[Peptide Atlas]</description> +<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:" />