Mercurial > repos > proteore > proteore_ms_observation_pepatlas
changeset 7:3e9ea4797b00 draft
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
| author | proteore |
|---|---|
| date | Fri, 28 Jun 2019 05:10:43 -0400 |
| parents | e77c0f3e9bab |
| children | 8fdde324e99e |
| files | Get_ms-ms_observations.R Get_ms-ms_observations.xml |
| diffstat | 2 files changed, 19 insertions(+), 5 deletions(-) [+] |
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--- a/Get_ms-ms_observations.R Thu May 02 05:08:06 2019 -0400 +++ b/Get_ms-ms_observations.R Fri Jun 28 05:10:43 2019 -0400 @@ -76,6 +76,16 @@ return (c(date,tissue,file_name,path)) } +clean_ids <- function(ids){ + + ids = gsub(" ","",ids) + ids = ids[which(ids!="")] + ids = ids[which(ids!="NA")] + ids = ids[!is.na(ids)] + + return(ids) +} + main = function() { args <- commandArgs(TRUE) if(length(args)<1) { @@ -105,7 +115,7 @@ # Extract input input_type = args$input_type if (input_type == "list") { - input = strsplit(args$input, "[ \t\n]+")[[1]] + input = unlist(strsplit(strsplit(args$input, "[ \t\n]+")[[1]],";")) } else if (input_type == "file") { filename = args$input ncol = args$column @@ -120,7 +130,7 @@ file = one_id_one_line(file,ncol) #only one id per line input = sapply(file[,ncol],function(x) strsplit(as.character(x),";")[[1]][1],USE.NAMES = F) } - + input = clean_ids(input) output = args$output #data_frame building
--- a/Get_ms-ms_observations.xml Thu May 02 05:08:06 2019 -0400 +++ b/Get_ms-ms_observations.xml Fri Jun 28 05:10:43 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.05.01"> +<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.06.27"> <description>[Peptide Atlas]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> @@ -89,6 +89,10 @@ If your input file or list contains other type of IDs, please use the ID_Converter tool. +.. class:: warningmark + +In copy/paste mode, the number of IDs considered in input is limited to 5000. + ---- **Parameters** @@ -134,13 +138,13 @@ **Authors** -T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR This work has been partially funded through the French National Agency for Research (ANR) IFB project. -Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. +Help: contact@proteore.org for any questions or concerns about this tool. ]]></help> <citations>