Mercurial > repos > immport-devteam > flowai
diff FCSflowAI.R @ 2:fab7c5deeb65 draft
planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
| author | azomics |
|---|---|
| date | Tue, 26 Sep 2023 23:19:04 +0000 |
| parents | 34397a84faf1 |
| children |
line wrap: on
line diff
--- a/FCSflowAI.R Tue Jun 23 18:34:02 2020 -0400 +++ b/FCSflowAI.R Tue Sep 26 23:19:04 2023 +0000 @@ -7,7 +7,7 @@ # Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen, # Joao Pedro de Magalhaes and Anis Larbi # Bioinformatics (2016) -# doi: 10.1093/bioinformatics/btw191 +# doi 10.1093/bioinformatics/btw191 # library(flowAI) @@ -17,22 +17,22 @@ args <- commandArgs(trailingOnly = TRUE) -remFS <- if(args[4]) c("FSC", "SSC") else NULL +rem_fs <- if (args[4]) c("FSC", "SSC") else NULL flow_auto_qc( - fcsfiles = args[1], - remove_from = args[2], - alphaFR = as.numeric(args[3]), - ChRemoveFS = remFS, - outlierFS = args[5], - pen_valueFS = as.numeric(args[6]), - sideFM = args[7], - fcs_QC = ifelse(args[9] == "None", FALSE, "_QC"), - fcs_highQ = ifelse(args[10] == "None", FALSE, "_highQ"), - fcs_lowQ = ifelse(args[11] == "None", FALSE, "_lowQ"), - folder_results = FALSE) + fcsfiles = args[1], + remove_from = args[2], + alphaFR = as.numeric(args[3]), + ChRemoveFS = rem_fs, + outlierFS = args[5], + pen_valueFS = as.numeric(args[6]), + sideFM = args[7], + fcs_QC = ifelse(args[9] == "None", FALSE, "_QC"), + fcs_highQ = ifelse(args[10] == "None", FALSE, "_highQ"), + fcs_lowQ = ifelse(args[11] == "None", FALSE, "_lowQ"), + folder_results = FALSE) -try(file.rename(dir(".", pattern = ".*_QC.html"), args[8]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[9]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[10]), silent =TRUE) -try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[11]), silent =TRUE) +try(file.rename(dir(".", pattern = ".*_QC.html"), args[8]), silent = TRUE) +try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[9]), silent = TRUE) +try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[10]), silent = TRUE) +try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[11]), silent = TRUE)