Mercurial > repos > immport-devteam > flowai

comparison FCSflowAI.R @ 1:34397a84faf1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
author azomics
date Tue, 23 Jun 2020 18:34:02 -0400
parents
children fab7c5deeb65
comparison
equal deleted inserted replaced
0:60aa5e56531a 1:34397a84faf1
1 #!/usr/bin/env Rscript
2 #
3 # Authors: Gianni Monaco
4 #
5 # Reference: flowAI: automatic and interactive anomaly discerning
6 # tools for flow cytometry data.
7 # Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen,
8 # Joao Pedro de Magalhaes and Anis Larbi
9 # Bioinformatics (2016)
10 # doi: 10.1093/bioinformatics/btw191
11 #
12
13 library(flowAI)
14 library(methods)
15
16 # parse arguments
17
18 args <- commandArgs(trailingOnly = TRUE)
19
20 remFS <- if(args[4]) c("FSC", "SSC") else NULL
21
22 flow_auto_qc(
23 fcsfiles = args[1],
24 remove_from = args[2],
25 alphaFR = as.numeric(args[3]),
26 ChRemoveFS = remFS,
27 outlierFS = args[5],
28 pen_valueFS = as.numeric(args[6]),
29 sideFM = args[7],
30 fcs_QC = ifelse(args[9] == "None", FALSE, "_QC"),
31 fcs_highQ = ifelse(args[10] == "None", FALSE, "_highQ"),
32 fcs_lowQ = ifelse(args[11] == "None", FALSE, "_lowQ"),
33 folder_results = FALSE)
34
35 try(file.rename(dir(".", pattern = ".*_QC.html"), args[8]), silent =TRUE)
36 try(file.rename(dir(".", pattern = ".*_QC.fcs"), args[9]), silent =TRUE)
37 try(file.rename(dir(".", pattern = ".*_highQ.fcs"), args[10]), silent =TRUE)
38 try(file.rename(dir(".", pattern = ".*_lowQ.fcs"), args[11]), silent =TRUE)