annotate scater-normalize.R @ 1:058b40656107 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author iuc
date Tue, 03 Sep 2019 14:26:50 -0400
parents a8290d207005
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
1 #!/usr/bin/env Rscript
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
2 #Normalises a SingleCellExperiment object
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
3
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
4 # Load optparse we need to check inputs
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
5 library(optparse)
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
6 library(workflowscriptscommon)
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
7 library(LoomExperiment)
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
8 library(scater)
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
9
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
10 # parse options
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
11 option_list = list(
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
12 make_option(
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
13 c("-i", "--input-loom"),
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
14 action = "store",
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
15 default = NA,
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
16 type = 'character',
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
17 help = "A SingleCellExperiment object file in Loom format."
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
18 ),
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
19 make_option(
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
20 c("-o", "--output-loom"),
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
21 action = "store",
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
22 default = NA,
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
23 type = 'character',
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
24 help = "File name in which to store the SingleCellExperiment object in Loom format."
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
25 )
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
26 )
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
27
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
28 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_loom'))
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
29
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
30 # Check parameter values
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
31
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
32 if ( ! file.exists(opt$input_loom)){
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
33 stop((paste('File', opt$input_loom, 'does not exist')))
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
34 }
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
35
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
36 # Input from Loom format
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
37
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
38 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
39 print(paste("Normalising...."))
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
40
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
41 #Normalise
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
42 scle <- normalize(scle, exprs_values = 1)
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
43
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
44 print(paste("Finished normalising"))
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
45
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
46 # Output to a Loom file
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
47 if (file.exists(opt$output_loom)) {
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
48 file.remove(opt$output_loom)
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
49 }
a8290d207005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
50 export(scle, opt$output_loom, format='loom')