annotate scripts/dropletutils.Rscript @ 8:a9caad671439 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc"
author iuc
date Mon, 05 Jul 2021 13:40:00 +0000
parents 2c1200fba922
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
1 ## Load in data
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
2 args <- commandArgs(trailingOnly = T)
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
3 if (length(args) != 1) {
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
4 stop("Please provide the config file")
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
5 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
6
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
7 suppressWarnings(suppressPackageStartupMessages(require(DropletUtils)))
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
8 suppressWarnings(suppressPackageStartupMessages(require(Matrix)))
1
cfe1e6c28d95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf"
iuc
parents: 0
diff changeset
9 suppressWarnings(suppressPackageStartupMessages(require(scater)))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
10
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
11 source(args[1])
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
12
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
13 ## Helper functions
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
14 set_sparse <- function(obj) {
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
15 return(as(obj, "dgCMatrix"))
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
16 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
17
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
18 write_tsv <- function(fileout, obj) {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
19 write.table(as.matrix(obj), file = fileout,
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
20 col.names = NA, sep = "\t", quote = FALSE)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
21 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
22
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
23 determine_geneids <- function(object) {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
24 if (!is.null(rowData(object)$Symbol)) {
3
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
iuc
parents: 2
diff changeset
25 return(rowData(object)$Symbol)
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
iuc
parents: 2
diff changeset
26 }
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
iuc
parents: 2
diff changeset
27 return(rownames(object))
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
iuc
parents: 2
diff changeset
28 }
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
iuc
parents: 2
diff changeset
29
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
30 get_counts <- function(object) {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
31 return(Matrix(counts(object), sparse = TRUE))
3
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
iuc
parents: 2
diff changeset
32 }
f0de368eabca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit a4cee4cac5097029188d836d5b904b605dbb943d"
iuc
parents: 2
diff changeset
33
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
34 write_out <- function(object, fileout, typeout) {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
35 if (typeout == "tsv") {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
36 write_tsv(fileout, get_counts(object))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
37 }
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
38 else if (typeout == "h5") {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
39 write10xCounts(fileout, get_counts(object),
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
40 type = "HDF5",
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
41 gene.symbol = determine_geneids(object),
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
42 overwrite = TRUE)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
43 }
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
44 else if (typeout == "directory") {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
45 write10xCounts(fileout, get_counts(object),
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
46 type = "sparse",
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
47 gene.symbol = determine_geneids(object),
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
48 overwrite = TRUE)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
49 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
50 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
51
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
52 read_10x_files <- function(filein, typein) {
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
53 sce <- NULL
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
54 if (typein == "tsv") {
1
cfe1e6c28d95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf"
iuc
parents: 0
diff changeset
55 ## Exploding memory problems occured here
cfe1e6c28d95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf"
iuc
parents: 0
diff changeset
56 ## - solution is to use the readSparseCounts function from scater
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
57 sce <- SingleCellExperiment(assays =
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
58 list(counts = readSparseCounts(filein)))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
59 }
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
60 else if (typein == "h5") {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
61 # use barcodes.tsv as column names
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
62 sce <- read10xCounts(filein, col.names = T, type = "HDF5")
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
63 }
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
64 else if (typein == "directory") {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
65 sce <- read10xCounts(filein, col.names = T, type = "sparse")
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
66 }
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
67 counts(sce) <- set_sparse(counts(sce))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
68 return(sce)
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
69 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
70
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
71
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
72 ## Methods
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
73
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
74
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
75 do_empty_drops <- function(files, eparams, intype = "directory",
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
76 outtype = "h5", fdr_threshold = 0.01) {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
77 sce <- read_10x_files(files$infile, intype)
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
78
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
79 eparams$... <- NULL ## hack to remove other parameters from being
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
80 eparams$m <- Matrix(counts(sce), sparse = TRUE)
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
81
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
82 ## Determine sensible lowerbound
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
83 m_stats <- summary(colSums(counts(sce)))
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
84 print("Cell Library Size Distribution:")
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
85 print(m_stats)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
86
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
87 if (m_stats["Min."] > eparams$lower) {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
88 print(paste0("CAUTION: Min. Lib. Size (", m_stats["Min."]
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
89 , ") < requested lowerbound (", eparams$lower, ")"))
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
90 message(paste0("Setting lowerbound to Mean: ", m_stats["Mean"]))
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
91 eparams$lower <- m_stats["Mean"]
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
92 }
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
93
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
94 e_out <- do.call(emptyDrops, c(eparams))
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
95
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
96 bar_names <- colnames(sce)
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
97 if (length(bar_names) != nrow(e_out)) {
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
98 stop("Length of barcodes and output metrics don't match.")
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
99 }
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
100 e_out <- cbind(bar_names, e_out)
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
101 e_out$is_cell <- e_out$FDR <= fdr_threshold
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
102 e_out$is_cellandlimited <- e_out$is_cell & e_out$Limited
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
103
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
104 ## Write to Plot
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
105 e_out$is_cell[is.na(e_out$is_cell)] <- FALSE
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
106 xlim_dat <- e_out[complete.cases(e_out), ]$Total
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
107
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
108 ## Write to table
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
109 write_tsv(files$table, e_out[complete.cases(e_out), ])
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
110
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
111 png(files$plot)
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
112 plot(e_out$Total, -e_out$LogProb, col = ifelse(e_out$is_cell,
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
113 "red", "black"),
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
114 xlab = "Total UMI count", ylab = "-Log Probability",
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
115 xlim = c(min(xlim_dat), max(xlim_dat)))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
116 dev.off()
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
117
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
118 ## Filtered
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
119 called <- NULL
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
120 if (fdr_threshold != 0) {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
121 called <- e_out$is_cellandlimited
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
122 } else {
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
123 called <- e_out$is_cell
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
124 }
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
125 called[is.na(called)] <- FALSE # replace NA's with FALSE
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
126 sce_filtered <- sce[, called]
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
127
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
128 write_out(sce_filtered, files$out, outtype)
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
129
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
130 message(paste("Cells:", sum(na.omit(e_out$is_cell))))
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
131 message(paste("Cells and Limited:", sum(na.omit(e_out$is_cellandlimited))))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
132 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
133
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
134
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
135 do_default_drops <- function(files, dparams,
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
136 intype = "directory", outtype = "h5") {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
137 sce <- read_10x_files(files$infile, intype)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
138
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
139 dparams$m <- counts(sce)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
140 called <- do.call(defaultDrops, c(dparams))
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
141
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
142 # Filtered
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
143 sce_filtered <- sce[, called]
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
144
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
145 write_out(sce_filtered, files$out, outtype)
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
146
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
147 message(paste("Cells:", sum(called)))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
148 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
149
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
150 do_barcode_rankings <- function(files, bparams, intype = "directory") {
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
151 sce <- read_10x_files(files$infile, intype)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
152
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
153 bparams$... <- NULL ## hack
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
154 bparams$m <- counts(sce)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
155
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
156 brout <- do.call(barcodeRanks, c(bparams))
2
a8aa294401be "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents: 1
diff changeset
157
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
158 png(files$plot)
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
159 plot(brout$rank, brout$total, log = "xy",
7
2c1200fba922 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 0a1586a00f94215b8182423e4b2f34fdf706a47d"
iuc
parents: 6
diff changeset
160 xlab = "(log) Rank", ylab = "(log) Total UMI Counts")
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
161 o <- order(brout$rank)
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
162 lines(brout$rank[o], brout$fitted[o], col = "red")
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
163
8
a9caad671439 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc"
iuc
parents: 7
diff changeset
164 abline(h = metadata(brout)$knee, col = "dodgerblue", lty = 2)
a9caad671439 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc"
iuc
parents: 7
diff changeset
165 abline(h = metadata(brout)$inflection, col = "forestgreen", lty = 2)
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
166 legend("bottomleft", lty = 2, col = c("dodgerblue", "forestgreen"),
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
167 legend = c("knee", "inflection"))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
168 dev.off()
8
a9caad671439 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 9d465ee72398a8a74fe499a2e4b74f507a5845cc"
iuc
parents: 7
diff changeset
169 print(paste("knee =", metadata(brout)$knee, ", inflection = ", metadata(brout)$inflection))
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
170 }
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
171
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
172 ## Main
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
173 set.seed(seed.val)
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
174
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
175 if (do.method == "barcodeRankings") {
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
176 do_barcode_rankings(files, bparams, intype)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
177
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
178 } else if (do.method == "defaultDrops") {
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
179 do_default_drops(files, dparams, intype, outtype)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
180
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
181 } else if (do.method == "emptyDrops") {
6
8855361fcfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
iuc
parents: 5
diff changeset
182 do_empty_drops(files, eparams, intype, outtype, empty_fdr_threshold)
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff changeset
183 }