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Updated waveica for new outputs from recetox-aplcms #378

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merged 8 commits into from
Jun 23, 2023
Merged

Updated waveica for new outputs from recetox-aplcms #378

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7a26724
added tranpose functionality, fixed linting
zargham-ahmad Jun 22, 2023
4c79898
added transpose option, added test
zargham-ahmad Jun 22, 2023
2ada2fd
bump galaxy version
zargham-ahmad Jun 22, 2023
a54098b
added bio.tools ref
zargham-ahmad Jun 22, 2023
786545a
Update tools/waveica/waveica.xml
zargham-ahmad Jun 22, 2023
288aaae
updated help text
zargham-ahmad Jun 22, 2023
0a908bc
Merge branch 'issue365' of https://github.com/zargham-ahmad/galaxytoo…
zargham-ahmad Jun 22, 2023
8cd2c06
updated transpose_feature_table help
zargham-ahmad Jun 22, 2023
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6 changes: 6 additions & 0 deletions tools/waveica/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,12 @@
</creator>
</xml>

<xml name="annotation">
<xrefs>
<xref type="bio.tools">waveica</xref>
</xrefs>
</xml>

<xml name="input_data">
<param type="data" name="data" label="Feature table" format="csv,tsv,parquet" help=""/>
</xml>
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5 changes: 5 additions & 0 deletions tools/waveica/test-data/feature_table_transpose_version.csv
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@@ -0,0 +1,5 @@
id,VT_160120_002,VT_160120_004,VT_160120_006,VT_160120_008,VT_160120_010
M85T34,228520.06430737,90217.384387202,235656.75288383896,16622.9351783435,62385.0742465736
M86T41,35646729.21543971,35735702.457215995,37021134.452711605,44302499.262606,44639738.0735709
M86T518,2386896.97966461,2456290.69621518,8873450.40260241,2466946.89667101,2389372.85729467
M86T539,1026645.83653468,1089246.46040563,837856.449608585,994979.069689685,954938.131337246
Binary file added tools/waveica/test-data/feature_table_transpose_version.parquet
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51 changes: 42 additions & 9 deletions tools/waveica/waveica.xml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy2" python_template_version="3.5">
<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy3" python_template_version="3.5">
<description>removal of batch effects for untargeted metabolomics data</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="annotation"/>
<expand macro="creator"/>

<requirements>
Expand All @@ -19,6 +20,7 @@
#if $input_num.input_choice == "2":
metadata = "$input_num.input_metadata.metadata",
ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
transpose = $input_num.transpose_feature_table,
#else:
ext = "$input_num.data.ext",
#end if
Expand All @@ -36,6 +38,7 @@
#if $input_num.input_choice == "2":
metadata = "$input_num.input_metadata.metadata",
ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext",
transpose = $input_num.transpose_feature_table,
#else:
ext = "$input_num.data.ext",
#end if
Expand All @@ -61,10 +64,12 @@
<expand macro="input_data"/>
</when>
<when value="2">
<expand macro="input_data"/>
<section name="input_metadata" title="Input metadata table" expanded="true">
<param name="metadata" label="Input metadata" type="data" format="csv,tsv,parquet" help="" />
</section>
<expand macro="input_data"/>
</section>
<param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false"
truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." />
</when>
</conditional>
<expand macro="general_parameters"/>
Expand Down Expand Up @@ -93,7 +98,7 @@
<param name="data" value="input_data.csv" ftype="csv"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
<param name="filter_length" value="2"/>
<param name="wavelet_length" value="2"/>
<param name="k" value="20"/>
<param name="t" value="0.05"/>
<param name="t2" value="0.05"/>
Expand All @@ -104,7 +109,7 @@
<param name="data" value="input_data.tsv" ftype="tsv"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
<param name="filter_length" value="2"/>
<param name="wavelet_length" value="2"/>
<param name="k" value="20"/>
<param name="t" value="0.05"/>
<param name="t2" value="0.05"/>
Expand All @@ -115,7 +120,7 @@
<param name="data" value="input_data.parquet" ftype="parquet"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
<param name="filter_length" value="2"/>
<param name="wavelet_length" value="2"/>
<param name="k" value="20"/>
<param name="t" value="0.05"/>
<param name="t2" value="0.05"/>
Expand All @@ -128,7 +133,7 @@
<param name="metadata" value="metadata.csv" ftype="csv"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
<param name="filter_length" value="2"/>
<param name="wavelet_length" value="2"/>
<param name="k" value="20"/>
<param name="t" value="0.05"/>
<param name="t2" value="0.05"/>
Expand All @@ -141,7 +146,7 @@
<param name="metadata" value="metadata.tsv" ftype="tsv"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
<param name="filter_length" value="2"/>
<param name="wavelet_length" value="2"/>
<param name="k" value="20"/>
<param name="t" value="0.05"/>
<param name="t2" value="0.05"/>
Expand All @@ -154,13 +159,41 @@
<param name="metadata" value="metadata.csv" ftype="csv"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
<param name="filter_length" value="2"/>
<param name="wavelet_length" value="2"/>
<param name="k" value="20"/>
<param name="t" value="0.05"/>
<param name="t2" value="0.05"/>
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/>
</test>
<test><!-- TEST 7 -->
<param name="input_choice" value="2"/>
<param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/>
<param name="metadata" value="metadata.parquet" ftype="parquet"/>
<param name="transpose_feature_table" value="TRUE"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
<param name="wavelet_length" value="2"/>
<param name="k" value="20"/>
<param name="t" value="0.05"/>
<param name="t2" value="0.05"/>
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/>
</test>
<test><!-- TEST 8 -->
<param name="input_choice" value="2"/>
<param name="data" value="feature_table_transpose_version.csv" ftype="csv"/>
<param name="metadata" value="metadata.csv" ftype="csv"/>
<param name="transpose_feature_table" value="TRUE"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
<param name="wavelet_length" value="2"/>
<param name="k" value="20"/>
<param name="t" value="0.05"/>
<param name="t2" value="0.05"/>
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.csv"/>
</test>
<!-- The following test has different results on three platform I've tried -->
<!-- <test>
<param name="data" value="input_data_nobatch.csv" ftype="csv"/>
Expand Down
82 changes: 69 additions & 13 deletions tools/waveica/waveica_wrapper.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,14 @@
read_file <- function(file, metadata, ft_ext, mt_ext) {
read_file <- function(file, metadata, ft_ext, mt_ext, transpose) {
data <- read_data(file, ft_ext)

if (transpose) {
col_names <- c("sampleName", data[[1]])
t_data <- data[-1]
t_data <- t(t_data)
data <- data.frame(rownames(t_data), t_data)
colnames(data) <- col_names
}

if (!is.na(metadata)) {
mt_data <- read_data(metadata, mt_ext)
data <- merge(mt_data, data, by = "sampleName")
Expand All @@ -24,24 +32,27 @@ read_data <- function(file, ext) {
waveica <- function(file,
metadata = NA,
ext,
transpose = FALSE,
wavelet_filter,
wavelet_length,
k,
t,
t2,
alpha,
exclude_blanks) {

# get input from the Galaxy, preprocess data
ext <- strsplit(x = ext, split = "\\,")[[1]]

ft_ext <- ext[1]
mt_ext <- ext[2]

data <- read_file(file, metadata, ft_ext, mt_ext)
data <- read_file(file, metadata, ft_ext, mt_ext, transpose)

required_columns <- c("sampleName", "class", "sampleType", "injectionOrder", "batch")
verify_input_dataframe(data, required_columns)
required_columns <- c(
"sampleName", "class", "sampleType",
"injectionOrder", "batch"
)
data <- verify_input_dataframe(data, required_columns)

data <- sort_by_injection_order(data)

Expand Down Expand Up @@ -76,28 +87,30 @@ waveica <- function(file,
waveica_singlebatch <- function(file,
metadata = NA,
ext,
transpose = FALSE,
wavelet_filter,
wavelet_length,
k,
alpha,
cutoff,
exclude_blanks) {

# get input from the Galaxy, preprocess data
ext <- strsplit(x = ext, split = "\\,")[[1]]

ft_ext <- ext[1]
mt_ext <- ext[2]

data <- read_file(file, metadata, ft_ext, mt_ext)
data <- read_file(file, metadata, ft_ext, mt_ext, transpose)

required_columns <- c("sampleName", "class", "sampleType", "injectionOrder")
optional_columns <- c("batch")
verify_input_dataframe(data, required_columns)

data <- verify_input_dataframe(data, required_columns)

data <- sort_by_injection_order(data)

feature_columns <- colnames(data)[!colnames(data) %in% c(required_columns, optional_columns)]
feature_columns <- colnames(data)[!colnames(data) %in%
c(required_columns, optional_columns)]
features <- data[, feature_columns]
injection_order <- data$injectionOrder

Expand All @@ -112,7 +125,7 @@ waveica_singlebatch <- function(file,
)

data[, feature_columns] <- features

group <- enumerate_groups(as.character(data$sampleType))
# remove blanks from dataset
if (exclude_blanks) {
data <- exclude_group(data, group)
Expand Down Expand Up @@ -142,9 +155,49 @@ verify_input_dataframe <- function(data, required_columns) {
stop("Error: dataframe cannot contain NULL values!
Make sure that your dataframe does not contain empty cells")
} else if (!all(required_columns %in% colnames(data))) {
stop("Error: missing metadata!
Make sure that the following columns are present in your dataframe: ", paste(required_columns, collapse = ", "))
stop(
"Error: missing metadata!
Make sure that the following columns are present in your dataframe: ",
paste(required_columns, collapse = ", ")
)
}

data <- verify_column_types(data, required_columns)

return(data)
}

verify_column_types <- function(data, required_columns) {
# Specify the column names and their expected types
column_types <- list(
"sampleName" = c("character", "factor"),
"class" = c("character", "factor"),
"sampleType" = c("character", "factor"),
"injectionOrder" = "integer",
"batch" = "integer"
)

column_types <- column_types[required_columns]

for (col_name in names(data)) {
actual_type <- class(data[[col_name]])
if (col_name %in% names(column_types)) {
expected_types <- column_types[[col_name]]

if (!actual_type %in% expected_types) {
stop(
"Column ", col_name, " is of type ", actual_type,
" but expected type is ",
paste(expected_types, collapse = " or "), "\n"
)
}
} else {
if (actual_type != "numeric") {
data[[col_name]] <- as.numeric(as.character(data[[col_name]]))
}
}
}
return(data)
}


Expand Down Expand Up @@ -187,7 +240,10 @@ store_data <- function(data, output, ext) {
if (ext == "csv") {
write.csv(data, file = output, row.names = FALSE, quote = FALSE)
} else if (ext == "tsv") {
write.table(data, file = output, sep = "\t", row.names = FALSE, quote = FALSE)
write.table(data,
file = output, sep = "\t",
row.names = FALSE, quote = FALSE
)
} else {
arrow::write_parquet(data, sink = output)
}
Expand Down
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