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WaveICA: Added boolean parameter to output feature table and metadata table separately #555

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merged 7 commits into from
Jun 6, 2024
Merged

WaveICA: Added boolean parameter to output feature table and metadata table separately #555

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d0776d7
added option to output feature table and metadata table separately
zargham-ahmad Jun 6, 2024
2ae069b
lint R script
zargham-ahmad Jun 6, 2024
6c834bd
Update tools/waveica/macros.xml
hechth Jun 6, 2024
57da999
Update tools/waveica/macros.xml
hechth Jun 6, 2024
60a95a9
Update tools/waveica/waveica.xml
hechth Jun 6, 2024
531aad6
Update tools/waveica/macros.xml
hechth Jun 6, 2024
6b9f862
fixed test
zargham-ahmad Jun 6, 2024
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12 changes: 11 additions & 1 deletion tools/waveica/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -96,10 +96,20 @@
</when>
</conditional>
</xml>
<xml name="split_output">
<param name = "keep_two_output" label="Keep Two Output in recetox-aplcms format" type="boolean" checked="false"
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truevalue="TRUE" falsevalue="FALSE" help="keep two outputs, one is feature table and second is metadata table" />
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</xml>

<xml name="outputs">
<outputs>
<data name="normalized_data" format="tsv">
<data name="normalized_data" format="tsv" label="Normalized table of ${on_string}">
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<change_format>
<when input_dataset="data" attribute="ext" value="parquet" format="parquet" />
</change_format>
</data>
<data name="metadata" format="tsv" label="Metadata table of ${on_string}">
<filter>keep_two_output</filter>
<change_format>
<when input_dataset="data" attribute="ext" value="parquet" format="parquet" />
</change_format>
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5 changes: 5 additions & 0 deletions tools/waveica/test-data/test10_output1.tsv
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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 355200.506508035 216897.826587868 362337.195084504 143303.377379009 189065.516447239
M86T41 75115889.9077485 75204863.1495248 76490295.1450204 83771659.9549148 84108898.7658797
M86T518 6101488.54615418 6170882.26270475 12588041.969092 6181538.46316058 6103964.42378424
M86T539 2007379.02604984 2069979.64992079 1818589.63912375 1975712.25920485 1935671.32085241
6 changes: 6 additions & 0 deletions tools/waveica/test-data/test10_output2.tsv
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@@ -0,0 +1,6 @@
sampleName class sampleType injectionOrder batch
VT_160120_002 sample sample 1 1
VT_160120_004 sample sample 2 1
VT_160120_006 sample sample 3 1
VT_160120_008 sample sample 4 1
VT_160120_010 sample sample 5 1
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61 changes: 47 additions & 14 deletions tools/waveica/waveica.xml
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@@ -1,4 +1,4 @@
<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy6" profile="21.09">
<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy7" profile="21.09">
<description>removal of batch effects for untargeted metabolomics data</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -51,14 +51,14 @@
)'
#end if

-e 'store_data(normalized_data, "$normalized_data", "$input_num.data.ext")'
-e 'store_data(normalized_data, "$normalized_data", "$metadata", "$input_num.data.ext", $keep_two_output)'
]]></command>

<inputs>
<conditional name="input_num">
<param name="input_choice" type="select" label="Choose input files:">
<option value="1" selected="true">1</option>
<option value="2">2</option>
<option value="1" selected="true">1: intensity-by-feature table with metadata</option>
<option value="2">2: intensity-by-feature table and metadata table separately</option>
</param>
<when value="1">
<expand macro="input_data"/>
Expand Down Expand Up @@ -89,12 +89,13 @@
</when>
</conditional>
<expand macro="exclude_blanks"/>
<expand macro="split_output"/>
</inputs>

<expand macro="outputs"/>

<tests>
<test><!-- TEST 1 -->
<test expect_num_outputs="1"><!-- TEST 1 -->
<param name="data" value="input_data.csv" ftype="csv"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
Expand All @@ -105,7 +106,7 @@
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
</test>
<test><!-- TEST 2 -->
<test expect_num_outputs="1"><!-- TEST 2 -->
<param name="data" value="input_data.tsv" ftype="tsv"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
Expand All @@ -116,7 +117,7 @@
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
</test>
<test><!-- TEST 3 -->
<test expect_num_outputs="1"><!-- TEST 3 -->
<param name="data" value="input_data.parquet" ftype="parquet"/>
<param name="mode" value="batchwise"/>
<param name="wavelet_filter" value="d"/>
Expand All @@ -127,7 +128,7 @@
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.parquet" ftype="parquet"/>
</test>
<test><!-- TEST 4 -->
<test expect_num_outputs="1"><!-- TEST 4 -->
<param name="input_choice" value="2"/>
<param name="data" value="feature_table.csv" ftype="csv"/>
<param name="metadata" value="metadata.csv" ftype="csv"/>
Expand All @@ -140,7 +141,7 @@
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
</test>
<test><!-- TEST 5 -->
<test expect_num_outputs="1"><!-- TEST 5 -->
<param name="input_choice" value="2"/>
<param name="data" value="feature_table.tsv" ftype="tsv"/>
<param name="metadata" value="metadata.tsv" ftype="tsv"/>
Expand All @@ -153,7 +154,7 @@
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
</test>
<test><!-- TEST 6 -->
<test expect_num_outputs="1"><!-- TEST 6 -->
<param name="input_choice" value="2"/>
<param name="data" value="feature_table.parquet" ftype="parquet"/>
<param name="metadata" value="metadata.csv" ftype="csv"/>
Expand All @@ -166,7 +167,7 @@
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
</test>
<test><!-- TEST 7 -->
<test expect_num_outputs="1"><!-- 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"/>
Expand All @@ -180,7 +181,7 @@
<param name="alpha" value="0"/>
<output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
</test>
<test><!-- TEST 8 -->
<test expect_num_outputs="1"><!-- 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"/>
Expand All @@ -205,10 +206,42 @@
<param name="cutoff" value="0"/>
<output name="normalized_data" file="normalized_data_nobatch.tsv"/>
</test> -->
<test expect_failure="true">
<test expect_num_outputs="2"><!-- TEST 9 -->
<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"/>
<param name="keep_two_output" value="TRUE"/>
<output name="normalized_data" file="test9_output1.parquet" ftype="parquet"/>
<output name="metadata" file="test9_output2.parquet" ftype="parquet"/>
</test>
<test expect_num_outputs="2"><!-- TEST 10 -->
<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"/>
<param name="keep_two_output" value="TRUE"/>
<output name="normalized_data" file="test10_output1.tsv" ftype="tsv"/>
<output name="metadata" file="test10_output2.tsv" ftype="tsv"/>
</test>
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<test expect_failure="true"><!-- TEST 11 -->
<param name="data" value="na_data.csv" ftype="csv"/>
</test>
<test expect_failure="true">
<test expect_failure="true"><!-- TEST 12 -->
<param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>
</test>
</tests>
Expand Down
70 changes: 55 additions & 15 deletions tools/waveica/waveica_wrapper.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,7 @@ read_file <- function(file, metadata, ft_ext, mt_ext, transpose) {

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
data <- tranpose_data(data, col_names)
}

if (!is.na(metadata)) {
Expand Down Expand Up @@ -133,7 +130,6 @@ waveica_singlebatch <- function(file,
return(data)
}


sort_by_injection_order <- function(data) {
if ("batch" %in% colnames(data)) {
data <- data[order(data[, "batch"], data[, "injectionOrder"], decreasing = FALSE), ]
Expand All @@ -143,7 +139,6 @@ sort_by_injection_order <- function(data) {
return(data)
}


verify_input_dataframe <- function(data, required_columns) {
if (anyNA(data)) {
stop("Error: dataframe cannot contain NULL values!
Expand Down Expand Up @@ -194,7 +189,6 @@ verify_column_types <- function(data, required_columns) {
return(data)
}


# Match group labels with [blank/sample/qc] and enumerate them
enumerate_groups <- function(group) {
group[grepl("blank", tolower(group))] <- 0
Expand All @@ -204,7 +198,6 @@ enumerate_groups <- function(group) {
return(group)
}


# Create appropriate input for R wavelets function
get_wf <- function(wavelet_filter, wavelet_length) {
wf <- paste(wavelet_filter, wavelet_length, sep = "")
Expand All @@ -217,7 +210,6 @@ get_wf <- function(wavelet_filter, wavelet_length) {
return(wf)
}


# Exclude blanks from a dataframe
exclude_group <- function(data, group) {
row_idx_to_exclude <- which(group %in% 0)
Expand All @@ -230,14 +222,62 @@ exclude_group <- function(data, group) {
}
}

store_data <- function(data, output, ext) {
store_data <- function(data, feature_output, metadata_output, ext, split_output = FALSE) {
if (ext == "parquet") {
arrow::write_parquet(data, output)
if (split_output == TRUE) {
split_df <- split_output(data)
arrow::write_parquet(split_df$metadata, metadata_output)
arrow::write_parquet(split_df$feature_table, feature_output)
} else {
arrow::write_parquet(data, feature_output)
}
} else {
write.table(data,
file = output, sep = "\t",
row.names = FALSE, quote = FALSE
)
if (split_output == TRUE) {
split_df <- split_output(data)
write.table(split_df$metadata,
file = metadata_output, sep = "\t",
row.names = FALSE, quote = FALSE
)
write.table(split_df$feature_table,
file = feature_output, sep = "\t",
row.names = FALSE, quote = FALSE
)
} else {
write.table(data,
file = feature_output, sep = "\t",
row.names = FALSE, quote = FALSE
)
}
}
cat("Normalization has been completed.\n")
}

split_output <- function(df) {
required_columns_set1 <- c("sampleName", "class", "sampleType", "injectionOrder", "batch")
required_columns_set2 <- c("sampleName", "class", "sampleType", "injectionOrder")

if (all(required_columns_set1 %in% colnames(df))) {
metadata_df <- df[, required_columns_set1, drop = FALSE]
df <- df[, -c(2:5)]
} else if (all(required_columns_set2 %in% colnames(df))) {
metadata_df <- df[, required_columns_set2, drop = FALSE]
df <- df[, -c(2:4)]
} else {
stop("Neither set of required columns is present in the dataframe.")
}

# Transpose the feature table
col_names <- c("id", as.vector(df[[1]]))
feature_table <- tranpose_data(df, col_names)

return(list(metadata = metadata_df, feature_table = feature_table))
}

tranpose_data <- function(data, column_names) {
t_data <- data[-1]
t_data <- t(t_data)
tranposed_data <- data.frame(rownames(t_data), t_data)
colnames(tranposed_data) <- column_names

return(tranposed_data)
}
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