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Updated RAMClustR to allow tsv for rectetox-aplcms inputs #539

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merged 3 commits into from
May 22, 2024
Merged

Updated RAMClustR to allow tsv for rectetox-aplcms inputs #539

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1451499
updated ramclustr to allow tsv for rectetox-aplcms inputs
zargham-ahmad May 21, 2024
2533ebe
Update tools/ramclustr/macros.xml
hechth May 21, 2024
25f2e23
Update tools/ramclustr/macros.xml
hechth May 21, 2024
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4 changes: 2 additions & 2 deletions tools/ramclustr/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -67,9 +67,9 @@

<xml name="parameters_recetox_aplcms">
<section name="ms_dataframe" title="Input MS Data as parquet (output from recetox-aplcms)" expanded="true">
<param label="Input MS1 featureDefinitions" name="ms1_featureDefinitions" type="data" format="parquet"
<param label="Input MS1 featureDefinitions" name="ms1_featureDefinitions" type="data" format="parquet,tabular"
help="Metadata with columns: mz, rt, feature names containing MS data."/>
<param label="Input MS1 featureValues" name="ms1_featureValues" type="data" format="parquet"
<param label="Input MS1 featureValues" name="ms1_featureValues" type="data" format="parquet,tabular"
help="data with rownames = sample names, colnames = feature names containing MS data."/>
<param label="phenoData" name="df_phenoData" type="data" format="tsv,csv" optional="true"
help="CSV/TSV file containing phenoData (optional)."/>
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4 changes: 3 additions & 1 deletion tools/ramclustr/ramclustr.xml
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@@ -1,4 +1,4 @@
<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy5" profile="21.09">
<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy6" profile="21.09">
<description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -56,6 +56,8 @@
ramclustObj = read_ramclustr_aplcms(
ms1_featuredefinitions = "$filetype.ms_dataframe.ms1_featureDefinitions",
ms1_featurevalues = "$filetype.ms_dataframe.ms1_featureValues",
ms1_featuredefinitions_ext = "$filetype.ms_dataframe.ms1_featureDefinitions.ext",
ms1_featurevalues_ext = "$filetype.ms_dataframe.ms1_featureValues.ext",
#if $filetype.ms_dataframe.df_phenoData:
df_phenodata = "$filetype.ms_dataframe.df_phenoData",
phenodata_ext = "${filetype.ms_dataframe.df_phenoData.ext}",
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19 changes: 16 additions & 3 deletions tools/ramclustr/ramclustr_wrapper.R
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Expand Up @@ -46,9 +46,22 @@ read_ramclustr_aplcms <- function(ms1_featuredefinitions = NULL,
phenodata_ext = NULL,
exp_des = NULL,
st = NULL,
ensure_no_na = TRUE) {
ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions)
ms1_featurevalues <- arrow::read_parquet(ms1_featurevalues)
ensure_no_na = TRUE,
ms1_featuredefinitions_ext = "parquet",
ms1_featurevalues_ext = "parquet") {
if (ms1_featuredefinitions_ext == "parquet") {
ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions)
} else {
ms1_featuredefinitions <- read.csv(ms1_featuredefinitions,
header = TRUE, sep = "\t"
)
}

if (ms1_featurevalues_ext == "parquet") {
ms1_featurevalues <- arrow::read_parquet(ms1_featurevalues)
} else {
ms1_featurevalues <- read.csv(ms1_featurevalues, header = TRUE, sep = "\t")
}

if (!is.null(df_phenodata)) {
if (phenodata_ext == "csv") {
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