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RAMClustR: fixed sample name reading for tabular inputs #541

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May 27, 2024
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RAMClustR: fixed sample name reading for tabular inputs #541

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2 changes: 1 addition & 1 deletion tools/ramclustr/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@
</xml>

<xml name="parameters_recetox_aplcms">
<section name="ms_dataframe" title="Input MS Data as parquet (output from recetox-aplcms)" expanded="true">
<section name="ms_dataframe" title="Input MS Data as parquet/tabular (output from recetox-aplcms)" expanded="true">
<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,tabular"
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2 changes: 1 addition & 1 deletion tools/ramclustr/ramclustr.xml
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@@ -1,4 +1,4 @@
<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy6" profile="21.09">
<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy7" profile="21.09">
<description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
<macros>
<import>macros.xml</import>
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7 changes: 5 additions & 2 deletions tools/ramclustr/ramclustr_wrapper.R
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Expand Up @@ -53,14 +53,17 @@ read_ramclustr_aplcms <- function(ms1_featuredefinitions = NULL,
ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions)
} else {
ms1_featuredefinitions <- read.csv(ms1_featuredefinitions,
header = TRUE, sep = "\t"
header = TRUE, sep = "\t", check.names = FALSE
)
}

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

if (!is.null(df_phenodata)) {
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