Mercurial > repos > recetox > ramclustr
changeset 10:2d94da58904b draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit dc508ea3521991cd42ff6c1aa8aa845b36412771
| author | recetox |
|---|---|
| date | Wed, 22 May 2024 08:04:21 +0000 |
| parents | d70dd1d6ac4d |
| children | da7722f665f4 |
| files | macros.xml ramclustr.xml ramclustr_wrapper.R |
| diffstat | 3 files changed, 21 insertions(+), 6 deletions(-) [+] |
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--- a/macros.xml Wed Apr 17 07:51:23 2024 +0000 +++ b/macros.xml Wed May 22 08:04:21 2024 +0000 @@ -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)."/>
--- a/ramclustr.xml Wed Apr 17 07:51:23 2024 +0000 +++ b/ramclustr.xml Wed May 22 08:04:21 2024 +0000 @@ -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> @@ -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}",
--- a/ramclustr_wrapper.R Wed Apr 17 07:51:23 2024 +0000 +++ b/ramclustr_wrapper.R Wed May 22 08:04:21 2024 +0000 @@ -46,9 +46,22 @@ 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") {