add: implement tool to add rank names to phyloseq object

tools/phyloseq/add_rank_names_to_phyloseq.R

@@ -0,0 +1,67 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("phyloseq"))
+suppressPackageStartupMessages(library("tidyverse"))
+
+# Option parsing
+option_list <- list(
+    make_option(c("--input"),
+        action = "store", dest = "input",
+        help = "Input file containing a phyloseq object"
+    ),
+    make_option(c("--output"), action = "store", dest = "output", help = "Output file for the updated phyloseq object")
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args <- parse_args(parser, positional_arguments = TRUE)
+opt <- args$options
+
+cat("Input file: ", opt$input, "\n")
+cat("Output file: ", opt$output, "\n")
+
+# Lade das Phyloseq-Objekt
+physeq <- readRDS(opt$input)
+
+# Überprüfen, ob das Phyloseq-Objekt erfolgreich geladen wurde
+if (is.null(physeq)) {
+    stop("Error: Failed to load the Phyloseq object. Check the input file.")
+}
+
+cat("Phyloseq object successfully loaded.\n")
+cat("Class of loaded object: ", class(physeq), "\n")
+
+# Überprüfe das aktuelle Taxonomy Table
+cat("Current tax_table:\n")
+print(tax_table(physeq))
+
+# Zuordnung der Rangnamen
+rank_names <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") # Anpassen je nach Bedarf
+
+# Füge eine leere Spalte für Species hinzu, falls sie fehlt
+if (ncol(tax_table(physeq)) == 6) {
+    tax_table(physeq) <- cbind(tax_table(physeq), Species = NA)
+}
+
+# Überprüfen, ob die Anzahl der Spalten mit der Anzahl der Rangnamen übereinstimmt
+if (ncol(tax_table(physeq)) != length(rank_names)) {
+    stop("Error: Number of columns in tax_table does not match the length of rank_names.")
+}
+
+# Setzen der Spaltennamen
+colnames(tax_table(physeq)) <- rank_names
+
+# Bestätige die Änderungen
+cat("Updated tax_table:\n")
+print(tax_table(physeq))
+
+# Extrahiere das erste Zeichen aus dem ersten Eintrag des tax_table (z.B. Kingdom)
+first_char <- substr(tax_table(physeq)[1, 1], 1, 1)
+cat("Extracted first character: ", first_char, "\n")
+
+# Speichere das aktualisierte Phyloseq-Objekt
+saveRDS(physeq, file = opt$output, compress = TRUE)
+cat("Updated Phyloseq object saved to: ", opt$output, "\n")
+
+# Gib das erste Zeichen zurück (es wird später in der XML-Datei verwendet)
+cat(first_char, "\n")

tools/phyloseq/add_rank_names_to_phyloseq.xml

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+<tool id="add_rank_names_to_phyloseq" name="Add Rank Names to Phyloseq Object" version="1.0">
+    <description>Add taxonomy rank names to a phyloseq object</description> 
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '${__tool_directory__}/add_rank_names_to_phyloseq.R' --input '$input' --output '$output'
+]]></command>
+
+    <inputs>
+        <expand macro="phyloseq_input"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="phyloseq"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+            <output name="output" ftype="phyloseq">
+                <!-- Check if the output contains the first character -->
+                <assert_contents>
+                    <has_text text="B"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help>
+    This tool adds taxonomy rank names to a phyloseq object in the `tax_table` slot.
+    </help>
+    <expand macro="citations"/>
+</tool>