From 79169e6b7f1f393107b0f4986d23e7deef9aa3de Mon Sep 17 00:00:00 2001
From: MaraBesemer <deine.email@beispiel.com>
Date: Sun, 1 Dec 2024 21:44:43 +0100
Subject: [PATCH] fix inputs

---
 tools/phyloseq/phyloseq_plot_bar.R   | 10 ++--------
 tools/phyloseq/phyloseq_plot_bar.xml | 11 ++---------
 2 files changed, 4 insertions(+), 17 deletions(-)

diff --git a/tools/phyloseq/phyloseq_plot_bar.R b/tools/phyloseq/phyloseq_plot_bar.R
index af86b57fd1a..d0d5830f39a 100755
--- a/tools/phyloseq/phyloseq_plot_bar.R
+++ b/tools/phyloseq/phyloseq_plot_bar.R
@@ -16,8 +16,8 @@ option_list <- list(
         help = "Variable for x-axis (e.g., 'Sample', 'Phylum')"
     ),
     make_option(c("--fill"),
-        action = "store", dest = "fill",
-        help = "Variable for fill color (e.g., 'Genus', 'Order')"
+        action = "store", dest = "fill", default = NULL,
+        help = "Variable for fill color (e.g., 'Genus', 'Order') (optional)"
     ),
     make_option(c("--facet"),
         action = "store", dest = "facet", default = NULL,
@@ -41,9 +41,6 @@ if (is.null(opt$input) || opt$input == "") {
 if (is.null(opt$x) || opt$x == "") {
     stop("Error: X-axis variable is required.")
 }
-if (is.null(opt$fill) || opt$fill == "") {
-    stop("Error: Fill variable is required.")
-}
 if (is.null(opt$output) || opt$output == "") {
     stop("Error: Output file is required.")
 }
@@ -57,9 +54,6 @@ sample_vars <- colnames(sample_data(physeq))
 if (!opt$x %in% sample_vars) {
     stop(paste("Error: X-axis variable", opt$x, "does not exist in the sample data."))
 }
-if (!opt$fill %in% sample_vars) {
-    stop(paste("Error: Fill variable", opt$fill, "does not exist in the sample data."))
-}
 
 # Generate bar plot
 p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
diff --git a/tools/phyloseq/phyloseq_plot_bar.xml b/tools/phyloseq/phyloseq_plot_bar.xml
index e91dc9dfcaf..9ef0713f6fe 100644
--- a/tools/phyloseq/phyloseq_plot_bar.xml
+++ b/tools/phyloseq/phyloseq_plot_bar.xml
@@ -36,14 +36,7 @@ Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
             </assert_contents>
         </output>
     </test>
-    <!-- Test 2: Missing x and fill parameters -->
-    <test>
-        <param name="input" value="output.phyloseq" ftype="phyloseq"/>
-        <param name="x" value="Number"/>
-        <param name="fill" value=""/>
-        <expect_exit_code>1</expect_exit_code>
-    </test>
-    <!-- Test 3: Valid parameters without facet -->
+    <!-- Test 2: Valid parameters without facet -->
     <test>
         <param name="input" value="output.phyloseq" ftype="phyloseq"/>
         <param name="x" value="Property"/>
@@ -67,7 +60,7 @@ Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
 
     - **Input**: A phyloseq object in RDS format.
     - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
-    - **Fill variable**: The variable to use for the bar fill colors (e.g., Genus, Order).
+    - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order).
     - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
 
     **Outputs**