--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_plot_bar.xml	Tue Dec 03 17:45:48 2024 +0000
@@ -0,0 +1,76 @@
+<tool id="phyloseq_plot_bar" name="Phyloseq: Bar Chart" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+  <description>Generate bar charts from a phyloseq object</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
+--input '$input'
+--x '$x'
+--fill '$fill'
+--facet '${facet}'
+--output '$output'
+  ]]></command>
+  <inputs>
+    <expand macro="phyloseq_input"/>
+    <param name="x" type="text" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum)" />
+    <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)" />
+    <param name="facet" type="text" optional="true" label="Facet by variable" help="Optional: Variable to facet the chart by (e.g., SampleType)" />
+  </inputs>
+  <outputs>
+    <data name="output" format="pdf" label="Bar Chart (PDF)" />
+  </outputs>
+   <tests>
+    <!-- Test 1: Default parameters -->
+    <test>
+        <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+        <param name="x" value="Property"/>
+        <param name="fill" value="Number"/>
+        <param name="facet" value="Property"/>
+        <output name="output" ftype="pdf">
+            <assert_contents>
+                <has_text text="%PDF"/>
+                <has_text text="%%EOF"/>
+            </assert_contents>
+        </output>
+    </test>
+    <!-- Test 2: Valid parameters without facet -->
+    <test>
+        <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+        <param name="x" value="Property"/>
+        <param name="fill" value="Number"/>
+        <param name="facet" value=""/>
+        <output name="output" ftype="pdf">
+            <assert_contents>
+                <has_text text="%PDF"/>
+                <has_text text="%%EOF"/>
+            </assert_contents>
+        </output>
+    </test>
+</tests>
+
+  <help>
+    **Description**
+
+    This tool generates bar charts from a phyloseq object using the `plot_bar` function.
+
+    **Inputs**
+
+    - **Input**: A phyloseq object in RDS format.
+    - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
+    - **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**
+
+    - A PDF file containing the bar chart.
+
+    **Usage Notes**
+
+    Ensure that the input file is a valid phyloseq object in RDS format.
+  </help>
+  <expand macro="citations"/>
+</tool>
+