--- a/phyloseq_plot_bar.xml	Tue Jan 07 17:58:06 2025 +0000
+++ b/phyloseq_plot_bar.xml	Fri Jan 10 14:58:52 2025 +0000
@@ -12,44 +12,66 @@
 --fill '$fill'
 --facet '${facet}'
 --output '$output'
+--topX '${topX}'
+--keepOthers '${keepOthers}'
+--keepNonAssigned '${keepNonAssigned}'
+--normalize '${normalize}'
+--width '${width}'
+--height '${height}'
+--device '${device}'
   ]]></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)" />
+    <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum). If not specified, the Samples are taken." />
+    <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="Variable to facet the chart by (e.g., SampleType)." />
+    <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." />
+    <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
+    <param name="keepNonAssigned" type="boolean" label="Keep Non Assigned" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." />
+    <param name="normalize" type="boolean" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
+    <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
+    <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
+    <param name="device" type="select" value="pdf" label="Output Device" help="Device to use for the output file. Options include pdf, png, and others.">
+      <option value="pdf">PDF</option>
+      <option value="png">PNG</option>
+      <option value="jpeg">JPEG</option>
+      <option value="tiff">TIFF</option>
+    </param>
   </inputs>
   <outputs>
     <data name="output" format="pdf" label="Bar Chart (PDF)" />
   </outputs>
-   <tests>
-    <!-- Test 1: Default parameters -->
+  <tests>
+    <!-- Test 1: Basic functionality with x and fill variables -->
     <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>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="x" value="Property"/>
+      <param name="fill" value="Phylum"/>
+      <param name="device" value="pdf"/>
+      <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 2: TopX filtering and normalization -->
     <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>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="x" value="Property"/>
+      <param name="fill" value="Genus"/>
+      <param name="facet" value="SampleType"/>
+      <param name="topX" value="10"/>
+      <param name="normalize" value="true"/>
+      <output name="output" ftype="pdf">
+        <assert_contents>
+          <has_text text="%PDF"/>
+          <has_text text="%%EOF"/>
+        </assert_contents>
+      </output>
     </test>
-</tests>
+  </tests>
 
   <help>
     **Description**
@@ -62,10 +84,12 @@
     - **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).
+    - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
+    - **Device**: Output format (e.g., pdf, png, jpeg, tiff).
 
     **Outputs**
 
-    - A PDF file containing the bar chart.
+    - A file containing the bar chart in the specified format.
 
     **Usage Notes**
 
@@ -73,4 +97,3 @@
   </help>
   <expand macro="citations"/>
 </tool>
-