diff phyloseq_plot_bar.xml @ 5:94563110275d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d6888da7aba38b97f6cb827355f2de436565684a

--- a/phyloseq_plot_bar.xml	Sat Jan 25 17:11:49 2025 +0000
+++ b/phyloseq_plot_bar.xml	Tue Feb 04 14:39:08 2025 +0000
@@ -19,6 +19,7 @@
 --width '${width}'
 --height '${height}'
 --device '${device}'
+--nolines '${nolines}'
   ]]></command>
   <inputs>
     <expand macro="phyloseq_input"/>
@@ -37,10 +38,20 @@
       <option value="jpeg">JPEG</option>
       <option value="tiff">TIFF</option>
     </param>
+    <param name="nolines" type="boolean" label="Remove Separation Lines" help="Do not add separation lines between bars in the chart." />
   </inputs>
   <outputs>
-    <data name="output" format="pdf" label="Bar Chart (PDF)" />
+    <data name="output" format="pdf" label="Bar Chart (${device})">
+      <change_format>
+        <when format="pdf" value="pdf"/>
+        <when format="png" value="png"/>
+        <when format="jpeg" value="jpeg"/>
+        <when format="tiff" value="tiff"/>
+      </change_format>
+
+    </data>
   </outputs>
+
   <tests>
     <!-- Test 1: Basic functionality with x and fill variables -->
     <test>
@@ -71,6 +82,36 @@
         </assert_contents>
       </output>
     </test>
+
+    <!-- Test 3: without OTU lines, Others and non assigned -->
+      <test>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="x" value="Sample"/>
+      <param name="fill" value="Genus"/>
+      <param name="facet" value=""/>
+      <param name="topX" value="10"/>
+      <param name="normalize" value="false"/>
+      <param name="keepOthers" value="false"/>
+      <param name="keepNonAssigned" value="false"/>
+      <param name="nolines" value="true"/>
+      <param name="device" value="pdf"/>
+      <output name="output" file="expected_output.pdf" ftype="pdf" compare="sim_size"/>
+    </test>
+
+    <!-- Test 4: with normalization, Others and non assigned -->
+      <test>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="x" value="Sample"/>
+      <param name="fill" value="Genus"/>
+      <param name="facet" value=""/>
+      <param name="topX" value="10"/>
+      <param name="normalize" value="true"/>
+      <param name="keepOthers" value="true"/>
+      <param name="keepNonAssigned" value="true"/>
+      <param name="nolines" value="false"/>
+      <param name="device" value="pdf"/>
+      <output name="output" file="expected_output_normalize.pdf" ftype="pdf" compare="sim_size"/>
+    </test>
   </tests>
 
   <help>