fix review comments

Author: Anup Kumar

tools/bioimaging/bioimage_inference.xml

@@ -2,7 +2,7 @@
     <description>with PyTorch</description>
     <macros>
         <token name="@TOOL_VERSION@">2.4.1</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
     </macros>
     <creator>
         <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
@@ -38,9 +38,8 @@
         <param name="input_image_file" type="data" format="tiff,png" label="Input image" help="Please provide an input image for the analysis."/>
         <param name="input_image_input_size" type="text" optional="false" label="Size of the input image" help="Provide the size of the input image. See the chosen model's RDF file to find the correct input size. For example: for the BioImage.IO model MitochondriaEMSegmentationBoundaryModel, the input size is 256 x 256 x 32 x 1. Enter the size as 256,256,32,1."/>
         <param name="input_image_input_axes" type="select" label="Axes of the input image" optional="false" help="Provide the input axes of the input image. See the chosen model's RDF file to find the correct axes. For example: for the BioImage.IO model MitochondriaEMSegmentationBoundaryModel, the input axes is 'bczyx'">
-            <option value="bczyx">bczyx</option>
-            <option value="bcyx">bcyx</option>
-            <option value="byxc">byxc</option>
+            <option value="bcyx">Four axes (e.g., bcyx, byxc)</option>
+            <option value="bczyx">Five axes (e.g., bczyx)</option>
         </param>
     </inputs>
     <outputs>
@@ -53,7 +52,7 @@
             <param name="input_image_file" value="input_image_file.tif" location="https://zenodo.org/api/records/6647674/files/sample_input_0.tif/content"/>
             <param name="input_image_input_size" value="256,256,1,1"/>
             <param name="input_image_input_axes" value="bcyx"/>
-            <output name="output_predicted_image" ftype="tiff">
+            <output name="output_predicted_image" ftype="tiff" file="output_nucleisegboundarymodel.tiff" compare="image_diff">
                 <assert_contents>
                     <has_size size="524846" delta="110" />
                 </assert_contents>
@@ -69,7 +68,7 @@
             <param name="input_image_file" value="input_nucleisegboundarymodel.png"/>
             <param name="input_image_input_size" value="256,256,1,1"/>
             <param name="input_image_input_axes" value="bcyx"/>
-            <output name="output_predicted_image" ftype="tiff">
+            <output name="output_predicted_image" ftype="tiff" file="output_nucleisegboundarymodel.tiff" compare="image_diff">
                 <assert_contents>
                     <has_size size="524846" delta="110" />
                 </assert_contents>