--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/image_math.xml	Fri Mar 06 17:31:48 2026 +0000
@@ -0,0 +1,215 @@
+<tool id="image_math" name="Process images using arithmetic expressions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
+    <description>with NumPy</description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">2.3.5</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv"/>
+        <expand macro="creators/kostrykin"/>
+    </creator>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">numpy</requirement>
+        <requirement type="package" version="0.7.3">giatools</requirement>
+    </requirements>
+    <required_files>
+        <include type="glob" path="*.py"/>
+    </required_files>
+    <command><![CDATA[
+    
+    ## Inputs
+    
+    python '$__tool_directory__/image_math.py'
+    --expression='$expression'
+    #if '$dtype' != '':
+        --dtype='$dtype'
+    #end if
+    #for $item in $inputs:
+        --input='$item.name:$item.image'
+    #end for
+    
+    ## Outputs
+    
+    --output='./result.tiff'
+    
+    ]]>
+    </command>
+    <inputs>
+        <param argument="--expression" type="text" label="Expression" optional="false">
+            <validator type="regex">^[a-zA-Z0-9-_\*\+ \(\)/\.]+$</validator>
+        </param>
+        <param name="dtype" type="select" label="Data type of the produced TIFF image">
+            <option value="" selected="true">Determine automatically</option>
+            <option value="float16">16-bit floating point</option>
+            <option value="float32">32-bit floating point</option>
+            <option value="float64">64-bit floating point</option>
+            <option value="int8">8-bit signed integer</option>
+            <option value="int16">16-bit signed integer</option>
+            <option value="int32">32-bit signed integer</option>
+            <option value="uint8">8-bit unsigned integer</option>
+            <option value="uint16">16-bit unsigned integer</option>
+            <option value="uint32">32-bit unsigned integer</option>
+        </param>
+        <repeat name="inputs" title="Input images" min="1">
+            <param name="image" type="data" format="png,tiff" label="Image" />
+            <param name="name" type="text" label="Variable for representation of the image within the expression" optional="false">
+                <validator type="regex">^[a-zA-Z_][a-zA-Z0-9_]*$</validator>
+            </param>
+        </repeat>
+    </inputs>
+    <outputs>
+       <data format="tiff" name="result" from_work_dir="result.tiff" />
+    </outputs>
+    <tests>
+        <!-- Multiplication with a scalar -->
+        <test>
+            <!--
+                GIA204: :relax_indent:
+                python '$__tool_directory__/image_math.py'
+                    ––expression='input1 * 2'
+                    ––dtype=''
+                    ––input='input1:input1.tiff'
+                    ––output='./result.tiff'
+            -->
+            <param name="expression" value="input1 * 2" />
+            <repeat name="inputs">
+                <param name="image" value="input1.tiff" />
+                <param name="name" value="input1" />
+            </repeat>
+            <expand macro="tests/intensity_image_diff" name="result" value="input1_times_2.tiff" ftype="tiff"/>
+        </test>
+        <!-- Unary negation operator -->
+        <test>
+            <!--
+                GIA204: :relax_indent:
+                python '$__tool_directory__/image_math.py'
+                    ––expression='-input1'
+                    ––dtype=''
+                    ––input='input1:input1.tiff'
+                    ––output='./result.tiff'
+            -->
+            <param name="expression" value="-input1" />
+            <repeat name="inputs">
+                <param name="image" value="input1.tiff" />
+                <param name="name" value="input1" />
+            </repeat>
+            <expand macro="tests/intensity_image_diff" name="result" value="minus_input1.tiff" ftype="tiff"/>
+        </test>
+        <!-- Binary addition, neutral element, addition with scalar -->
+        <test>
+            <!--
+                GIA204: :relax_indent:
+                python '$__tool_directory__/image_math.py'
+                    ––expression='input1 + input2 + 1'
+                    ––dtype=''
+                    ––input='input1:input1.tiff'
+                    ––input='input2:minus_input1.tiff'
+                    ––output='./result.tiff'
+            -->
+            <param name="expression" value="input1 + input2 + 1" />
+            <repeat name="inputs">
+                <param name="image" value="input1.tiff" />
+                <param name="name" value="input1" />
+            </repeat>
+            <repeat name="inputs">
+                <param name="image" value="minus_input1.tiff" />
+                <param name="name" value="input2" />
+            </repeat>
+            <expand macro="tests/intensity_image_diff" name="result" value="ones.tiff" ftype="tiff"/>
+        </test>
+        <!-- Parentheses -->
+        <test>
+            <!--
+                GIA204: :relax_indent:
+                python '$__tool_directory__/image_math.py'
+                    ––expression='(input1 + input2) / 2'
+                    ––dtype=''
+                    ––input='input1:input1.tiff'
+                    ––input='input2:ones.tiff'
+                    ––output='./result.tiff'
+            -->
+            <param name="expression" value="(input1 + input2) / 2" />
+            <repeat name="inputs">
+                <param name="image" value="input1.tiff" />
+                <param name="name" value="input1" />
+            </repeat>
+            <repeat name="inputs">
+                <param name="image" value="ones.tiff" />
+                <param name="name" value="input2" />
+            </repeat>
+            <expand macro="tests/intensity_image_diff" name="result" value="half_of_input1_plus_one.tiff" ftype="tiff"/>
+        </test>
+        <!-- Abs -->
+        <test>
+            <!--
+                GIA204: :relax_indent:
+                python '$__tool_directory__/image_math.py'
+                    ––expression='abs(input)'
+                    ––dtype=''
+                    ––input='input:input1.tiff'
+                    ––output='./result.tiff'
+            -->
+            <param name="expression" value="abs(input)" />
+            <repeat name="inputs">
+                <param name="image" value="input1.tiff" />
+                <param name="name" value="input" />
+            </repeat>
+            <expand macro="tests/intensity_image_diff" name="result" value="input1_abs.tiff" ftype="tiff"/>
+        </test>
+        <!-- Decimal, conversion to explicit `dtype` -->
+        <test>
+            <!--
+                GIA204: :relax_indent:
+                python '$__tool_directory__/image_math.py'
+                    ––expression='input1 / 0.5'
+                    ––dtype='uint8'
+                    ––input='input1:input1.tiff'
+                    ––output='./result.tiff'
+            -->
+            <param name="expression" value="input1 / 0.5" />
+            <param name="dtype" value="uint8" />
+            <repeat name="inputs">
+                <param name="image" value="input1.tiff" />
+                <param name="name" value="input1" />
+            </repeat>
+            <expand macro="tests/intensity_image_diff" name="result" value="input1_times_2_uint8.tiff" ftype="tiff"/>
+        </test>
+    </tests>
+    <help>
+
+        **Processes images according to pixel-wise arithmetic expressions.**
+
+        The supported pixel-wise expressions are:
+
+        - Addition, subtraction, multiplication, and division (``+``, ``-``, ``*``, ``/``)
+        - Integer division (e.g., ``input // 2``)
+        - Power (e.g., ``input ** 2``)
+        - Negation (e.g., ``-input``)
+        - Absolute values (e.g., ``abs(input)``)
+        - Square root (e.g., ``sqrt(input)``)
+        - Combinations of the above (also using parentheses)
+
+        Examples:
+
+        - **Negate an image.**
+          Expression: ``-image``
+          where ``image`` is an arbitrary input image.
+
+        - **Mean of two images.**
+          Expression: ``(image1 + image2) / 2``
+          where ``image1`` and `image2` are two arbitrary input images.
+
+        - **Perform division avoiding division-by-zero.**
+          Expression: ``image1 / (abs(image2) + 1e-8)``
+          where ``image1`` and `image2` are two arbitrary input images.
+
+    </help>
+    <citations>
+        <citation type="doi">10.1038/s41586-020-2649-2</citation>
+    </citations>
+</tool>