--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Jun 22 12:25:34 2025 +0000
@@ -0,0 +1,147 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.3.0</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">23.0</token>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">quay.io/bgruening/vpt:1.3.0-1</container>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="creator">
+        <creator>
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+            <person givenName="Amirhossein" familyName="Naghsh Nilchi" email="nilchia@informatik.uni-freiburg.de" />
+            <person givenName="Pavan" familyName="Videm" email="videmp@informatik.uni-freiburg.de" />
+            <person givenName="Björn" familyName="Grüning" email="gruening@informatik.uni-freiburg.de" />
+        </creator>
+    </xml>
+    <token name="@CMD@"><![CDATA[
+        mkdir -p 'input/images' 'output/' &&
+        #for $image in $input_images:
+            ln -s '$image' 'input/images/${image.element_identifier}.${image.ext}' &&
+        #end for
+        ln -s '$input_micron_to_mosaic' 'input/micron_to_mosaic_pixel_transform.csv' &&
+        ]]></token>
+    <token name="@COMMON_ARGS@"><![CDATA[
+        --processes \${GALAXY_SLOTS:-10}
+        --verbose
+        --log-file 'output/log'
+    ]]>
+    </token>
+    <xml name="common_input">
+        <param argument="--input_images" type="data" format="tiff" multiple="true" label="MEROSCOPE tiff images"/>
+        <param argument="--input_micron_to_mosaic" type="data" format="csv" label="Micron to mosaic mapping file"/>
+    </xml>
+    <xml name="normalization_param" token_label="Normalization">
+        <param name="normalization" type="select" label="@LABEL@">
+            <option value="default">default (min-max range normalization)</option>
+            <option value="CLAHE">CLAHE (Contrast Limited Adaptive Histogram Equalization)</option>
+        </param>
+    </xml>
+    <xml name="channel_options_basic">
+            <yield/>
+            <option value="Cellbound1">Cellbound1</option>
+            <option value="Cellbound2">Cellbound2</option>
+            <option value="Cellbound3">Cellbound3</option>
+        </xml>
+    <xml name="channel_options_none">
+        <expand macro="channel_options_basic">
+            <option value="None" selected="true">None</option>
+            <option value="DAPI">DAPI</option>
+            <option value="PolyT">PolyT</option>
+            <yield/>
+        </expand>
+</xml>
+    <xml name="advanced_output">
+        <section name="advanced_output" title="Advanced output options">
+            <param name="log" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Output log?"/>
+        </section>
+    </xml>
+    <xml name="common_output">
+        <data name="vpt_log" format="txt" from_work_dir="output/log" label="${tool.name} on ${on_string}: VPT log">
+            <filter>advanced_output['log']</filter>
+        </data>
+    </xml>
+    <xml name="task_input_data">
+        <conditional name="normalize_conditional">
+            <param name="normalize_select" type="select" label="Perform Normalization?">
+                <option value="Yes" selected="true">Yes</option>
+                <option value="No">No</option>
+            </param>
+            <when value="Yes">
+                <conditional name="normalize_type_conditional" label="Select normalization method">
+                    <expand macro="normalization_param"/>
+                    <when value="default"/>
+                    <when value="CLAHE">
+                        <param name="clip_limit" type="float" min="0" max="1" value="0.01" label="Clip limit" help="higher values give more contrast"/>
+                        <param name="filter_size" type="integer" min="1" value="100" label="Tile grid size"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="No"/>
+        </conditional>
+        <conditional name="blur_conditional">
+            <param name="blur_select" type="select" label="Perform Blur?">
+                <option value="Yes">Yes</option>
+                <option value="No" selected="true">No</option>
+            </param>
+            <when value="Yes">
+                <param name="blur_options" type="select" label="Blur options">
+                    <option value="average">average</option>
+                    <option value="median">median</option>
+                    <option value="gaussian">gaussian</option>
+                </param>
+                <param name="kernel_size" type="integer" min="0" value="5" label="Kernel size in pixel"/>
+            </when>
+            <when value="No"/>
+        </conditional>
+        <conditional name="downsample_conditional">
+            <param name="downsample_select" type="select" label="Perform downsample?">
+                <option value="Yes">Yes</option>
+                <option value="No" selected="true">No</option>
+            </param>
+            <when value="Yes">
+                <param name="scale" type="float" min="0" value="2.0" label="Downsample" help="Reduces the size of the images during segmentation to decrease processing time" />
+            </when>
+            <when value="No"/>
+        </conditional>
+    </xml>
+    <xml name="channel_map_conditional_childs">
+        <when value="None"/>
+        <when value="DAPI">
+            <expand macro="task_input_data"/>
+        </when>
+        <when value="PolyT">
+            <expand macro="task_input_data"/>
+        </when>
+        <when value="Cellbound1">
+            <expand macro="task_input_data"/>
+        </when>
+        <when value="Cellbound2">
+            <expand macro="task_input_data"/>
+        </when>
+        <when value="Cellbound3">
+            <expand macro="task_input_data"/>
+        </when>
+    </xml>
+    <xml name="sanitize_digits">
+        <sanitizer invalid_char="">
+            <valid initial="string.digits">
+                <add value=","/>
+                <add value="."/>
+            </valid>
+       </sanitizer>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@Manual{github,
+                title = {Vizgen Post-processing Tool},
+                author = {Vizgen},
+                organization = {Vizgen},
+                year = {2022},
+                url = {https://github.com/Vizgen/vizgen-postprocessing}}
+            </citation>
+        </citations>
+    </xml>
+</macros>