--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vpt_extract.xml	Sun Jun 22 12:25:39 2025 +0000
@@ -0,0 +1,85 @@
+<tool id="vpt_extract" name="Vizgen VPT - Extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>image patches</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="creator" />
+    <command detect_errors="exit_code"><![CDATA[
+        @CMD@
+        vpt
+            @COMMON_ARGS@
+            extract-image-patch
+            --input-images 'input/images/'
+            --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
+            --output-patch 'output/patch1.png'
+            --center-x $center_x
+            --center-y $center_y
+            --size-x $size_x
+            --size-y $size_y
+            --input-z-index $input_z_index
+            #if $red_stain_name != "None":
+                --red-stain-name $red_stain_name
+            #end if
+            #if $green_stain_name != "None":
+                --green-stain-name $green_stain_name
+            #end if
+            #if $blue_stain_name != "None":
+                --blue-stain-name $blue_stain_name
+            #end if
+            --normalization $normalization
+    ]]></command>
+    <inputs>
+        <expand macro="common_input"/>
+        <param argument="--center-x" type="integer" value="0" label="X coordinate in micron space"/>
+        <param argument="--center-y" type="integer" value="0" label="Y coordinate in micron space"/>
+        <param argument="--size-x" type="integer" min="1" value="108" label="Width of the patch in micron space"/>
+        <param argument="--size-y" type="integer" min="1" value="108" label="Height of the patch in micron space"/>
+        <param argument="--input_z_index" type="integer" min="0" value="2" label="The Z plane of the mosaic tiff images to use for the patch"/>
+        <param argument="--red-stain-name" type="select" label="The stain that will be used for red channel of the patch">
+            <expand macro="channel_options_none"/>
+        </param>
+        <param argument="--green-stain-name" type="select" label="The stain that will be used for green channel of the patch">
+            <expand macro="channel_options_none"/>
+        </param>
+        <param argument="--blue-stain-name" type="select" label="The stain that will be used for blue channel of the patch">
+            <expand macro="channel_options_none"/>
+        </param>
+        <expand macro="normalization_param" label="Normalization method that will be used on each channel of the patch"/>
+        <expand macro="advanced_output"/>
+    </inputs>
+    <outputs>
+        <data name="patch_image" format="png" from_work_dir="output/patch1.png" label="${tool.name} on ${on_string}: Patched image"/>
+        <expand macro="common_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
+            <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
+            <param name="center_x" value="200"/>
+            <param name="center_y" value="200"/>
+            <param name="size_x" value="208"/>
+            <param name="size_y" value="208"/>
+            <param name="input_z_index" value="2"/>
+            <param name="red_stain_name" value="Cellbound1"/>
+            <param name="green_stain_name" value="Cellbound3"/>
+            <param name="blue_stain_name" value="DAPI"/>
+            <param name="normalization" value="CLAHE"/>
+            <section name="advanced_output">
+                <param name="log" value="true"/>
+            </section>
+            <output name="patch_image" location="https://zenodo.org/records/15319018/files/patch1.png" ftype="png" compare="image_diff"/>
+            <output name="vpt_log">
+                <assert_contents>
+                    <has_text_matching expression="Extract image patch finished"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+The Vizgen Post-processing Tool (VPT) is a scalable and reproducible tool which enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
+
+The extract-image-patch tool extracts a patch from the mosaic image at the specified coordinates and size. The patch is saved as a PNG image. It can be used for manual segmentation or for training machine learning models.
+    </help>
+    <expand macro="citations" />
+</tool>
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