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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
author bgruening
date Sun, 22 Jun 2025 12:25:39 +0000
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e08b21abb96d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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1 <tool id="vpt_extract" name="Vizgen VPT - Extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>image patches</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="creator" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @CMD@
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10 vpt
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11 @COMMON_ARGS@
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12 extract-image-patch
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13 --input-images 'input/images/'
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14 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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15 --output-patch 'output/patch1.png'
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16 --center-x $center_x
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17 --center-y $center_y
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18 --size-x $size_x
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19 --size-y $size_y
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20 --input-z-index $input_z_index
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21 #if $red_stain_name != "None":
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22 --red-stain-name $red_stain_name
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23 #end if
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24 #if $green_stain_name != "None":
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25 --green-stain-name $green_stain_name
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26 #end if
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27 #if $blue_stain_name != "None":
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28 --blue-stain-name $blue_stain_name
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29 #end if
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30 --normalization $normalization
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31 ]]></command>
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32 <inputs>
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33 <expand macro="common_input"/>
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34 <param argument="--center-x" type="integer" value="0" label="X coordinate in micron space"/>
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35 <param argument="--center-y" type="integer" value="0" label="Y coordinate in micron space"/>
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36 <param argument="--size-x" type="integer" min="1" value="108" label="Width of the patch in micron space"/>
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37 <param argument="--size-y" type="integer" min="1" value="108" label="Height of the patch in micron space"/>
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38 <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"/>
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39 <param argument="--red-stain-name" type="select" label="The stain that will be used for red channel of the patch">
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40 <expand macro="channel_options_none"/>
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41 </param>
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42 <param argument="--green-stain-name" type="select" label="The stain that will be used for green channel of the patch">
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43 <expand macro="channel_options_none"/>
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44 </param>
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45 <param argument="--blue-stain-name" type="select" label="The stain that will be used for blue channel of the patch">
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46 <expand macro="channel_options_none"/>
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47 </param>
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48 <expand macro="normalization_param" label="Normalization method that will be used on each channel of the patch"/>
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49 <expand macro="advanced_output"/>
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50 </inputs>
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51 <outputs>
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52 <data name="patch_image" format="png" from_work_dir="output/patch1.png" label="${tool.name} on ${on_string}: Patched image"/>
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53 <expand macro="common_output"/>
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54 </outputs>
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55 <tests>
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56 <test expect_num_outputs="2">
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57 <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"/>
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58 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
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59 <param name="center_x" value="200"/>
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60 <param name="center_y" value="200"/>
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61 <param name="size_x" value="208"/>
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62 <param name="size_y" value="208"/>
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63 <param name="input_z_index" value="2"/>
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64 <param name="red_stain_name" value="Cellbound1"/>
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65 <param name="green_stain_name" value="Cellbound3"/>
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66 <param name="blue_stain_name" value="DAPI"/>
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67 <param name="normalization" value="CLAHE"/>
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68 <section name="advanced_output">
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69 <param name="log" value="true"/>
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70 </section>
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71 <output name="patch_image" location="https://zenodo.org/records/15319018/files/patch1.png" ftype="png" compare="image_diff"/>
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72 <output name="vpt_log">
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73 <assert_contents>
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74 <has_text_matching expression="Extract image patch finished"/>
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75 </assert_contents>
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76 </output>
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77 </test>
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78 </tests>
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79 <help>
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80 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.
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81
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82 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.
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83 </help>
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84 <expand macro="citations" />
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85 </tool>