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Merge pull request #1614 from nilchia/vpt
add vpt
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‎tools/vpt/.shed.yml‎

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name: vpt
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owner: bgruening
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description: Vizgen Post-processing Tool
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homepage_url: https://vizgen.github.io/vizgen-postprocessing/
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long_description: |
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The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments. VPT is a command line tool that emphasizes scalable, reproducible analysis, and can be run on a workstation, a cluster, or be deployed in a cloud computing environment.
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remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/vpt
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type: unrestricted
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categories:
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- Single Cell
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- Spatial Omics
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- Transcriptomics
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- Imaging
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auto_tool_repositories:
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name_template: "{{ tool_id }}"
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description_template: "Wrapper for {{ tool_name }}."
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suite:
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name: "suite_vpt"
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description: "A suite of Galaxy tools designed to work with the vpt-tools collection."
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type: repository_suite_definition

‎tools/vpt/macros.xml‎

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<macros>
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<token name="@TOOL_VERSION@">1.3.0</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<token name="@PROFILE@">23.0</token>
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<xml name="requirements">
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<requirements>
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<container type="docker">quay.io/bgruening/vpt:1.3.0-1</container>
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<yield/>
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</requirements>
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</xml>
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<xml name="creator">
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<creator>
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<organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
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<person givenName="Amirhossein" familyName="Naghsh Nilchi" email="nilchia@informatik.uni-freiburg.de" />
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<person givenName="Pavan" familyName="Videm" email="videmp@informatik.uni-freiburg.de" />
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<person givenName="Björn" familyName="Grüning" email="gruening@informatik.uni-freiburg.de" />
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</creator>
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</xml>
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<token name="@CMD@"><![CDATA[
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mkdir -p 'input/images' 'output/' &&
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#for $image in $input_images:
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ln -s '$image' 'input/images/${image.element_identifier}.${image.ext}' &&
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#end for
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ln -s '$input_micron_to_mosaic' 'input/micron_to_mosaic_pixel_transform.csv' &&
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]]></token>
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<token name="@COMMON_ARGS@"><![CDATA[
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--processes \${GALAXY_SLOTS:-10}
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--verbose
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--log-file 'output/log'
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]]>
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</token>
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<xml name="common_input">
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<param argument="--input_images" type="data" format="tiff" multiple="true" label="MEROSCOPE tiff images"/>
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<param argument="--input_micron_to_mosaic" type="data" format="csv" label="Micron to mosaic mapping file"/>
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</xml>
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<xml name="normalization_param" token_label="Normalization">
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<param name="normalization" type="select" label="@LABEL@">
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<option value="default">default (min-max range normalization)</option>
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<option value="CLAHE">CLAHE (Contrast Limited Adaptive Histogram Equalization)</option>
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</param>
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</xml>
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<xml name="channel_options_basic">
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<yield/>
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<option value="Cellbound1">Cellbound1</option>
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<option value="Cellbound2">Cellbound2</option>
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<option value="Cellbound3">Cellbound3</option>
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</xml>
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<xml name="channel_options_none">
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<expand macro="channel_options_basic">
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<option value="None" selected="true">None</option>
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<option value="DAPI">DAPI</option>
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<option value="PolyT">PolyT</option>
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<yield/>
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</expand>
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</xml>
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<xml name="advanced_output">
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<section name="advanced_output" title="Advanced output options">
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<param name="log" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Output log?"/>
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</section>
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</xml>
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<xml name="common_output">
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<data name="vpt_log" format="txt" from_work_dir="output/log" label="${tool.name} on ${on_string}: VPT log">
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<filter>advanced_output['log']</filter>
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</data>
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</xml>
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<xml name="sanitize_digits">
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<sanitizer invalid_char="">
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<valid initial="string.digits">
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<add value=","/>
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<add value="."/>
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</valid>
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</sanitizer>
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</xml>
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<xml name="citations">
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<citations>
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<citation type="bibtex">@Manual{github,
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title = {Vizgen Post-processing Tool},
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author = {Vizgen},
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organization = {Vizgen},
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year = {2022},
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url = {https://github.com/Vizgen/vizgen-postprocessing}}
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</citation>
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</citations>
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</xml>
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</macros>

‎tools/vpt/vpt_extract.xml‎

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<tool id="vpt_extract" name="Vizgen VPT - Extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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<description>image patches</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="requirements" />
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<expand macro="creator" />
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<command detect_errors="exit_code"><![CDATA[
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@CMD@
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vpt
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@COMMON_ARGS@
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extract-image-patch
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--input-images 'input/images/'
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--input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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--output-patch 'output/patch1.png'
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--center-x $center_x
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--center-y $center_y
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--size-x $size_x
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--size-y $size_y
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--input-z-index $input_z_index
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#if $red_stain_name != "None":
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--red-stain-name $red_stain_name
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#end if
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#if $green_stain_name != "None":
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--green-stain-name $green_stain_name
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#end if
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#if $blue_stain_name != "None":
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--blue-stain-name $blue_stain_name
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#end if
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--normalization $normalization
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]]></command>
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<inputs>
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<expand macro="common_input"/>
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<param argument="--center-x" type="integer" label="X coordinate in micron space"/>
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<param argument="--center-y" type="integer" label="Y coordinate in micron space"/>
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<param argument="--size-x" type="integer" min="1" value="108" label="Width of the patch in micron space"/>
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<param argument="--size-y" type="integer" min="1" value="108" label="Height of the patch in micron space"/>
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<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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<param argument="--red-stain-name" type="select" label="The stain that will be used for red channel of the patch">
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<expand macro="channel_options_none"/>
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</param>
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<param argument="--green-stain-name" type="select" label="The stain that will be used for green channel of the patch">
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<expand macro="channel_options_none"/>
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</param>
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<param argument="--blue-stain-name" type="select" label="The stain that will be used for blue channel of the patch">
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<expand macro="channel_options_none"/>
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</param>
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<expand macro="normalization_param" label="Normalization method that will be used on each channel of the patch"/>
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<expand macro="advanced_output"/>
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</inputs>
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<outputs>
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<data name="patch_image" format="png" from_work_dir="output/patch1.png" label="${tool.name} on ${on_string}: Patched image"/>
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<expand macro="common_output"/>
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</outputs>
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<tests>
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<test expect_num_outputs="2">
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<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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<param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
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<param name="center_x" value="200"/>
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<param name="center_y" value="200"/>
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<param name="size_x" value="208"/>
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<param name="size_y" value="208"/>
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<param name="input_z_index" value="2"/>
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<param name="red_stain_name" value="Cellbound1"/>
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<param name="green_stain_name" value="Cellbound3"/>
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<param name="blue_stain_name" value="DAPI"/>
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<param name="normalization" value="CLAHE"/>
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<section name="advanced_output">
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<param name="log" value="true"/>
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</section>
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<output name="patch_image" location="https://zenodo.org/records/15319018/files/patch1.png" ftype="png" compare="image_diff"/>
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<output name="vpt_log">
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<assert_contents>
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<has_text_matching expression="Extract image patch finished"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help>
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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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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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</help>
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<expand macro="citations" />
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</tool>

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