Mercurial > repos > bgruening > vpt_extract
changeset 0:e08b21abb96d draft default tip
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 |
| parents | |
| children | |
| files | macros.xml vpt_extract.xml |
| diffstat | 2 files changed, 232 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jun 22 12:25:39 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>
--- /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> \ No newline at end of file