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Merged
merged 13 commits into from
May 3, 2025
Merged

add bellavista prepare #6946

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4d4a300
add bellavista prepare
nilchia Apr 30, 2025
0f6af69
add first test
nilchia Apr 30, 2025
171aa14
add test
nilchia May 1, 2025
a248674
correct archive path
nilchia May 1, 2025
53591c2
add shed.yml
nilchia May 2, 2025
26fe6d0
correct tool directory
nilchia May 2, 2025
ce9e1ee
Update tools/bellavista/bellavista_prepare.xml
nilchia May 2, 2025
3a728f8
turn off all plots
nilchia May 2, 2025
4ec64ec
add timeout
nilchia May 2, 2025
aa0f821
check output
nilchia May 2, 2025
cbd095d
correct path
nilchia May 3, 2025
25523cd
add hidden timeout param
nilchia May 3, 2025
6c9ac97
correct param
nilchia May 3, 2025
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16 changes: 16 additions & 0 deletions tools/bellavista/.shed.yml
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name: bellavista
owner: iuc
description: Open-Source Visualization for Imaging-Based Spatial Transcriptomics
homepage_url: https://github.com/pkosurilab/BellaVista
long_description: |
BellaVista is an open-source Python package developed for 10x Genomics Xenium, Vizgen MERSCOPE, and custom (home-built) MERFISH datasets utilizing napari for interactive data exploration.
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bellavista
type: unrestricted
categories:
- Single Cell
- Spatial Omics
- Transcriptomics
- Imaging
auto_tool_repositories:
name_template: "{{ tool_id }}"
description_template: "Wrapper for {{ tool_name }}."
17 changes: 17 additions & 0 deletions tools/bellavista/bellavista.bash
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#!/usr/bin/bash

cd "$BELLAVISTA_DIR" &&
touch './bellavista.log' &&
/opt/bellavista/bellavista/bin/bellavista "./config.json" | tee './bellavista.log' &&
TOOL_PID=$!

while sleep 1; do
if grep -q "OME-Zarr image saved successfully" './bellavista.log'; then
echo "Bella Vista input files created! Stopping the tool..."
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I think you need an additional safe-guards here.

What happens if this string never appears? Should we kill the tool after X hours? The X hours can be taken optionally from an ENV var, so the admin can overwrite it?

Also would it make sense to actually check if the result file exist?

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I added a timeout to the script.
For the output I'm not sure how to check. the main output would be the image in zarr format.
Now I just check if the directory and .zgroup file exists

kill -INT $TOOL_PID
break
fi
done &&

wait $TOOL_PID &&
echo "Bella Vista stopped."
180 changes: 180 additions & 0 deletions tools/bellavista/bellavista_prepare.xml
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<tool id="bellavista_prepare" name="Bellavista" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Prepare large images for bellavista visualizer</description>
<creator>
<organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
<person givenName="Amirhossein" familyName="Naghsh Nilchi" email="[email protected]" />
<person givenName="Pavan" familyName="Videm" email="[email protected]" />
<person givenName="Björn" familyName="Grüning" email="[email protected]" />
</creator>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
export BELLAVISTA_DIR=`pwd`/input/ &&
mkdir -p 'input' 'input/BellaVista_output' &&
chmod -R 777 'input/' &&
#if $technology_conditional.plot_genes.plot_transcripts == "true":
ln -s '$technology_conditional.plot_genes.transcript_filename' './input/${technology_conditional.plot_genes.transcript_filename.element_identifier}.${technology_conditional.plot_genes.transcript_filename.ext}' &&
#end if
#for $image in $technology_conditional.images:
ln -s '$image' 'input/${image.element_identifier}.${image.ext}' &&
#end for
ln -s '$bellavista_config_file' './input/config.json' &&
#if $technology_conditional.plot_cell_segmentation.plot_cell_seg == "true":
ln -s '$technology_conditional.plot_cell_segmentation.cell_segmentation' './input/${technology_conditional.plot_cell_segmentation.cell_segmentation.element_identifier}.${technology_conditional.plot_cell_segmentation.cell_segmentation.ext}' &&
#end if
#if $technology_conditional.plot_nuclear_segmentation.plot_nuclear_seg == "true":
ln -s '$technology_conditional.plot_nuclear_segmentation.nuclear_segmentation' './input/${technology_conditional.plot_nuclear_segmentation.nuclear_segmentation.element_identifier}.${technology_conditional.plot_nuclear_segmentation.nuclear_segmentation.ext}' &&
#end if
#if $technology_conditional.technology == "MERSCOPE":
ln -s '$technology_conditional.um_to_px_transform' './input/micron_to_mosaic_pixel_transform.csv' &&
#end if
cat ./input/config.json &&

bash '$__tool_directory__/bellavista.bash'

cd ../ &&
tar -czf 'bellavista.tar.gz' 'input/BellaVista_output'
]]></command>
<configfiles>
<configfile name="bellavista_config_file"><![CDATA[
{
"system": "$technology",
"data_folder": "./",
"create_bellavista_inputs": true,

"visualization_parameters": {
"plot_image": true,
#if $technology_conditional.plot_genes.plot_transcripts == "true":
"plot_transcripts": true,
#else
"plot_transcripts": false,
#end if
#if $technology_conditional.plot_cell_segmentation.plot_cell_seg == "true":
"plot_cell_seg": true,
#else
"plot_cell_seg": false,
#end if
#if $technology_conditional.plot_nuclear_segmentation.plot_nuclear_seg == "true":
"plot_nuclear_seg": true,
#else
"plot_nuclear_seg": false,
#end if
"genes_visible_on_startup": false,
#if $technology_conditional.plot_genes.plot_all_genes.all_genes == "Yes":
"plot_allgenes": true,
#else
"plot_allgenes": false,
#set $gene_list = ['"' + str(x.strip()) + '"' for x in str($technology_conditional.plot_genes.plot_all_genes.selected_genes).split(',')]
#set $genes = ','.join($gene_list)
"selected_genes": $genes,
#end if
"rotate_angle": $rotate_angle,
"transcript_point_size": $transcript_point_size
},

"input_files": {
#set $last_index = len($technology_conditional.images) - 1
"images": [
#for $i in range(len($images)):
"$images[$i].element_identifier.$images[$i].ext"#if $i != $last_index#,#end if
#end for
],
#if $technology_conditional.plot_cell_segmentation.plot_cell_seg == "true":
"cell_segmentation": "${technology_conditional.plot_cell_segmentation.cell_segmentation.element_identifier}.${technology_conditional.plot_cell_segmentation.cell_segmentation.ext}",
#end if
#if $technology_conditional.plot_nuclear_segmentation.plot_nuclear_seg == "true":
"nuclear_segmentation": "${technology_conditional.plot_nuclear_segmentation.nuclear_segmentation.element_identifier}.${technology_conditional.plot_nuclear_segmentation.nuclear_segmentation.ext}",
#end if
#if $technology_conditional.technology == "MERSCOPE":
"um_to_px_transform": "micron_to_mosaic_pixel_transform.csv",
#end if
#if $technology_conditional.plot_genes.plot_transcripts == "true":
"transcript_filename": "${technology_conditional.plot_genes.transcript_filename.element_identifier}.${technology_conditional.plot_genes.transcript_filename.ext}",
#end if
"z_plane": $technology_conditional.z_plane
}
}
]]></configfile>
</configfiles>
<inputs>
<conditional name="technology_conditional">
<param name="technology" type="select" label="Spatial transcriptomic technology">
<option value="Xenium">Xenium</option>
<option value="MERSCOPE" selected="true">MERSCOPE</option>
</param>
<when value="Xenium">
<expand macro="common_param"/>
</when>
<when value="MERSCOPE">
<expand macro="common_param">
<param name="um_to_px_transform" type="data" format="csv" optional="false" label="micron to pixel transformations"/>
</expand>
</when>
</conditional>
<section name="advanced_output" title="Advanced output options">
<param name="config" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Output config file?"/>
</section>
</inputs>
<outputs>
<data name="bellavista_output" format="tar.gz" label="${tool.name} on ${on_string}: Bellavista prepared inputs" from_work_dir="./bellavista.tar.gz" />
<data name="config" format="json" label="${tool.name} on ${on_string}: config file" from_work_dir="input/config.json">
<filter>advanced_output['config']</filter>
</data>
</outputs>
<tests>
<test expect_num_outputs="2">
<conditional name="technology_conditional">
<param name="technology" value="MERSCOPE"/>
<param name="images" location="https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif"/>
<conditional name="plot_genes">
<param name="plot_transcripts" value="true"/>
<param name="transcript_filename" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
</conditional>
<conditional name="plot_cell_segmentation">
<param name="plot_cell_seg" value="false"/>
</conditional>
<conditional name="plot_nuclear_segmentation">
<param name="plot_nuclear_seg" value="false"/>
</conditional>
<param name="um_to_px_transform" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
<param name="z_plane" value="3"/>
<param name="transcript_point_size" value="1"/>
<param name="rotate_angle" value="0"/>
</conditional>
<section name="advanced_output">
<param name="config" value="true"/>
</section>
<output name="bellavista_output">
<assert_contents>
<has_archive_member path="input/BellaVista_output/gene_dict.pkl"/>
<has_archive_member path="input/BellaVista_output/OMEzarrImages"/>
<has_archive_member path="input/BellaVista_output/um_to_px_transforms.pkl"/>
</assert_contents>
</output>
<output name="config">
<assert_contents>
<has_text text="MERSCOPE"/>
<has_text text="&quot;create_bellavista_inputs&quot;: true"/>
<has_text text="&quot;plot_cell_seg&quot;: false"/>
</assert_contents>
</output>
<assert_stdout>
<has_text text="Creating Bella Vista input files for Vizgen MERSCOPE"/>
<has_text text="Bella Vista input files created!"/>
</assert_stdout>
</test>
</tests>
<help><![CDATA[
BellaVista is an open-source visualization tool for imaging-based spatial transcriptomics data. It allows users to visualize and explore spatial transcriptomics data in a user-friendly interface. The tool supports MERSCOPE and Xenium imaging-based spatial transcriptomics technologies.

Users can customize the visualization by selecting specific genes, adjusting image rotation angles, and controlling the size of transcript points. BellaVista also provides options for plotting cell and nuclear segmentation, enhancing the exploration of spatial transcriptomics data.

.. image:: https://raw.githubusercontent.com/pkosurilab/BellaVista/c8129bb8954c92962a87606595c09b35cc414295/images/bellavista_figure.png
:height: 500
:width: 700
]]>
</help>
<expand macro="citations"/>
</tool>
73 changes: 73 additions & 0 deletions tools/bellavista/macros.xml
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<macros>
<token name="@TOOL_VERSION@">0.0.2</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">23.0</token>
<xml name="requirements">
<requirements>
<container type="docker">quay.io/bgruening/bellavista:0.0.2-3</container>
<yield/>
</requirements>
</xml>
<xml name="common_param">
<param name="images" type="data" format="tiff,ome.tiff" multiple="true" optional="false" label="Images"/>
<conditional name="plot_genes">
<param name="plot_transcripts" type="select" label="Plot transcripts?">
<option value="false">No</option>
<option value="true" selected="true">Yes</option>
</param>
<when value="false"></when>
<when value="true">
<param name="transcript_filename" type="data" format="csv,parquet" optional="false" label="transcript spatial locations"/>
<conditional name="plot_all_genes">
<param name="all_genes" type="select" label="Plot all genes?">
<option value="Yes" selected="true">Yes</option>
<option value="No">No</option>
</param>
<when value="Yes"/>
<when value="No">
<param name="selected_genes" type="text" optional="false" value="" label="Comma separated list of custom genes">
<sanitizer>
<valid initial="string.printable">
<remove value="&apos;"/>
</valid>
</sanitizer>
</param>
</when>
</conditional>
</when>
</conditional>
<conditional name="plot_cell_segmentation">
<param name="plot_cell_seg" type="select" label="Plot cell segmentation?">
<option value="false">No</option>
<option value="true" selected="true">Yes</option>
</param>
<when value="false"></when>
<when value="true">
<param name="cell_segmentation" type="data" format="parquet,zarr" optional="false" label="Cell segmentations"/>
</when>
</conditional>
<conditional name="plot_nuclear_segmentation">
<param name="plot_nuclear_seg" type="select" label="Plot nuclear segmentation?">
<option value="false" selected="true">No</option>
<option value="true">Yes</option>
</param>
<when value="false"></when>
<when value="true">
<param name="nuclear_segmentation" type="data" format="parquet,zarr" optional="false" label="Nuclear segmentations"/>
</when>
</conditional>
<yield />
<param name="z_plane" type="integer" min="0" value="0" label="z-plane of image to be visualize"/>
<param name="transcript_point_size" type="integer" min="0" value="1" label="Size of the points representing individual transcripts"/>
<param name="rotate_angle" type="integer" min="-180" max="180" value="0" label="Image rotation angle in degrees"/>
</xml>
<xml name="citations">
<citations>
<citation type="doi">10.1016/j.bpj.2024.11.3199</citation>
<citation type="bibtex">@Manual{github,
title = {Open-source Visualization for Imaging-Based Spatial Transcriptomics},
url = {https://github.com/pkosurilab/BellaVista}}
</citation>
</citations>
</xml>
</macros>