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update bellavista - include inputs to tar file #6951

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26 changes: 17 additions & 9 deletions tools/bellavista/bellavista_prepare.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,28 +16,30 @@
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}' &&
cp '$technology_conditional.plot_genes.transcript_filename' './input/${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}' &&
cp '$image' 'input/${image.element_identifier}.${image.ext}' &&
#end for
ln -s '$bellavista_config_file' './input/config.json' &&
cp '$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}' &&
cp '$technology_conditional.plot_cell_segmentation.cell_segmentation' './input/${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}' &&
cp '$technology_conditional.plot_nuclear_segmentation.nuclear_segmentation' './input/${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' &&
cp '$technology_conditional.um_to_px_transform' './input/micron_to_mosaic_pixel_transform.csv' &&
#end if
cat ./input/config.json &&
cat './input/config.json' &&

cp './input/config.json' './input/config_orig.json' &&

cd "\$BELLAVISTA_DIR" &&
bash '$__tool_directory__/bellavista.bash' &&
cd .. &&

tar -czf 'bellavista.tar.gz' 'input/BellaVista_output'
tar -czf 'bellavista.tar.gz' 'input/'
]]></command>
<configfiles>
<configfile name="bellavista_config_file"><![CDATA[
Expand Down Expand Up @@ -122,7 +124,7 @@
</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 ${on_string}: config file" from_work_dir="input/config.json">
<data name="config" format="json" label="${tool.name} on ${on_string}: config file" from_work_dir="input/config_orig.json">
<filter>advanced_output['config']</filter>
</data>
</outputs>
Expand Down Expand Up @@ -151,8 +153,12 @@
</section>
<output name="bellavista_output">
<assert_contents>
<has_archive_member path="input/config_orig.json"/>
<has_archive_member path="input/mosaic_PolyT_z3.tif"/>
<has_archive_member path="input/micron_to_mosaic_pixel_transform.csv"/>
<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/OMEzarrImages/.zgroup"/>
<has_archive_member path="input/BellaVista_output/um_to_px_transforms.pkl"/>
</assert_contents>
</output>
Expand Down Expand Up @@ -204,6 +210,8 @@ BellaVista is an open-source visualization tool for imaging-based spatial transc

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.

For large images, it is highly recommended to use the Bellavista Prepare tool to preprocess the inputs with high computing power. The tool will create a tarball with all the necessary processed files and it can be used directly for bellavista interactive tool.

.. image:: https://raw.githubusercontent.com/pkosurilab/BellaVista/c8129bb8954c92962a87606595c09b35cc414295/images/bellavista_figure.png
:height: 500
:width: 700
Expand Down
2 changes: 1 addition & 1 deletion tools/bellavista/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">0.0.2</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">23.0</token>
<xml name="requirements">
<requirements>
Expand Down