Mercurial > repos > goeckslab > gate_finder
diff main_macros.xml @ 4:5f4a4dd06bc9 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit bc4c0bb6784a55399241f99a29b176541a164a18
| author | goeckslab |
|---|---|
| date | Thu, 20 Feb 2025 19:47:28 +0000 |
| parents | 80102785f5ff |
| children |
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--- a/main_macros.xml Thu May 30 17:24:31 2024 +0000 +++ b/main_macros.xml Thu Feb 20 19:47:28 2025 +0000 @@ -1,11 +1,11 @@ <macros> - <token name="@TOOL_VERSION@">1.0.4</token> - <token name="@VERSION_SUFFIX@">5</token> - <token name="@PROFILE@">20.01</token> + <token name="@TOOL_VERSION@">3.5.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> <xml name="vitessce_requirements"> <requirements> - <container type="docker">quay.io/goeckslab/vitessce:@TOOL_VERSION@v3</container> + <container type="docker">quay.io/goeckslab/vitessce:@TOOL_VERSION@</container> </requirements> </xml> @@ -23,11 +23,11 @@ mkdir -p '${output.files_path}/A/0' && ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' && #if $masks - info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff') && - echo '>showinf -nopix -nometa -noflat \$image' && + info=\$(showinf -nopix -nometa -noflat -no-upgrade '${output.files_path}/A/0/image01.ome.tiff') && + echo '>showinf -nopix -nometa -noflat -no-upgrade \$image' && echo "\$info\n" && - masks_info=\$(showinf -nopix -nometa -noflat '$masks') && - echo '>showinf -nopix -nometa -noflat \$masks' && + masks_info=\$(showinf -nopix -nometa -noflat -no-upgrade '$masks') && + echo '>showinf -nopix -nometa -noflat -no-upgrade \$masks' && echo "\$masks_info\n" && masks_n_resolutions=\$(echo "\$masks_info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) && if [ -z \$masks_n_resolutions ]; then @@ -51,14 +51,14 @@ fi; fi; fi; - tile_info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff' | grep '^\s*Tile\ssize\s*=' -m1); + tile_info=\$(showinf -nopix -nometa -noflat -no-upgrade '${output.files_path}/A/0/image01.ome.tiff' | grep '^\s*Tile\ssize\s*=' -m1); tile_x=\$(echo "\$tile_info" | cut -d' ' -f4); tile_y=\$(echo "\$tile_info" | cut -d' ' -f6); - convert_cmd="bfconvert -pyramid-resolutions \$n_resolutions -pyramid-scale \$pyramid_scale -noflat -tilex \$tile_x -tiley \$tile_y '$masks' '${output.files_path}/A/0/masks01.ome.tiff'"; + convert_cmd="bfconvert -no-upgrade -pyramid-resolutions \$n_resolutions -pyramid-scale \$pyramid_scale -noflat -tilex \$tile_x -tiley \$tile_y '$masks' '${output.files_path}/A/0/masks01.ome.tiff'"; echo "\n>\$convert_cmd"; eval \$convert_cmd; - masks_info_new=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'); - echo "\n>showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'"; + masks_info_new=\$(showinf -nopix -nometa -noflat -no-upgrade '${output.files_path}/A/0/masks01.ome.tiff'); + echo "\n>showinf -nopix -nometa -noflat -no-upgrade '${output.files_path}/A/0/masks01.ome.tiff'"; echo "\$masks_info_new\n"; else ln -sf '$masks' '${output.files_path}/A/0/masks01.ome.tiff'; @@ -68,6 +68,7 @@ --inputs '$inputs' --output '${output.files_path}' --image '${output.files_path}/A/0/image01.ome.tiff' + --offsets '$image.metadata.offsets' #if $masks --masks '${output.files_path}/A/0/masks01.ome.tiff' #end if @@ -75,9 +76,9 @@ --anndata '$anndata' #end if && - cp -R '$__tool_directory__/static' '${output.files_path}' && cp '$__tool_directory__/index.html' '$output'; - + echo "export var config = \$(cat ${output.files_path}/config.json)" >> '${output.files_path}/config.js'; + cat '${output.files_path}/config.json' >> '$vitessce_config'; ]]> </command> </xml>