Mercurial > repos > goeckslab > gate_finder
diff main_macros.xml @ 0:6df8d6e42152 draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
| author | goeckslab |
|---|---|
| date | Thu, 08 Sep 2022 17:22:53 +0000 |
| parents | |
| children | 8097f9124f87 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/main_macros.xml Thu Sep 08 17:22:53 2022 +0000 @@ -0,0 +1,84 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> + + <xml name="vitessce_requirements"> + <requirements> + <container type="docker">quay.io/goeckslab/vitessce:@TOOL_VERSION@</container> + </requirements> + </xml> + + <xml name="macro_stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> + </stdio> + </xml> + + <xml name="vitessce_cmd" token_tool_id="vitessce_spatial"> + <command> + <![CDATA[ + export BF_MAX_MEM="\${GALAXY_MEMORY_MB}m" && + 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' && + echo "\$info\n" && + masks_info=\$(showinf -nopix -nometa -noflat '$masks') && + echo '>showinf -nopix -nometa -noflat \$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 + n_resolutions=\$(echo "\$info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) && + pyramid_scale=1 && + if [ -z "\$n_resolutions" ]; then + echo "Warning: Failded to retrieve the number of pyramid resolutions. Set pyramid resolutions to 4 and scale to 2!"; + n_resolutions=4; + pyramid_scale=2; + else + echo "Found the number of pyramid resolutions: \$n_resolutions"; + if [ "\$n_resolutions" -gt 1 ]; then + sizeX0=\$(echo "\$info" | grep '^\s*sizeX\[0\]\s*=' -m1 | cut -d'=' -f2 | xargs) ; + sizeX1=\$(echo "\$info" | grep '^\s*sizeX\[1\]\s*=' -m1 | cut -d'=' -f2 | xargs) ; + if [ "\$sizeX0" -gt 0 ] && [ "\$sizeX1" -gt 0 ]; then + pyramid_scale=\$(((\$sizeX0 + \$sizeX1 / 2 ) / \$sizeX1)); + echo "Calculate pyramid scale: \$sizeX0 / \$sizeX1 ~= \$pyramid_scale."; + else + pyramid_scale=2; + echo "Warning: Failed to calculate the pyramid scale; set it to 2!"; + fi; + fi; + fi; + tile_info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff' | grep '^\s*Tile\ssize\s*=' -m1); + tile_x=\$(echo "\$tile_info" | cut -d' ' -f4); + tile_y=\$(echo "\$tile_info" | cut -d' ' -f6); + convert_cmd="bfconvert -pyramid-resolutions \$n_resolutions -pyramid-scale \$pyramid_scale -noflat -tilex \$tile_x -tiley \$tile_y '$masks' '${output.files_path}/A/0/masks01.ome.tiff'"; + echo "\n>\$convert_cmd"; + eval \$convert_cmd; + masks_info_new=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'); + echo "\n>showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'"; + echo "\$masks_info_new\n"; + else + ln -sf '$masks' '${output.files_path}/A/0/masks01.ome.tiff'; + fi && + #end if + python '$__tool_directory__/@TOOL_ID@.py' + --inputs '$inputs' + --output '${output.files_path}' + --image '${output.files_path}/A/0/image01.ome.tiff' + #if $masks + --masks '${output.files_path}/A/0/masks01.ome.tiff' + #end if + #if $do_phenotyping.phenotyping_choice + --anndata '$anndata' + #end if + && + cp -R '$__tool_directory__/static' '${output.files_path}' && + cp '$__tool_directory__/index.html' '$output'; + + ]]> + </command> + </xml> + +</macros>