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comparison main_macros.xml @ 4:5f4a4dd06bc9 draft default tip

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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
comparison
equal deleted inserted replaced
3:80102785f5ff 4:5f4a4dd06bc9
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.0.4</token> 2 <token name="@TOOL_VERSION@">3.5.1</token>
3 <token name="@VERSION_SUFFIX@">5</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">20.01</token> 4 <token name="@PROFILE@">22.01</token>
5 5
6 <xml name="vitessce_requirements"> 6 <xml name="vitessce_requirements">
7 <requirements> 7 <requirements>
8 <container type="docker">quay.io/goeckslab/vitessce:@TOOL_VERSION@v3</container> 8 <container type="docker">quay.io/goeckslab/vitessce:@TOOL_VERSION@</container>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 11
12 <xml name="macro_stdio"> 12 <xml name="macro_stdio">
13 <stdio> 13 <stdio>
21 MAX_MEM=\${GALAXY_MEMORY_MB:-2000} && 21 MAX_MEM=\${GALAXY_MEMORY_MB:-2000} &&
22 export BF_MAX_MEM="\$((\$MAX_MEM/2))m" && 22 export BF_MAX_MEM="\$((\$MAX_MEM/2))m" &&
23 mkdir -p '${output.files_path}/A/0' && 23 mkdir -p '${output.files_path}/A/0' &&
24 ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' && 24 ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' &&
25 #if $masks 25 #if $masks
26 info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff') && 26 info=\$(showinf -nopix -nometa -noflat -no-upgrade '${output.files_path}/A/0/image01.ome.tiff') &&
27 echo '>showinf -nopix -nometa -noflat \$image' && 27 echo '>showinf -nopix -nometa -noflat -no-upgrade \$image' &&
28 echo "\$info\n" && 28 echo "\$info\n" &&
29 masks_info=\$(showinf -nopix -nometa -noflat '$masks') && 29 masks_info=\$(showinf -nopix -nometa -noflat -no-upgrade '$masks') &&
30 echo '>showinf -nopix -nometa -noflat \$masks' && 30 echo '>showinf -nopix -nometa -noflat -no-upgrade \$masks' &&
31 echo "\$masks_info\n" && 31 echo "\$masks_info\n" &&
32 masks_n_resolutions=\$(echo "\$masks_info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) && 32 masks_n_resolutions=\$(echo "\$masks_info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) &&
33 if [ -z \$masks_n_resolutions ]; then 33 if [ -z \$masks_n_resolutions ]; then
34 n_resolutions=\$(echo "\$info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) && 34 n_resolutions=\$(echo "\$info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) &&
35 pyramid_scale=1 && 35 pyramid_scale=1 &&
49 pyramid_scale=2; 49 pyramid_scale=2;
50 echo "Warning: Failed to calculate the pyramid scale; set it to 2!"; 50 echo "Warning: Failed to calculate the pyramid scale; set it to 2!";
51 fi; 51 fi;
52 fi; 52 fi;
53 fi; 53 fi;
54 tile_info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff' | grep '^\s*Tile\ssize\s*=' -m1); 54 tile_info=\$(showinf -nopix -nometa -noflat -no-upgrade '${output.files_path}/A/0/image01.ome.tiff' | grep '^\s*Tile\ssize\s*=' -m1);
55 tile_x=\$(echo "\$tile_info" | cut -d' ' -f4); 55 tile_x=\$(echo "\$tile_info" | cut -d' ' -f4);
56 tile_y=\$(echo "\$tile_info" | cut -d' ' -f6); 56 tile_y=\$(echo "\$tile_info" | cut -d' ' -f6);
57 convert_cmd="bfconvert -pyramid-resolutions \$n_resolutions -pyramid-scale \$pyramid_scale -noflat -tilex \$tile_x -tiley \$tile_y '$masks' '${output.files_path}/A/0/masks01.ome.tiff'"; 57 convert_cmd="bfconvert -no-upgrade -pyramid-resolutions \$n_resolutions -pyramid-scale \$pyramid_scale -noflat -tilex \$tile_x -tiley \$tile_y '$masks' '${output.files_path}/A/0/masks01.ome.tiff'";
58 echo "\n>\$convert_cmd"; 58 echo "\n>\$convert_cmd";
59 eval \$convert_cmd; 59 eval \$convert_cmd;
60 masks_info_new=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'); 60 masks_info_new=\$(showinf -nopix -nometa -noflat -no-upgrade '${output.files_path}/A/0/masks01.ome.tiff');
61 echo "\n>showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'"; 61 echo "\n>showinf -nopix -nometa -noflat -no-upgrade '${output.files_path}/A/0/masks01.ome.tiff'";
62 echo "\$masks_info_new\n"; 62 echo "\$masks_info_new\n";
63 else 63 else
64 ln -sf '$masks' '${output.files_path}/A/0/masks01.ome.tiff'; 64 ln -sf '$masks' '${output.files_path}/A/0/masks01.ome.tiff';
65 fi && 65 fi &&
66 #end if 66 #end if
67 python '$__tool_directory__/@TOOL_ID@.py' 67 python '$__tool_directory__/@TOOL_ID@.py'
68 --inputs '$inputs' 68 --inputs '$inputs'
69 --output '${output.files_path}' 69 --output '${output.files_path}'
70 --image '${output.files_path}/A/0/image01.ome.tiff' 70 --image '${output.files_path}/A/0/image01.ome.tiff'
71 --offsets '$image.metadata.offsets'
71 #if $masks 72 #if $masks
72 --masks '${output.files_path}/A/0/masks01.ome.tiff' 73 --masks '${output.files_path}/A/0/masks01.ome.tiff'
73 #end if 74 #end if
74 #if $do_phenotyping.phenotyping_choice == 'add_h5ad' 75 #if $do_phenotyping.phenotyping_choice == 'add_h5ad'
75 --anndata '$anndata' 76 --anndata '$anndata'
76 #end if 77 #end if
77 && 78 &&
78 cp -R '$__tool_directory__/static' '${output.files_path}' &&
79 cp '$__tool_directory__/index.html' '$output'; 79 cp '$__tool_directory__/index.html' '$output';
80 80 echo "export var config = \$(cat ${output.files_path}/config.json)" >> '${output.files_path}/config.js';
81 cat '${output.files_path}/config.json' >> '$vitessce_config';
81 ]]> 82 ]]>
82 </command> 83 </command>
83 </xml> 84 </xml>
84 85
85 </macros> 86 </macros>