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comparison main_macros.xml @ 0:6df8d6e42152 draft

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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
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children 8097f9124f87
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-1:000000000000 0:6df8d6e42152
1 <macros>
2 <token name="@TOOL_VERSION@">1.0.4</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">20.01</token>
5
6 <xml name="vitessce_requirements">
7 <requirements>
8 <container type="docker">quay.io/goeckslab/vitessce:@TOOL_VERSION@</container>
9 </requirements>
10 </xml>
11
12 <xml name="macro_stdio">
13 <stdio>
14 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
15 </stdio>
16 </xml>
17
18 <xml name="vitessce_cmd" token_tool_id="vitessce_spatial">
19 <command>
20 <![CDATA[
21 export BF_MAX_MEM="\${GALAXY_MEMORY_MB}m" &&
22 mkdir -p '${output.files_path}/A/0' &&
23 ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' &&
24 #if $masks
25 info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff') &&
26 echo '>showinf -nopix -nometa -noflat \$image' &&
27 echo "\$info\n" &&
28 masks_info=\$(showinf -nopix -nometa -noflat '$masks') &&
29 echo '>showinf -nopix -nometa -noflat \$masks' &&
30 echo "\$masks_info\n" &&
31 masks_n_resolutions=\$(echo "\$masks_info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) &&
32 if [ -z \$masks_n_resolutions ]; then
33 n_resolutions=\$(echo "\$info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) &&
34 pyramid_scale=1 &&
35 if [ -z "\$n_resolutions" ]; then
36 echo "Warning: Failded to retrieve the number of pyramid resolutions. Set pyramid resolutions to 4 and scale to 2!";
37 n_resolutions=4;
38 pyramid_scale=2;
39 else
40 echo "Found the number of pyramid resolutions: \$n_resolutions";
41 if [ "\$n_resolutions" -gt 1 ]; then
42 sizeX0=\$(echo "\$info" | grep '^\s*sizeX\[0\]\s*=' -m1 | cut -d'=' -f2 | xargs) ;
43 sizeX1=\$(echo "\$info" | grep '^\s*sizeX\[1\]\s*=' -m1 | cut -d'=' -f2 | xargs) ;
44 if [ "\$sizeX0" -gt 0 ] && [ "\$sizeX1" -gt 0 ]; then
45 pyramid_scale=\$(((\$sizeX0 + \$sizeX1 / 2 ) / \$sizeX1));
46 echo "Calculate pyramid scale: \$sizeX0 / \$sizeX1 ~= \$pyramid_scale.";
47 else
48 pyramid_scale=2;
49 echo "Warning: Failed to calculate the pyramid scale; set it to 2!";
50 fi;
51 fi;
52 fi;
53 tile_info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff' | grep '^\s*Tile\ssize\s*=' -m1);
54 tile_x=\$(echo "\$tile_info" | cut -d' ' -f4);
55 tile_y=\$(echo "\$tile_info" | cut -d' ' -f6);
56 convert_cmd="bfconvert -pyramid-resolutions \$n_resolutions -pyramid-scale \$pyramid_scale -noflat -tilex \$tile_x -tiley \$tile_y '$masks' '${output.files_path}/A/0/masks01.ome.tiff'";
57 echo "\n>\$convert_cmd";
58 eval \$convert_cmd;
59 masks_info_new=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff');
60 echo "\n>showinf -nopix -nometa -noflat '${output.files_path}/A/0/masks01.ome.tiff'";
61 echo "\$masks_info_new\n";
62 else
63 ln -sf '$masks' '${output.files_path}/A/0/masks01.ome.tiff';
64 fi &&
65 #end if
66 python '$__tool_directory__/@TOOL_ID@.py'
67 --inputs '$inputs'
68 --output '${output.files_path}'
69 --image '${output.files_path}/A/0/image01.ome.tiff'
70 #if $masks
71 --masks '${output.files_path}/A/0/masks01.ome.tiff'
72 #end if
73 #if $do_phenotyping.phenotyping_choice
74 --anndata '$anndata'
75 #end if
76 &&
77 cp -R '$__tool_directory__/static' '${output.files_path}' &&
78 cp '$__tool_directory__/index.html' '$output';
79
80 ]]>
81 </command>
82 </xml>
83
84 </macros>