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comparison main_macros.xml @ 2:764f6363e2a9 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit a6714d257c45c11d999c7cc2241c89da193cae15
author goeckslab
date Fri, 10 May 2024 17:21:02 +0000
parents 8097f9124f87
children 80102785f5ff
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1:8097f9124f87 2:764f6363e2a9
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.0.4</token> 2 <token name="@TOOL_VERSION@">1.0.4</token>
3 <token name="@VERSION_SUFFIX@">3</token> 3 <token name="@VERSION_SUFFIX@">4</token>
4 <token name="@PROFILE@">20.01</token> 4 <token name="@PROFILE@">20.01</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@</container> 8 <container type="docker">quay.io/goeckslab/vitessce:@TOOL_VERSION@v2</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>
16 </xml> 16 </xml>
17 17
18 <xml name="vitessce_cmd" token_tool_id="vitessce_spatial"> 18 <xml name="vitessce_cmd" token_tool_id="vitessce_spatial">
19 <command detect_errors="aggressive"> 19 <command detect_errors="aggressive">
20 <![CDATA[ 20 <![CDATA[
21 export BF_MAX_MEM="\${GALAXY_MEMORY_MB}m" && 21 MAX_MEM=\${GALAXY_MEMORY_MB:-2000} &&
22 export BF_MAX_MEM="\$((\$MAX_MEM/2))m" &&
22 mkdir -p '${output.files_path}/A/0' && 23 mkdir -p '${output.files_path}/A/0' &&
23 ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' && 24 ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' &&
24 #if $masks 25 #if $masks
25 info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff') && 26 info=\$(showinf -nopix -nometa -noflat '${output.files_path}/A/0/image01.ome.tiff') &&
26 echo '>showinf -nopix -nometa -noflat \$image' && 27 echo '>showinf -nopix -nometa -noflat \$image' &&