Mercurial > repos > goeckslab > vitessce_spatial

comparison main_macros.xml @ 1:4bf852448b5d draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 130ef7e8ae6cab35866b72617e53d35acc11475a
author goeckslab
date Wed, 28 Feb 2024 20:52:55 +0000
parents 9f60ef2d586e
children 4f43e11fb3c9
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0:9f60ef2d586e 1:4bf852448b5d
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@">0</token> 3 <token name="@VERSION_SUFFIX@">3</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@</container>
14 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 14 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
15 </stdio> 15 </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> 19 <command detect_errors="aggressive">
20 <![CDATA[ 20 <![CDATA[
21 export BF_MAX_MEM="\${GALAXY_MEMORY_MB}m" && 21 export BF_MAX_MEM="\${GALAXY_MEMORY_MB}m" &&
22 mkdir -p '${output.files_path}/A/0' && 22 mkdir -p '${output.files_path}/A/0' &&
23 ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' && 23 ln -sf '$image' '${output.files_path}/A/0/image01.ome.tiff' &&
24 #if $masks 24 #if $masks
68 --output '${output.files_path}' 68 --output '${output.files_path}'
69 --image '${output.files_path}/A/0/image01.ome.tiff' 69 --image '${output.files_path}/A/0/image01.ome.tiff'
70 #if $masks 70 #if $masks
71 --masks '${output.files_path}/A/0/masks01.ome.tiff' 71 --masks '${output.files_path}/A/0/masks01.ome.tiff'
72 #end if 72 #end if
73 #if $do_phenotyping.phenotyping_choice 73 #if $do_phenotyping.phenotyping_choice == 'add_h5ad'
74 --anndata '$anndata' 74 --anndata '$anndata'
75 #end if 75 #end if
76 && 76 &&
77 cp -R '$__tool_directory__/static' '${output.files_path}' && 77 cp -R '$__tool_directory__/static' '${output.files_path}' &&
78 cp '$__tool_directory__/index.html' '$output'; 78 cp '$__tool_directory__/index.html' '$output';