annotate macros.xml @ 3:7ee5b6f7533e draft default tip

planemo upload for repository https://github.com/labsyspharm/basic-illumination commit 384bcb73bece365356d3aaaebffd545b01a35aa1
author goeckslab
date Wed, 21 Feb 2024 23:18:46 +0000
parents acc6f509968c
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
1
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5 <container type="docker">labsyspharm/basic-illumination:@TOOL_VERSION@</container>
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6 </requirements>
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7 </xml>
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8
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9 <xml name="version_cmd">
1
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10 <version_command>echo @TOOL_VERSION@</version_command>
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11 </xml>
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12 <xml name="citations">
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13 <citations>
1
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14 <citation type="doi">10.1038/ncomms14836</citation>
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15 </citations>
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16 </xml>
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17
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18 <token name="@TOOL_VERSION@">1.1.1</token>
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19 <token name="@VERSION_SUFFIX@">2</token>
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20 <token name="@PROFILE@">19.01</token>
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21 <token name="@CMD_BEGIN@"><![CDATA[
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22 ## if ImageJ isn't already present, this is the docker-dependency version
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23 ## as such, ImageJ needs to be registered as a global executable on $PATH
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24
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25 if ! [ -x "\$(which ImageJ)" ]; then
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26 ln -sf "\$(which ImageJ-linux64)" "ImageJ";
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27 export PATH="\$PATH:\$(pwd)/";
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28 fi &&
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30 BASIC_SCRIPT="" &&
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31 if [ -f "/opt/fiji/imagej_basic_ashlar.py" ]; then
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32 export BASIC_SCRIPT="/opt/fiji/imagej_basic_ashlar.py";
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33 else
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34 export BASIC_SCRIPT="${__tool_directory__}/imagej_basic_ashlar.py";
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35 fi &&
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37 ImageJ --ij2 --headless --run \$BASIC_SCRIPT
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38 ]]></token>
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39 </macros>