Mercurial > repos > perssond > basic_illumination

annotate macros.xml @ 1:db20f09300bd draft

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planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
author goeckslab
date Thu, 01 Sep 2022 22:46:21 +0000
parents fd8dfd64f25e
children acc6f509968c
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fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
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1 <?xml version="1.0"?>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
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2 <macros>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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3 <xml name="requirements">
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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4 <requirements>
1
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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5 <container type="docker">labsyspharm/basic-illumination:@TOOL_VERSION@</container>
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fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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6 </requirements>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
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7 </xml>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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8
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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9 <xml name="version_cmd">
1
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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10 <version_command>echo @TOOL_VERSION@</version_command>
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fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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11 </xml>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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12 <xml name="citations">
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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13 <citations>
1
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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14 <citation type="doi">10.1038/ncomms14836</citation>
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fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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15 </citations>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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16 </xml>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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17
1
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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18 <token name="@TOOL_VERSION@">1.0.3</token>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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19 <token name="@VERSION_SUFFIX@">0</token>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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20 <token name="@PROFILE@">19.01</token>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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21 <token name="@CMD_BEGIN@"><![CDATA[
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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22 ## if ImageJ isn't already present, this is the docker-dependency version
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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23 ## as such, ImageJ needs to be registered as a global executable on $PATH
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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25 if ! [ -x "\$(which ImageJ)" ]; then
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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26 ln -sf "\$(which ImageJ-linux64)" "ImageJ";
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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27 export PATH="\$PATH:\$(pwd)/";
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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28 fi &&
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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30 BASIC_SCRIPT="" &&
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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31 if [ -f "/opt/fiji/imagej_basic_ashlar.py" ]; then
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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32 export BASIC_SCRIPT="/opt/fiji/imagej_basic_ashlar.py";
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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33 else
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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34 export BASIC_SCRIPT="${__tool_directory__}/imagej_basic_ashlar.py";
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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35 fi &&
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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37 ImageJ --ij2 --headless --run \$BASIC_SCRIPT
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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38 ]]></token>
0
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
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39 </macros>