Mercurial > repos > perssond > basic_illumination
annotate macros.xml @ 3:7ee5b6f7533e draft default tip
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit 384bcb73bece365356d3aaaebffd545b01a35aa1
author | goeckslab |
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date | Wed, 21 Feb 2024 23:18:46 +0000 |
parents | acc6f509968c |
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rev | line source |
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fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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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
parents:
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2 <macros> |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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3 <xml name="requirements"> |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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4 <requirements> |
1
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents:
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5 <container type="docker">labsyspharm/basic-illumination:@TOOL_VERSION@</container> |
0
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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6 </requirements> |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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7 </xml> |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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8 |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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9 <xml name="version_cmd"> |
1
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents:
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10 <version_command>echo @TOOL_VERSION@</version_command> |
0
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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11 </xml> |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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12 <xml name="citations"> |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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13 <citations> |
1
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents:
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14 <citation type="doi">10.1038/ncomms14836</citation> |
0
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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15 </citations> |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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16 </xml> |
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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17 |
3
7ee5b6f7533e
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit 384bcb73bece365356d3aaaebffd545b01a35aa1
goeckslab
parents:
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18 <token name="@TOOL_VERSION@">1.1.1</token> |
7ee5b6f7533e
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit 384bcb73bece365356d3aaaebffd545b01a35aa1
goeckslab
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19 <token name="@VERSION_SUFFIX@">2</token> |
1
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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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:
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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
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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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24 |
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
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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
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27 export PATH="\$PATH:\$(pwd)/"; |
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents:
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28 fi && |
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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29 |
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:
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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
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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:
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33 else |
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents:
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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:
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35 fi && |
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents:
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36 |
db20f09300bd
planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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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:
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38 ]]></token> |
0
fd8dfd64f25e
"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
perssond
parents:
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39 </macros> |