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annotate basic_illumination.xml @ 0:fd8dfd64f25e draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
author perssond
date Fri, 12 Mar 2021 00:13:46 +0000
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children db20f09300bd
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fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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1 <tool id="basic_illumination" name="BaSiC Illumination" version="@VERSION@.3" profile="17.09">
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2 <description>ImageJ BaSiC shading correction for use with Ashlar</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6
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7 <expand macro="requirements"/>
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8 @VERSION_CMD@
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10 <command detect_errors="exit_code"><![CDATA[
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11 ln -s $in_files "${in_files.name}" &&
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12
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13 #set $outname = str($in_files.name).replace('.ome.tiff','')
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14
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15 @CMD_BEGIN@
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16
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17 "filename='${in_files.name}',output_dir='.',experiment_name='output'";
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18
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19 ]]></command>
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21 <inputs>
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22 <param type="data" name="in_files" format="tiff" label="Raw Cycle Images"/>
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23 </inputs>
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24
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25 <outputs>
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26 <data format="tiff" name="output_dfp" label="${tool.name} on ${on_string}: DFP" from_work_dir="output-dfp.tif"/>
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27 <data format="tiff" name="output_ffp" label="${tool.name} on ${on_string}: FFP" from_work_dir="output-ffp.tif"/>
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28 </outputs>
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29
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30 <help><![CDATA[
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31 basic-illumination
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32 ImageJ BaSiC shading correction for use with Ashlar
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33
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34 Running as a Docker container
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35 Create a container:
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37 docker run -it -v /path/to/data:/data labsyspharm/basic-illumination bash
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38 (where /path/to/data is the data directory on your local machine. Your data will be mapped to /data inside the container)
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39
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40 Once inside the container, do ls /data to ensure your data is there, followed by
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41
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42 ImageJ-linux64 --ij2 --headless --run imagej_basic_ashlar.py \
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43 "filename='/data/input.ome.tiff',output_dir='/data/',experiment_name='my_experiment'"
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44 for each input.ome.tiff in your data directory.
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46 OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/basic-illumination
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47 Conda Package Available From: https://anaconda.org/ohsu-comp-bio/basic-illumination
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>