Mercurial > repos > perssond > basic_illumination

annotate basic_illumination.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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db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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1 <tool id="basic_illumination" name="BaSiC Illumination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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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fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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7 <expand macro="requirements"/>
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db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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8 <expand macro="version_cmd"/>
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10 <command detect_errors="exit_code"><![CDATA[
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db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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11 ln -s '$in_files' '${in_files.name}' &&
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12
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db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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13 #set $outname = str('$in_files.name').replace('.ome.tiff','')
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15 @CMD_BEGIN@
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17 "filename='${in_files.name}',output_dir='.',experiment_name='output'";
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18
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19 ]]></command>
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21 <inputs>
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22 <param type="data" name="in_files" format="tiff" label="Raw Cycle Images"/>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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23 </inputs>
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24
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25 <outputs>
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26 <data format="tiff" name="output_dfp" label="${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"/>
fd8dfd64f25e "planemo upload for repository https://github.com/ohsu-comp-bio/basic-illumination commit a8d2367c8c66eecfc2586a593acc8547a7f8611c-dirty"
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28 </outputs>
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db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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29 <tests>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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30 <test>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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31 <param name="in_files" value="test.tiff" />
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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32 <output name="output_dfp" ftype="tiff">
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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33 <assert_contents>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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34 <has_size value="350000" delta="50000" />
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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35 </assert_contents>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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36 </output>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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37 <output name="output_ffp" ftype="tiff">
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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38 <assert_contents>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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39 <has_size value="350000" delta="50000" />
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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40 </assert_contents>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
parents: 0
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41 </output>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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42 </test>
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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43 </tests>
0
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44 <help><![CDATA[
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45 -------------------
0
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46 basic-illumination
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47 -------------------
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48
1
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goeckslab
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49 **ImageJ BaSiC shading correction for use with Ashlar**
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
goeckslab
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50 **basic-illumination** can read image data directly from BioFormats-supported microscope
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goeckslab
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51 vendor file formats as well as a directory of plain TIFF files. Output includes a flat field and
db20f09300bd planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761
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52 dark field image per input file.
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53 ]]></help>
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54 <expand macro="citations" />
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55 </tool>