Mercurial > repos > bgruening > cp_cellprofiler4

annotate macros.xml @ 0:b333df978624 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
author bgruening
date Mon, 25 Apr 2022 18:30:59 +0000
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children f0656d0f2a4d
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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1 <macros>
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2 <token name="@TOOL_VERSION@">4.2.1</token>
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3 <token name="@PY_VERSION@">3.8</token>
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4 <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token>
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5 <token name="@SPACES@">" "</token>
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6 <!-- four spaces needed for CP pipeline file -->
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7 <token name="@COMMON_HELP@">
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8 .. class:: infomark
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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10 **Input**
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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12 Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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14 .. class:: infomark
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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16 **Output**
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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18 The input CellProfiler pipeline file *(.cppipe)* in addition to the settings of this module.
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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20 .. class:: warningmark
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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22 **IMPORTANT**
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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24 The first tool in a CellProfiler workflow has to be **Starting modules** and the last one **CellProfiler**. You can also execute the entire pipeline with the final CellProfiler tool, in which you feed in the images you want to process as well.
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25 </token>
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27 <xml name="cp_requirements">
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28 <requirements>
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29 <requirement type="package" version="@TOOL_VERSION@">cellprofiler</requirement>
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30 </requirements>
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31 </xml>
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34 <xml name="py_requirements">
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35 <requirements>
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36 <requirement type="package" version="@PY_VERSION@">python</requirement>
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37 </requirements>
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38 </xml>
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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41 <xml name="citations">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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42 <citations>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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43 <citation type="bibtex">
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44 @article{McQuin_2018,
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45 title = {CellProfiler 3.0: Next-generation image processing for biology},
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46 author = {McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE},
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47 year = {2018},
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48 volume = {16(7):e2005970},
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49 DOI = {10.1371/journal.pbio.2005970},
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50 journal = {PLoS Biol.},
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51 url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970},
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52 }
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53 </citation>
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54 </citations>
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55 </xml>
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57 </macros>
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58