annotate macros.xml @ 0:b333df978624 draft

"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>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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5 <token name="@SPACES@">" "</token>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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6 <!-- four spaces needed for CP pipeline file -->
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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7 <token name="@COMMON_HELP@">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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8 .. class:: infomark
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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10 **Input**
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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12 Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
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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14 .. class:: infomark
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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16 **Output**
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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18 The input CellProfiler pipeline file *(.cppipe)* in addition to the settings of this module.
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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20 .. class:: warningmark
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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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.
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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25 </token>
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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27 <xml name="cp_requirements">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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28 <requirements>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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29 <requirement type="package" version="@TOOL_VERSION@">cellprofiler</requirement>
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30 </requirements>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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31 </xml>
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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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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34 <xml name="py_requirements">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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35 <requirements>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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36 <requirement type="package" version="@PY_VERSION@">python</requirement>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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37 </requirements>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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38 </xml>
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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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">
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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44 @article{McQuin_2018,
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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},
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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},
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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52 }
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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53 </citation>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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54 </citations>
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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55 </xml>
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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57 </macros>
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58