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annotate macros.xml @ 1:6d3851ac885f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 07:47:33 -0400
parents 2005f8058036
children
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1 <macros>
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2 <token name="@CP_VERSION@">3.1.9</token>
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3 <token name="@PY_VERSION@">3.7</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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2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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10 **Input**
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12 Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
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14 .. class:: infomark
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2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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16 **Output**
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2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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18 The input CellProfiler pipeline file *(.cppipe)* in addition to the settings of this module.
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20 .. class:: warningmark
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22 **IMPORTANT**
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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
1
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28 <xml name="output_pipeline_param">
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29 <data name="output_pipeline" from_work_dir="output.cppipe" format="txt"/>
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30 </xml>
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1
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33 <xml name="input_pipeline_param">
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34 <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/>
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35 </xml>
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38 <xml name="cp_requirements">
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39 <requirements>
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40 <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement>
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41 </requirements>
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42 </xml>
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2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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45 <xml name="py_requirements">
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46 <requirements>
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47 <requirement type="package" version="@PY_VERSION@">python</requirement>
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48 </requirements>
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49 </xml>
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2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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52 <xml name="citations">
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53 <citations>
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54 <citation type="bibtex">
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55 @article{McQuin_2018,
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56 title = {CellProfiler 3.0: Next-generation image processing for biology},
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57 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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58 year = {2018},
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59 volume = {16(7):e2005970},
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60 DOI = {10.1371/journal.pbio.2005970},
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61 journal = {PLoS Biol.},
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62 url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970},
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63 }
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64 </citation>
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65 </citations>
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66 </xml>
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67
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69 <xml name="cmd_modules">
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70 <command detect_errors="aggressive">
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71 <![CDATA[
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72 python '$script_file' '$inputs' '$input_pipeline'
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73 ]]>
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74 </command>
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75 </xml>
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78 <xml name="text_validator">
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79 <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>
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80 </xml>
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81
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83 <xml name="test_input_pipeline_param">
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84 <param name="input_pipeline" value="common.cppipe" />
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85 </xml>
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86
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87
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88 <xml name="test_out_file" token_file="common.cppipe">
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89 <output name="output_pipeline" ftype="txt" file="@FILE@" lines_diff="0"/>
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90 </xml>
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91
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92 </macros>
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93