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comparison macros.xml @ 0:644e5e32a83c draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:03:00 +0000
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-1:000000000000 0:644e5e32a83c
1 <macros>
2 <token name="@CP_VERSION@">3.1.9</token>
3 <token name="@PY_VERSION@">3.7</token>
4 <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token>
5 <token name="@SPACES@">" "</token>
6 <!-- four spaces needed for CP pipeline file -->
7 <token name="@COMMON_HELP@">
8 .. class:: infomark
9
10 **Input**
11
12 Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
13
14 .. class:: infomark
15
16 **Output**
17
18 The input CellProfiler pipeline file *(.cppipe)* in addition to the settings of this module.
19
20 .. class:: warningmark
21
22 **IMPORTANT**
23
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.
25 </token>
26
27
28 <xml name="output_pipeline_param">
29 <data name="output_pipeline" from_work_dir="output.cppipe" format="txt"/>
30 </xml>
31
32
33 <xml name="input_pipeline_param">
34 <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/>
35 </xml>
36
37
38 <xml name="cp_requirements">
39 <requirements>
40 <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement>
41 </requirements>
42 </xml>
43
44
45 <xml name="py_requirements">
46 <requirements>
47 <requirement type="package" version="@PY_VERSION@">python</requirement>
48 </requirements>
49 </xml>
50
51
52 <xml name="citations">
53 <citations>
54 <citation type="bibtex">
55 @article{McQuin_2018,
56 title = {CellProfiler 3.0: Next-generation image processing for biology},
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},
58 year = {2018},
59 volume = {16(7):e2005970},
60 DOI = {10.1371/journal.pbio.2005970},
61 journal = {PLoS Biol.},
62 url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970},
63 }
64 </citation>
65 </citations>
66 </xml>
67
68
69 <xml name="cmd_modules">
70 <command detect_errors="aggressive">
71 <![CDATA[
72 python '$script_file' '$inputs' '$input_pipeline'
73 ]]>
74 </command>
75 </xml>
76
77
78 <xml name="text_validator">
79 <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>
80 </xml>
81
82
83 <xml name="test_input_pipeline_param">
84 <param name="input_pipeline" value="common.cppipe" />
85 </xml>
86
87
88 <xml name="test_out_file" token_file="common.cppipe">
89 <output name="output_pipeline" ftype="txt" file="@FILE@" lines_diff="0"/>
90 </xml>
91
92 </macros>
93