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comparison macros.xml @ 2:c956182d4e2c draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author bgruening
date Thu, 16 Apr 2020 05:32:53 -0400
parents 10257d6d545b
children 72a7f23f3a79
comparison
equal deleted inserted replaced
1:c0759ca34e20 2:c956182d4e2c
1 <macros> 1 <macros>
2 <token name="@CP_VERSION@">3.1.9</token> 2 <token name="@CP_VERSION@">3.1.9</token>
3 <token name="@PY_VERSION@">2.7.16</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> 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
5 9
6 <token name="@SPACES@">" "</token> <!-- four spaces needed for CP pipeline file --> 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
7 27
8 <xml name="output_pipeline_macro"> 28 <xml name="output_pipeline_macro">
9 <data name="out_file" from_work_dir="output" format="txt" label="Output pipeline" /> 29 <data name="out_file" from_work_dir="output" format="txt"/>
10 </xml> 30 </xml>
11 31
32
12 <xml name="input_pipeline_macro"> 33 <xml name="input_pipeline_macro">
13 <param name="input_pipeline" type="data" format="data" label="Pipeline to select"/> 34 <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/>
14 </xml> 35 </xml>
36
15 37
16 <xml name="cp_requirements"> 38 <xml name="cp_requirements">
17 <requirements> 39 <requirements>
18 <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement> 40 <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement>
19 </requirements> 41 </requirements>
20 </xml> 42 </xml>
21 43
44
22 <xml name="py_requirements"> 45 <xml name="py_requirements">
23 <requirements> 46 <requirements>
24 <requirement type="package" version="@PY_VERSION@">python</requirement> 47 <requirement type="package" version="@PY_VERSION@">python</requirement>
25 </requirements> 48 </requirements>
26 </xml> 49 </xml>
27 50
51
28 <xml name="citations"> 52 <xml name="citations">
29 <citations> 53 <citations>
30 <citation type="bibtex"> 54 <citation type="bibtex">
31 @misc{galaxytoolscellprofiler, 55 @article{McQuin_2018,
32 author = {Sun, Yi}, 56 title = {CellProfiler 3.0: Next-generation image processing for biology},
33 year = {2020}, 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},
34 title = {Cellprofiler Galaxy tools}, 58 year = {2018},
35 publisher = {Github}, 59 volume = {16(7):e2005970},
36 journal = {Github repository}, 60 DOI = {10.1371/journal.pbio.2005970},
37 url = {https://github.com/bgruening/galaxytools/tools/cellrprofiler}, 61 journal = {PLoS Biol.},
38 } 62 url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970},
63 }
39 </citation> 64 </citation>
40 </citations> 65 </citations>
41 </xml> 66 </xml>
42 67
68
43 <xml name="cmd_modules"> 69 <xml name="cmd_modules">
44 <command detect_errors="aggressive"><![CDATA[ 70 <command detect_errors="aggressive">
45 python '$script_file' '$inputs' '$input_pipeline' 71 <![CDATA[
46 ]]></command> 72 python '$script_file' '$inputs' '$input_pipeline'
73 ]]>
74 </command>
47 </xml> 75 </xml>
76
48 77
49 <xml name="text_validator"> 78 <xml name="text_validator">
50 <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator> 79 <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>
51 </xml> 80 </xml>
52 81
82
53 <xml name="test_input_pipeline_param"> 83 <xml name="test_input_pipeline_param">
54 <param name="input_pipeline" value="common.txt" /> 84 <param name="input_pipeline" value="common.txt" />
55 </xml> 85 </xml>
56 86
87
57 <xml name="test_out_file" token_file="common.txt"> 88 <xml name="test_out_file" token_file="common.txt">
58 <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/> 89 <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/>
59 </xml> 90 </xml>
60 91
92
61 <xml name="help" token_module="common"> 93 <xml name="help" token_module="common">
62 <help> 94 <help>
63 This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe) 95 This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
64 96
65 Input: existing pipeline file 97 Input: existing pipeline file
66 98
67 Output: new pipeline file 99 Output: new pipeline file
68 100
69 Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone. 101 Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
70 </help> 102 </help>
71 </xml> 103 </xml>
72 </macros> 104 </macros>
73 105