Mercurial > repos > bgruening > cp_measure_image_quality
comparison macros.xml @ 2:4dcd464c22ff draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author | bgruening |
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date | Thu, 16 Apr 2020 05:33:18 -0400 |
parents | 26945c55ddff |
children | 08a2cf887a44 |
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1:e8a42b438de3 | 2:4dcd464c22ff |
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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 |