Mercurial > repos > bgruening > cp_identify_primary_objects

comparison macros.xml @ 0:6d011deed7cb draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 20:04:27 +0000
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children f42416baea78
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-1:000000000000 0:6d011deed7cb
1 <macros>
2 <token name="@CP_VERSION@">3.1.9</token>
3 <token name="@PY_VERSION@">2.7.16</token>
4 <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token>
5
6 <token name="@SPACES@">" "</token> <!-- four spaces needed for CP pipeline file -->
7
8 <xml name="output_pipeline_macro">
9 <data name="out_file" from_work_dir="output" format="txt" label="Output pipeline" />
10 </xml>
11
12 <xml name="input_pipeline_macro">
13 <param name="input_pipeline" type="data" format="data" label="Pipeline to select"/>
14 </xml>
15
16 <xml name="cp_requirements">
17 <requirements>
18 <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement>
19 </requirements>
20 </xml>
21
22 <xml name="py_requirements">
23 <requirements>
24 <requirement type="package" version="@PY_VERSION@">python</requirement>
25 </requirements>
26 </xml>
27
28 <xml name="citations">
29 <citations>
30 <citation type="bibtex">
31 @misc{galaxytoolscellprofiler,
32 author = {Sun, Yi},
33 year = {2020},
34 title = {Cellprofiler Galaxy tools},
35 publisher = {Github},
36 journal = {Github repository},
37 url = {https://github.com/bgruening/galaxytools/tools/cellrprofiler},
38 }
39 </citation>
40 </citations>
41 </xml>
42
43 <xml name="cmd_modules">
44 <command detect_errors="aggressive"><![CDATA[
45 python '$script_file' '$inputs' '$input_pipeline'
46 ]]></command>
47 </xml>
48
49 <xml name="text_validator">
50 <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>
51 </xml>
52
53 <xml name="test_input_pipeline_param">
54 <param name="input_pipeline" value="common.txt" />
55 </xml>
56
57 <xml name="test_out_file" token_file="common.txt">
58 <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/>
59 </xml>
60
61 <xml name="help" token_module="common">
62 <help>
63 This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
64
65 Input: existing pipeline file
66
67 Output: new pipeline file
68
69 Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
70 </help>
71 </xml>
72 </macros>
73