Mercurial > repos > bgruening > cp_measure_image_area_occupied

comparison macros.xml @ 3:7a08edbc790e 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 07:56:06 -0400
parents 534ed7b8ca34
children
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2:534ed7b8ca34 3:7a08edbc790e
23 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. 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> 25 </token>
26 26
27 27
28 <xml name="output_pipeline_macro"> 28 <xml name="output_pipeline_param">
29 <data name="out_file" from_work_dir="output" format="txt"/> 29 <data name="output_pipeline" from_work_dir="output.cppipe" format="txt"/>
30 </xml> 30 </xml>
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32 32
33 <xml name="input_pipeline_macro"> 33 <xml name="input_pipeline_param">
34 <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/> 34 <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/>
35 </xml> 35 </xml>
36 36
37 37
38 <xml name="cp_requirements"> 38 <xml name="cp_requirements">
79 <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>
80 </xml> 80 </xml>
81 81
82 82
83 <xml name="test_input_pipeline_param"> 83 <xml name="test_input_pipeline_param">
84 <param name="input_pipeline" value="common.txt" /> 84 <param name="input_pipeline" value="common.cppipe" />
85 </xml> 85 </xml>
86 86
87 87
88 <xml name="test_out_file" token_file="common.txt"> 88 <xml name="test_out_file" token_file="common.cppipe">
89 <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/> 89 <output name="output_pipeline" ftype="txt" file="@FILE@" lines_diff="0"/>
90 </xml> 90 </xml>
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92
93 <xml name="help" token_module="common">
94 <help>
95 This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
96
97 Input: existing pipeline file
98
99 Output: new pipeline file
100
101 Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
102 </help>
103 </xml>
104 </macros> 92 </macros>
105 93