Mercurial > repos > bgruening > cp_measure_object_size_shape

comparison measure_object_size_shape.xml @ 3:5c9549983af8 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 07:54:52 -0400
parents 5ef26243a4a5
children acf3aa487283
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2:5ef26243a4a5 3:5c9549983af8
1 <tool id="cp_measure_object_size_shape" name="MeasureObjectSizeShape" version="@CP_VERSION@"> 1 <tool id="cp_measure_object_size_shape" name="MeasureObjectSizeShape" version="@CP_VERSION@">
2 <description>measure area and shape features of identified objects</description> 2 <description>measure area and shape features of identified objects</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <expand macro="py_requirements"/> 8 <expand macro="py_requirements"/>
9 <expand macro="cmd_modules" /> 9 <expand macro="cmd_modules" />
10 10
11 <configfiles> 11 <configfiles>
12 <inputs name="inputs" /> 12 <inputs name="inputs" />
39 k, v = lines[4].strip().split(':') 39 k, v = lines[4].strip().split(':')
40 40
41 module_count = int(v) 41 module_count = int(v)
42 new_count = module_count + 1 42 new_count = module_count + 1
43 lines[4] = k + ":%d\n" % new_count 43 lines[4] = k + ":%d\n" % new_count
44 with open("output", "w") as f: 44 with open("output.cppipe", "w") as f:
45 f.writelines(lines) 45 f.writelines(lines)
46 f.write(writemoss()) 46 f.write(writemoss())
47 47
48 f.close() 48 f.close()
49 </configfile> 49 </configfile>
50 </configfiles> 50 </configfiles>
51 51
52 <inputs> 52 <inputs>
53 <expand macro="input_pipeline_macro" /> 53 <expand macro="input_pipeline_param" />
54 <repeat name="rpt_object" title="Add another object"> 54 <repeat name="rpt_object" title="new object" min="1">
55 <param name="objects_to_measure" label="Select objects to measure" type="text" > 55 <param name="objects_to_measure" label="Enter the name of the object to measure" type="text">
56 <expand macro="text_validator" /> 56 <expand macro="text_validator" />
57 </param> 57 </param>
58 </repeat> 58 </repeat>
59 <param name="zernike_feature" type="select" display="radio" label="Calculate the Zernike features?"> 59 <param name="zernike_feature" type="select" display="radio" label="Calculate the Zernike features?" help="Select 'Yes' to calculate the Zernike shape features. Because the first 10 Zernike polynomials (from order 0 to order 9) are calculated, this operation can be time-consuming if the image contains a lot of objects. Select 'No' if you are measuring 3D objects with this module.">
60 <option value="Yes">Yes</option> 60
61 <option value="No">No</option> 61 <option value="Yes">Yes</option>
62 </param> 62 <option value="No">No</option>
63 </param>
63 </inputs> 64 </inputs>
64 65
65 <outputs> 66 <outputs>
66 <expand macro="output_pipeline_macro" /> 67 <expand macro="output_pipeline_param" />
67 </outputs> 68 </outputs>
68 69
69 <tests> 70 <tests>
70 <test> 71 <test>
71 <expand macro="test_input_pipeline_param" /> 72 <expand macro="test_input_pipeline_param" />
74 </repeat> 75 </repeat>
75 <repeat name="rpt_object"> 76 <repeat name="rpt_object">
76 <param name="objects_to_measure" value="Nucleoli" /> 77 <param name="objects_to_measure" value="Nucleoli" />
77 </repeat> 78 </repeat>
78 <param name="zernike_feature" value="Yes" /> 79 <param name="zernike_feature" value="Yes" />
79 <expand macro="test_out_file" file="measure_object_size_shape.txt" /> 80 <expand macro="test_out_file" file="measure_object_size_shape.cppipe" />
80 </test> 81 </test>
81 </tests> 82 </tests>
83 <help>
84 <![CDATA[
82 85
83 <expand macro="help" module="MeasureObjectSizeShape" /> 86 .. class:: infomark
84 <expand macro="citations" /> 87
88 **What it does**
89
90 Given an image with identified objects (e.g., nuclei or cells), this module extracts area and shape features of each one. Note that these features are only reliable for objects that are completely inside the image borders, so you may wish to exclude objects touching the edge of the image using Identify settings for 2D objects, or by applying *FilterObjects* downstream.
91
92 The display window for this module shows per-image aggregates for the per-object measurements. If you want to view the per-object measurements themselves, you will need to use an *Export* module to export them, or use *DisplayDataOnImage* to display the object measurements of choice overlaid on an image of choice.
93
94 @COMMON_HELP@
95 ]]>
96 </help>
97 <expand macro="citations" />
85 98
86 </tool> 99 </tool>