Mercurial > repos > bgruening > cp_measure_image_area_occupied
comparison measure_image_area_occupied.xml @ 3:7a08edbc790e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author | bgruening |
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date | Mon, 11 May 2020 07:56:06 -0400 |
parents | 534ed7b8ca34 |
children | 91e03287f285 |
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2:534ed7b8ca34 | 3:7a08edbc790e |
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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" /> |
13 <configfile name="script_file"> | 13 <configfile name="script_file"> |
14 import json | 14 import json |
15 import sys | 15 import sys |
16 import os | 16 import os |
17 | 17 |
18 FOURSPACES=@SPACES@ | 18 FOURSPACES=@SPACES@ |
38 _str += FOURSPACES + "Select objects to measure:%s\n" % area['con_area']['objects_to_measure'] | 38 _str += FOURSPACES + "Select objects to measure:%s\n" % area['con_area']['objects_to_measure'] |
39 _str += FOURSPACES + "Select a binary image to measure:None\n" | 39 _str += FOURSPACES + "Select a binary image to measure:None\n" |
40 else: | 40 else: |
41 _str += FOURSPACES + "Select objects to measure:None\n" | 41 _str += FOURSPACES + "Select objects to measure:None\n" |
42 _str += FOURSPACES + "Select a binary image to measure:%s\n" % area['con_area']['image_to_measure'] | 42 _str += FOURSPACES + "Select a binary image to measure:%s\n" % area['con_area']['image_to_measure'] |
43 | 43 |
44 return _str | 44 return _str |
45 | 45 |
46 | 46 |
47 with open(input_pipeline) as fin: | 47 with open(input_pipeline) as fin: |
48 lines = fin.readlines() | 48 lines = fin.readlines() |
50 k, v = lines[4].strip().split(':') | 50 k, v = lines[4].strip().split(':') |
51 | 51 |
52 module_count = int(v) | 52 module_count = int(v) |
53 new_count = module_count + 1 | 53 new_count = module_count + 1 |
54 lines[4] = k + ":%d\n" % new_count | 54 lines[4] = k + ":%d\n" % new_count |
55 with open("output", "w") as f: | 55 with open("output.cppipe", "w") as f: |
56 f.writelines(lines) | 56 f.writelines(lines) |
57 f.write(writemiao()) | 57 f.write(writemiao()) |
58 | 58 |
59 f.close() | 59 f.close() |
60 </configfile> | 60 </configfile> |
61 </configfiles> | 61 </configfiles> |
62 | 62 |
63 <inputs> | 63 <inputs> |
64 <expand macro="input_pipeline_macro" /> | 64 <expand macro="input_pipeline_param" /> |
65 <repeat name="rpt_area" title="Add another area"> | 65 <repeat name="rpt_area" title="new area" min="1"> |
66 <conditional name="con_area"> | 66 <conditional name="con_area"> |
67 <param name="objects_or_image" label="Measure the area occupied in a binary image, or in objects?" type="select"> | 67 <param name="objects_or_image" label="Measure the area occupied in a binary image, or in objects?" type="select"> |
68 <help> | |
69 <![CDATA[ | |
70 The area can be measured in two ways: | |
71 <br> - Binary Image: The area occupied by the foreground in a binary (black and white) image. | |
72 <br> - Objects: The area occupied by previously-identified objects. | |
73 ]]> | |
74 </help> | |
68 <option value="Binary image">Binary image</option> | 75 <option value="Binary image">Binary image</option> |
69 <option value="Objects">Objects</option> | 76 <option value="Objects">Objects</option> |
70 </param> | 77 </param> |
71 <when value="Objects"> | 78 <when value="Objects"> |
72 <param name="objects_to_measure" label="Select objects to measure" type="text"> | 79 <param name="objects_to_measure" label="Enter the name of the objects to measure" type="text"> |
73 <expand macro="text_validator" /> | 80 <expand macro="text_validator" /> |
74 </param> | 81 </param> |
75 </when> | 82 </when> |
76 <when value="Binary image"> | 83 <when value="Binary image"> |
77 <param name="image_to_measure" label="Select a binary image to measure" type="text"> | 84 <param name="image_to_measure" label="Enter the name of a binary image to measure" type="text"> |
78 <expand macro="text_validator" /> | 85 <expand macro="text_validator" /> |
79 </param> | 86 </param> |
80 </when> | 87 </when> |
81 </conditional> | 88 </conditional> |
82 </repeat> | 89 </repeat> |
83 </inputs> | 90 </inputs> |
84 | 91 |
85 <outputs> | 92 <outputs> |
86 <expand macro="output_pipeline_macro" /> | 93 <expand macro="output_pipeline_param" /> |
87 </outputs> | 94 </outputs> |
88 | 95 |
89 <tests> | 96 <tests> |
90 <test> | 97 <test> |
91 <expand macro="test_input_pipeline_param" /> | 98 <expand macro="test_input_pipeline_param" /> |
99 <conditional name="con_area"> | 106 <conditional name="con_area"> |
100 <param name="objects_or_image" value="Objects" /> | 107 <param name="objects_or_image" value="Objects" /> |
101 <param name="objects_to_measure" value="Nucleoli" /> | 108 <param name="objects_to_measure" value="Nucleoli" /> |
102 </conditional> | 109 </conditional> |
103 </repeat> | 110 </repeat> |
104 <expand macro="test_out_file" file="measure_image_area_occupied.txt" /> | 111 <expand macro="test_out_file" file="measure_image_area_occupied.cppipe" /> |
105 </test> | 112 </test> |
106 </tests> | 113 </tests> |
107 | 114 |
108 <expand macro="help" module="MeasureImageAreaOccupied" /> | 115 <help> |
116 <![CDATA[ | |
117 | |
118 .. class:: infomark | |
119 | |
120 **What it does** | |
121 This tool reports the sum of the areas and perimeters of the objects defined by one of the Identify modules, or the area of the foreground in a binary image. | |
122 If the input image has a mask (for example, created by the MaskImage module), the measurements made by this module will take the mask into account by ignoring the pixels outside the mask. | |
123 You can use this tool to measure the number of pixels above a given threshold if you precede it with thresholding performed by Threshold, and then select the binary image output by Threshold to be measured by this module. | |
124 | |
125 @COMMON_HELP@ | |
126 ]]> | |
127 </help> | |
128 | |
109 <expand macro="citations" /> | 129 <expand macro="citations" /> |
110 </tool> | 130 </tool> |