Mercurial > repos > bgruening > cp_measure_object_intensity
comparison measure_object_intensity.xml @ 0:1373b765c8f9 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author | bgruening |
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date | Thu, 26 Mar 2020 17:07:39 -0400 |
parents | |
children | ae299f107121 |
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-1:000000000000 | 0:1373b765c8f9 |
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1 <tool id="cp_measure_object_intensity" name="MeasureObjectIntensity" version="@CP_VERSION@"> | |
2 <description>measures several intensity features for identified objects</description> | |
3 | |
4 <macros><import>macros.xml</import></macros> | |
5 | |
6 <expand macro="py_requirements"/> | |
7 <expand macro="cmd_modules" /> | |
8 | |
9 <configfiles> | |
10 <inputs name="inputs" /> | |
11 <configfile name="script_file"> | |
12 import json | |
13 import sys | |
14 import os | |
15 | |
16 FOURSPACES=@SPACES@ | |
17 | |
18 input_json_path = sys.argv[1] | |
19 input_pipeline= sys.argv[2] | |
20 | |
21 params = json.load(open(input_json_path, "r")) | |
22 | |
23 def writemoi(): | |
24 _str = "\nMeasureObjectIntensity:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count | |
25 | |
26 hidden = len(params['rpt_image']) | |
27 | |
28 _str += FOURSPACES + "Hidden:%d\n" % hidden | |
29 | |
30 for img in params['rpt_image']: | |
31 _str += FOURSPACES + "Select an image to measure:%s\n" % img['image_to_measure'] | |
32 | |
33 for obj in params['rpt_object']: | |
34 _str += FOURSPACES + "Select objects to measure:%s\n" % obj['objects_to_measure'] | |
35 | |
36 return _str | |
37 | |
38 | |
39 with open(input_pipeline) as fin: | |
40 lines = fin.readlines() | |
41 | |
42 k, v = lines[4].strip().split(':') | |
43 | |
44 module_count = int(v) | |
45 new_count = module_count + 1 | |
46 lines[4] = k + ":%d\n" % new_count | |
47 with open("output", "w") as f: | |
48 f.writelines(lines) | |
49 f.write(writemoi()) | |
50 | |
51 f.close() | |
52 </configfile> | |
53 </configfiles> | |
54 | |
55 <inputs> | |
56 <expand macro="input_pipeline_macro" /> | |
57 <repeat name="rpt_image" title="Add another image"> | |
58 <param name="image_to_measure" label="Select an image to measure" type="text"> | |
59 <expand macro="text_validator" /> | |
60 </param> | |
61 </repeat> | |
62 | |
63 <repeat name="rpt_object" title="Add another object"> | |
64 <param name="objects_to_measure" label="Select objects to measure" type="text" > | |
65 <expand macro="text_validator" /> | |
66 </param> | |
67 </repeat> | |
68 </inputs> | |
69 | |
70 <outputs> | |
71 <expand macro="output_pipeline_macro" /> | |
72 </outputs> | |
73 | |
74 <tests> | |
75 <test> | |
76 <expand macro="test_input_pipeline_param" /> | |
77 <repeat name="rpt_image"> | |
78 <param name="image_to_measure" value="DNA"/> | |
79 </repeat> | |
80 <repeat name="rpt_object" > | |
81 <param name="objects_to_measure" value="Nuclei" /> | |
82 </repeat> | |
83 <expand macro="test_out_file" file="measure_object_intensity.txt" /> | |
84 </test> | |
85 </tests> | |
86 | |
87 <expand macro="help" module="MeasureObjectIntensity" /> | |
88 <expand macro="citations" /> | |
89 | |
90 </tool> |