Mercurial > repos > bgruening > cp_measure_object_size_shape

annotate 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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1 <tool id="cp_measure_object_size_shape" name="MeasureObjectSizeShape" version="@CP_VERSION@">
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2 <description>measure area and shape features of identified objects</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="py_requirements"/>
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9 <expand macro="cmd_modules" />
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11 <configfiles>
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12 <inputs name="inputs" />
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13 <configfile name="script_file">
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14 import json
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15 import sys
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16 import os
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18 FOURSPACES=@SPACES@
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20 input_json_path = sys.argv[1]
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21 input_pipeline= sys.argv[2]
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23 params = json.load(open(input_json_path, "r"))
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26 def writemoss():
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27 _str = "\nMeasureObjectSizeShape:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:1|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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29 for obj in params['rpt_object']:
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30 _str += FOURSPACES + "Select objects to measure:%s\n" % obj['objects_to_measure']
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32 _str += FOURSPACES + "Calculate the Zernike features?:%s\n" % params['zernike_feature']
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34 return _str
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36 with open(input_pipeline) as fin:
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37 lines = fin.readlines()
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39 k, v = lines[4].strip().split(':')
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41 module_count = int(v)
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42 new_count = module_count + 1
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43 lines[4] = k + ":%d\n" % new_count
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44 with open("output.cppipe", "w") as f:
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45 f.writelines(lines)
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46 f.write(writemoss())
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47
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48 f.close()
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49 </configfile>
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50 </configfiles>
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52 <inputs>
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53 <expand macro="input_pipeline_param" />
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54 <repeat name="rpt_object" title="new object" min="1">
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55 <param name="objects_to_measure" label="Enter the name of the object to measure" type="text">
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56 <expand macro="text_validator" />
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57 </param>
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58 </repeat>
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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.">
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60
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61 <option value="Yes">Yes</option>
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62 <option value="No">No</option>
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63 </param>
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64 </inputs>
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65
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66 <outputs>
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67 <expand macro="output_pipeline_param" />
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68 </outputs>
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70 <tests>
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71 <test>
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72 <expand macro="test_input_pipeline_param" />
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73 <repeat name="rpt_object">
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74 <param name="objects_to_measure" value="Nuclei" />
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75 </repeat>
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76 <repeat name="rpt_object">
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77 <param name="objects_to_measure" value="Nucleoli" />
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78 </repeat>
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79 <param name="zernike_feature" value="Yes" />
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80 <expand macro="test_out_file" file="measure_object_size_shape.cppipe" />
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81 </test>
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82 </tests>
3
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83 <help>
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84 <![CDATA[
0
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85
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86 .. class:: infomark
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87
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88 **What it does**
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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.
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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.
5c9549983af8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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93
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94 @COMMON_HELP@
5c9549983af8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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95 ]]>
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96 </help>
5c9549983af8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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97 <expand macro="citations" />
0
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98
eba2ec72f967 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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99 </tool>