Mercurial > repos > bgruening > cp_measure_object_intensity
annotate measure_object_intensity.xml @ 3:b867e9317a06 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 07:49:31 -0400 |
parents | ae299f107121 |
children | 407925835dd9 |
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0
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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1 <tool id="cp_measure_object_intensity" name="MeasureObjectIntensity" version="@CP_VERSION@"> |
2
ae299f107121
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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2 <description>measure several intensity features for identified objects</description> |
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3 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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4 <macros> |
b867e9317a06
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5 <import>macros.xml</import> |
b867e9317a06
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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6 </macros> |
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7 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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8 <expand macro="py_requirements"/> |
1373b765c8f9
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9 <expand macro="cmd_modules" /> |
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11 <configfiles> |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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12 <inputs name="inputs" /> |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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13 <configfile name="script_file"> |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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14 import json |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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15 import sys |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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16 import os |
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17 |
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18 FOURSPACES=@SPACES@ |
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20 input_json_path = sys.argv[1] |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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21 input_pipeline= sys.argv[2] |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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22 |
1373b765c8f9
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23 params = json.load(open(input_json_path, "r")) |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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24 |
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25 def writemoi(): |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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26 _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 |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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27 |
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28 hidden = len(params['rpt_image']) |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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29 |
1373b765c8f9
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30 _str += FOURSPACES + "Hidden:%d\n" % hidden |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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31 |
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32 for img in params['rpt_image']: |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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33 _str += FOURSPACES + "Select an image to measure:%s\n" % img['image_to_measure'] |
1373b765c8f9
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34 |
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35 for obj in params['rpt_object']: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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36 _str += FOURSPACES + "Select objects to measure:%s\n" % obj['objects_to_measure'] |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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37 |
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38 return _str |
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39 |
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40 |
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41 with open(input_pipeline) as fin: |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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42 lines = fin.readlines() |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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43 |
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44 k, v = lines[4].strip().split(':') |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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45 |
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46 module_count = int(v) |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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47 new_count = module_count + 1 |
1373b765c8f9
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48 lines[4] = k + ":%d\n" % new_count |
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49 with open("output.cppipe", "w") as f: |
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50 f.writelines(lines) |
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51 f.write(writemoi()) |
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52 |
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53 f.close() |
b867e9317a06
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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54 </configfile> |
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55 </configfiles> |
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56 |
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57 <inputs> |
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58 <expand macro="input_pipeline_param" /> |
b867e9317a06
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59 <repeat name="rpt_image" title="new image" min="1"> |
b867e9317a06
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60 <param name="image_to_measure" label="Enter the name of an image to measure" type="text"> |
b867e9317a06
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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61 <expand macro="text_validator" /> |
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62 </param> |
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63 </repeat> |
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64 |
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65 <repeat name="rpt_object" title="new object" min="1"> |
b867e9317a06
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66 <param name="objects_to_measure" label="Enter the name of the objects to measure" type="text"> |
b867e9317a06
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67 <expand macro="text_validator" /> |
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68 </param> |
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69 </repeat> |
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70 </inputs> |
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71 |
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72 <outputs> |
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73 <expand macro="output_pipeline_param" /> |
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74 </outputs> |
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75 |
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76 <tests> |
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77 <test> |
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78 <expand macro="test_input_pipeline_param" /> |
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79 <repeat name="rpt_image"> |
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80 <param name="image_to_measure" value="DNA"/> |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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81 </repeat> |
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82 <repeat name="rpt_object"> |
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83 <param name="objects_to_measure" value="Nuclei" /> |
1373b765c8f9
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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84 </repeat> |
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85 <expand macro="test_out_file" file="measure_object_intensity.cppipe" /> |
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86 </test> |
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87 </tests> |
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88 |
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89 <help> |
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90 <![CDATA[ |
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91 |
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92 .. class:: infomark |
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93 |
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94 **What it does** |
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95 |
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96 MeasureObjectIntensity measures several intensity features for identified objects. |
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97 |
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98 Given an image with objects identified (e.g., nuclei or cells), this module extracts intensity features for each object based on one or more corresponding grayscale images. |
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99 Measurements are recorded for each object. |
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100 Intensity measurements are made for all combinations of the images and objects entered. |
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101 If you want only specific image/object measurements, you can use multiple MeasureObjectIntensity modules for each group of measurements desired. |
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102 Note that for publication purposes, the units of intensity from microscopy images are usually described as “Intensity units” or “Arbitrary intensity units” because microscopes are not calibrated to an absolute scale. |
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103 Also, it is important to note whether you are reporting the mean vs. the integrated intensity, so specify “Mean intensity units” or “Integrated intensity units” accordingly. |
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104 Keep in mind that the default behavior in CellProfiler is to rescale the image intensity from 0 to 1 by dividing all pixels in the image by the maximum possible intensity value. |
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105 This “maximum possible” value is defined by the “Set intensity range from” setting in NamesAndTypes; see the help for that setting for more details. |
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106 |
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107 @COMMON_HELP@ |
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108 ]]> |
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109 </help> |
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110 |
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111 |
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112 |
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113 <expand macro="citations" /> |
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114 |
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115 </tool> |