Mercurial > repos > bgruening > cp_measure_object_size_shape
annotate measure_object_size_shape.xml @ 4:79e10d12d90a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author | bgruening |
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date | Sat, 06 Feb 2021 10:08:15 +0000 |
parents | 5c9549983af8 |
children | acf3aa487283 |
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eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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1 <tool id="cp_measure_object_size_shape" name="MeasureObjectSizeShape" version="@CP_VERSION@"> |
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5ef26243a4a5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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2 <description>measure area and shape features of identified objects</description> |
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eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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4 <macros> |
eba2ec72f967
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5 <import>macros.xml</import> |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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6 </macros> |
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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"/> |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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9 <expand macro="cmd_modules" /> |
eba2ec72f967
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10 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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11 <configfiles> |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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12 <inputs name="inputs" /> |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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13 <configfile name="script_file"> |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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14 import json |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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15 import sys |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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16 import os |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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17 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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18 FOURSPACES=@SPACES@ |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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20 input_json_path = sys.argv[1] |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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21 input_pipeline= sys.argv[2] |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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22 |
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23 params = json.load(open(input_json_path, "r")) |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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24 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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25 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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26 def writemoss(): |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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28 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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29 for obj in params['rpt_object']: |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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30 _str += FOURSPACES + "Select objects to measure:%s\n" % obj['objects_to_measure'] |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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31 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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32 _str += FOURSPACES + "Calculate the Zernike features?:%s\n" % params['zernike_feature'] |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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33 |
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34 return _str |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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35 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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36 with open(input_pipeline) as fin: |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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37 lines = fin.readlines() |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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38 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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39 k, v = lines[4].strip().split(':') |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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40 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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41 module_count = int(v) |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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42 new_count = module_count + 1 |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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43 lines[4] = k + ":%d\n" % new_count |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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44 with open("output.cppipe", "w") as f: |
5c9549983af8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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45 f.writelines(lines) |
5c9549983af8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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46 f.write(writemoss()) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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47 |
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48 f.close() |
5c9549983af8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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49 </configfile> |
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50 </configfiles> |
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51 |
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52 <inputs> |
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53 <expand macro="input_pipeline_param" /> |
5c9549983af8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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54 <repeat name="rpt_object" title="new object" min="1"> |
5c9549983af8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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55 <param name="objects_to_measure" label="Enter the name of the object to measure" type="text"> |
5c9549983af8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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56 <expand macro="text_validator" /> |
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57 </param> |
5c9549983af8
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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."> |
5c9549983af8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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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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69 |
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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"> |
eba2ec72f967
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74 <param name="objects_to_measure" value="Nuclei" /> |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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75 </repeat> |
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76 <repeat name="rpt_object"> |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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77 <param name="objects_to_measure" value="Nucleoli" /> |
eba2ec72f967
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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78 </repeat> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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> |
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83 <help> |
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84 <![CDATA[ |
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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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89 |
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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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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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91 |
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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. |
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93 |
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94 @COMMON_HELP@ |
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95 ]]> |
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96 </help> |
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97 <expand macro="citations" /> |
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98 |
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99 </tool> |