Mercurial > repos > bgruening > cp_measure_image_intensity

annotate measure_image_intensity.xml @ 0:e87d1fd2d673 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 17:43:18 -0400
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children 20525bc7f6f4
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e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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1 <tool id="cp_measure_image_intensity" name="MeasureImageIntensity" version="@CP_VERSION@">
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2 <description>measures several intensity features across an entire image (excluding masked pixels)</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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25 def writemii():
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26 _str = "\nMeasureImageIntensity:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:2|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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28 for intensity in params['rpt_intensity']:
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29 obj_flag = intensity['con_intensity']['only_from_objects']
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31 _str += FOURSPACES + "Select the image to measure:%s\n" % intensity['image_to_measure']
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32 _str += FOURSPACES + "Measure the intensity only from areas enclosed by objects?:%s\n" % obj_flag
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34 if obj_flag == "No":
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35 _str += FOURSPACES + "Select the input objects:None\n"
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36 else:
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37 _str += FOURSPACES + "Select the input objects:%s\n" % intensity['con_intensity']['input_objects']
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39 return _str
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41 with open(input_pipeline) as fin:
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42 lines = fin.readlines()
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44 k, v = lines[4].strip().split(':')
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46 module_count = int(v)
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47 new_count = module_count + 1
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48 lines[4] = k + ":%d\n" % new_count
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49 with open("output", "w") as f:
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50 f.writelines(lines)
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51 f.write(writemii())
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52
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53 f.close()
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54 </configfile>
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55 </configfiles>
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57 <inputs>
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58
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59 <expand macro="input_pipeline_macro" />
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60 <repeat name="rpt_intensity" title="Add another image">
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61 <param name="image_to_measure" label="Select image to measure" type="text" >
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62 <expand macro="text_validator" />
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63 </param>
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64 <conditional name="con_intensity">
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65 <param name="only_from_objects" label="Measure the intensity only from areas enclosed by objects?" display="radio" type="select">
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66 <option value="Yes">Yes</option>
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67 <option value="No">No</option>
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68 </param>
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69 <when value="Yes">
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70 <param name="input_objects" label="Select the input objects" type="text">
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71 <expand macro="text_validator" />
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72 </param>
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73 </when>
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74 <when value="No" />
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75 </conditional>
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76 </repeat>
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77 </inputs>
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78
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79 <outputs>
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80 <expand macro="output_pipeline_macro" />
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81 </outputs>
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82
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83 <tests>
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84 <test>
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85 <expand macro="test_input_pipeline_param" />
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86 <repeat name="rpt_intensity">
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87 <param name="image_to_measure" value="DNA" />
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88 <conditional name="con_intensity">
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89 <param name="only_from_objects" value="No" />
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90 </conditional>
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91 </repeat>
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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92 <repeat name="rpt_intensity">
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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93 <param name="image_to_measure" value="DNA" />
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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94 <conditional name="con_intensity">
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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95 <param name="only_from_objects" value="Yes" />
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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96 <param name="input_objects" value="Nuclei" />
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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97 </conditional>
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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98 </repeat>
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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99 <expand macro="test_out_file" file="measure_image_intensity.txt" />
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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100 </test>
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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101 </tests>
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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102 <expand macro="help" module="MeasureImageIntensity" />
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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103 <expand macro="citations" />
e87d1fd2d673 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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104 </tool>