Mercurial > repos > bgruening > cp_measure_granularity

annotate measure_granularity.xml @ 1:e336ff1955a0 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6a3036d24b5ec074936f8f8283b7e176f6f1ce70"
author bgruening
date Thu, 09 Apr 2020 08:14:44 -0400
parents 1062c9e44147
children 88dd3674c4d0
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1 <tool id="cp_measure_granularity" name="MeasureGranularity" version="@CP_VERSION@">
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2 <description>outputs spectra of size measurements of the textures in the image</description>
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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 writemg():
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26 _str = "\nMeasureGranularity:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\\'PARAMS\\x3A\\', \\'- Radius\\', \'- Range\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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28 image_count = len(params['rpt_image'])
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30 _str += FOURSPACES + "Image count:%d\n" % image_count
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32 for img in params['rpt_image']:
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33 obj_count = len(img['rpt_object'])
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35 _str += FOURSPACES + "Object count:%d\n" % obj_count
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37 _str += FOURSPACES + "Select an image to measure:%s\n" % img['image_to_measure']
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39 _str += FOURSPACES + "Subsampling factor for granularity measurements:%s\n" % img['subsampling_factor_granularity']
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41 _str += FOURSPACES + "Subsampling factor for background reduction:%.2f\n" % img['subsampling_factor_background_reduction']
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43 _str += FOURSPACES + "Radius of structuring element:%d\n" % img['radius']
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44 _str += FOURSPACES + "Range of the granular spectrum:%d\n" % img['range_granular_spectrum']
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46 for obj in img['rpt_object']:
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47 _str += FOURSPACES + "Select objects to meausre:%s\n" % obj['object_to_measure']
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49 return _str
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51 with open(input_pipeline) as fin:
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52 lines = fin.readlines()
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54 k, v = lines[4].strip().split(':')
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56 module_count = int(v)
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57 new_count = module_count + 1
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58 lines[4] = k + ":%d\n" % new_count
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59 with open("output", "w") as f:
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60 f.writelines(lines)
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61 f.write(writemg())
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63 f.close()
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64 </configfile>
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65 </configfiles>
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67 <inputs>
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68 <expand macro="input_pipeline_macro" />
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69 <repeat name="rpt_image" title="Add another image">
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70 <param name="image_to_measure" type="text" label="Select an image to measure">
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71 <expand macro="text_validator" />
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72 </param>
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74 <param name="subsampling_factor_granularity" type="float" value="0.25" label="Subsampling factor for granularity measurements" />
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76 <param name="subsampling_factor_background_reduction" type="float" value="0.25" min="0.125" max="0.25" label="Subsampling factor for background reduction" />
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78 <param name="radius" type="integer" value="10" label="Radius of structuring element" />
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80 <param name="range_granular_spectrum" type="integer" value="16" label="Range of the granular spectrum" />
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82 <repeat name="rpt_object" title="Add another object">
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83 <param name="object_to_measure" type="text" label="Select object to measure" >
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84 <expand macro="text_validator" />
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85 </param>
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86 </repeat>
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87 </repeat>
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88 </inputs>
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90 <outputs>
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91 <expand macro="output_pipeline_macro" />
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92 </outputs>
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93
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94 <tests>
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95 <test>
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96 <expand macro="test_input_pipeline_param" />
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97 <repeat name="rpt_image">
1062c9e44147 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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98 <param name="image_to_measure" value="DNA" />
1062c9e44147 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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99 <param name="subsampling_factor_granularity" value="0.25" />
1062c9e44147 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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100 <param name="subsampling_factor_background_reduction" value="0.25" />
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101 <param name="radius" value="10" />
1062c9e44147 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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102 <param name="range_granular_spectrum" value="16" />
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103 </repeat>
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104 <expand macro="test_out_file" file="measure_granularity.txt" />
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105 </test>
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106 </tests>
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107
1062c9e44147 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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108 <expand macro="help" module="MeasureGranularity" />
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109 <expand macro="citations" />
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110 </tool>