Mercurial > repos > bgruening > cp_mask_image

annotate mask_image.xml @ 0:54d7d3450800 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 17:47:02 -0400
parents
children baa3e6d4d99d
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54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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1 <tool id="cp_mask_image" name="MaskImage" version="@CP_VERSION@">
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2 <description>hides certain portions of an image based on previously identified objects or a binary image</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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54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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 writemi():
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26 _str = "\nMaskImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\'Keep only nucleoli inside the nuclei\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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28 _str += FOURSPACES + "Select the input image:%s\n" % params['input_image']
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29 _str += FOURSPACES + "Name the output image:%s\n" % params['name_output_image']
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31 img_obj = params['con_img_obj']['img_obj']
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54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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33 _str += FOURSPACES + "Use objects or an image as a mask?:%s\n" % params['con_img_obj']['img_obj']
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54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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35 if img_obj == "Objects":
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36 _str += FOURSPACES + "Select object for mask:%s\n" % params['con_img_obj']['select_obj']
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37 _str += FOURSPACES + "Select image for mask:None\n"
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38 else:
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39 _str += FOURSPACES + "Select object for mask:None\n"
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40 _str += FOURSPACES + "Select image for mask:%s\n" % params['con_img_obj']['select_img']
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54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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42 _str += FOURSPACES + "Invert the mask?:%s\n" % params['invert_mask']
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44 return _str
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54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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46 with open(input_pipeline) as fin:
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47 lines = fin.readlines()
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49 k, v = lines[4].strip().split(':')
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51 module_count = int(v)
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52 new_count = module_count + 1
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53 lines[4] = k + ":%d\n" % new_count
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55 with open("output", "w") as f:
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56 f.writelines(lines)
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57 f.write(writemi())
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59 f.close()
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60 </configfile>
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61 </configfiles>
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63 <inputs>
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64
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65 <expand macro="input_pipeline_macro" />
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66 <param name="input_image" label="Select input image" type="text">
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67 <expand macro="text_validator" />
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68 </param>
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69
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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70 <param name="name_output_image" type="text" label="Name the output image">
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71 <expand macro="text_validator" />
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72 </param>
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73
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74 <conditional name="con_img_obj">
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75 <param name="img_obj" label="Use objects or an image as a mask?" type="select">
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76 <option value="Objects">Objects</option>
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77 <option value="Image">Image</option>
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78 </param>
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79 <when value="Objects">
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80 <param name="select_obj" label="Select object for mask" type="text"/>
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81 </when>
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82 <when value="Image">
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83 <param name="select_img" label="Select image for mask" type="text"/>
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84 </when>
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85 </conditional>
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86 <param name="invert_mask" label="Invert the mask?" type="select" display="radio">
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87 <option value="Yes">Yes</option>
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88 <option value="No">No</option>
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89 </param>
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90 </inputs>
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91
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92 <outputs>
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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93 <expand macro="output_pipeline_macro" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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94 </outputs>
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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95
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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96 <tests>
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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97 <test>
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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98 <expand macro="test_input_pipeline_param"/>
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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99 <param name="input_image" value="DNAdarkholes" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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100 <param name="name_output_image" value="MaskDNAdarkholes" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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101 <conditional name="con_img_obj">
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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102 <param name="img_obj" value="Objects" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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103 <param name="select_obj" value="Nuclei" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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104 </conditional>
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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105 <param name="invert_mask" value="No" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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106 <expand macro="test_out_file" file="mask_image.txt" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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107 </test>
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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108 </tests>
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109
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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110 <expand macro="help" module="GrayToColor" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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111 <expand macro="citations" />
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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112
54d7d3450800 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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113 </tool>