Mercurial > repos > bgruening > cp_convert_objects_to_image

annotate convert_objects_to_image.xml @ 3:2690da374874 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 07:44:29 -0400
parents 1221c018f7be
children cdf8e3c57dae
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1 <tool id="cp_convert_objects_to_image" name="ConvertObjectsToImage" version="@CP_VERSION@">
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2 <description>convert the identified objects into an image</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="py_requirements"/>
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7 <expand macro="cmd_modules" />
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8 <configfiles>
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9 <inputs name="inputs" />
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10 <configfile name="script_file">
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11 import json
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12 import sys
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13 import os
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15 FOURSPACES=@SPACES@
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17 input_json_path = sys.argv[1]
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18 input_pipeline= sys.argv[2]
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20 params = json.load(open(input_json_path, "r"))
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23 def writecoti():
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24 _str = "\nConvertObjectsToImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:1|show_window:True|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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26 _str += FOURSPACES + "Select the input objects:%s\n" % params['input_object']
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27 _str += FOURSPACES + "Name the output image:%s\n" % params['name_output_image']
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29 color_format = params['con_color_format']['color_format']
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31 _str += FOURSPACES + "Select the color format:%s\n" % color_format
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33 if color_format == "Color":
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34 _str += FOURSPACES + "Select the colormap:%s\n" % params['con_color_format']['color_map']
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35 else:
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36 _str += FOURSPACES + "Select the colormap:Default\n"
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38 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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43 k, v = lines[4].strip().split(':')
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45 module_count = int(v)
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46 new_count = module_count + 1
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47 lines[4] = k + ":%d\n" % new_count
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48 with open("output.cppipe", "w") as f:
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49 f.writelines(lines)
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50 f.write(writecoti())
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52 f.close()
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53 </configfile>
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54 </configfiles>
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56 <inputs>
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57 <expand macro="input_pipeline_param" />
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58 <param name="input_object" type="text" label="Enter the name of the input objects you want to convert to an image" />
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59 <param name="name_output_image" type="text" label="Enter the name of the resulting image">
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60 <expand macro="text_validator" />
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61 </param>
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62
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63 <conditional name="con_color_format">
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64 <param name="color_format" type="select" label="Select the color format">
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65 <option value="Color">Color</option>
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66 <option value="Binary (black &amp; white)">Binary (black &amp; white)</option>
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67 <option value="Grayscale">Grayscale</option>
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68 <option value="unit16">unit16</option>
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69 <sanitizer sanitize="false"/>
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70 </param>
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71 <when value="Binary (black &amp; white)" />
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72 <when value="Grayscale" />
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73 <when value="unit16" />
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74 <when value="Color">
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75 <param name="color_map" type="select" label="Select the colormap" help="The colormap affects how the objects are colored." >
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76 <option value="Default">Default</option>
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77 <option value="Accent">Accent</option>
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78 <option value="Blues">Blues</option>
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79 <option value="BrBG">BrBG</option>
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80 <option value="BuGn">BuGn</option>
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81 <option value="BuPu">BuPu</option>
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82 <option value="Dark2">Dark2</option>
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83 <option value="GnBu">GnBu</option>
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84 <option value="Greens">Greens</option>
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85 <option value="Greys">Greys</option>
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86 <option value="OrRd">OrRd</option>
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87 <option value="Oranges">Oranges</option>
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88 <option value="PRGn">PRGn</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
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89 <option value="Paired">Paired</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
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90 <option value="Pastel1">Pastel1</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
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91 <option value="Pastel2">Pastel2</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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92 <option value="PiYG">PiYG</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
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93 <option value="PuBu">PuBu</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
94 <option value="PuBuGn">PuBuGn</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
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95 <option value="PuOr">PuOr</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
96 <option value="PuRd">PuRd</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
97 <option value="Purples">Purples</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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98 <option value="RdBu">RdBu</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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99 <option value="RdGy">RdGy</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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100 <option value="RdPu">RdPu</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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101 <option value="RdYIBu">RdYIBu</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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102 <option value="RdYiGn">RdYiGn</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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103 <option value="Reds">Reds</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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104 <option value="Set1">Set1</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
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105 <option value="Set2">Set2</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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106 <option value="Set3">Set3</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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107 <option value="Spectral">Spectral</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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108 <option value="YIGn">YIGn</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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109 <option value="YIGnBu">YIGnBu</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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110 <option value="YIOrBr">YIOrBr</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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111 <option value="YIOrRd">YIOrRd</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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112 <option value="autumn">autumn</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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113 <option value="binary">binary</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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114 <option value="bone">bone</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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115 <option value="cool">cool</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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116 <option value="copper">copper</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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117 <option value="flag">flag</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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118 <option value="gist_earth">gist_earth</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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119 <option value="gist_gray">gist_gray</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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120 <option value="gist_heat">gist_heat</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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121 <option value="gist_ncar">gist_ncar</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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122 <option value="gist_rainbow">gist_rainbow</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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123 <option value="gist_stern">gist_stern</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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124 <option value="gist_yarg">gist_yarg</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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125 <option value="gray">gray</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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126 <option value="hot">hot</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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127 <option value="hsv">hsv</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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128 <option value="jet">jet</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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129 <option value="pink">pink</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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130 <option value="prism">prism</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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131 <option value="spectral">spectral</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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132 <option value="spring">spring</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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133 <option value="summer">summer</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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134 <option value="winter">winter</option>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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135 </param>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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136 </when>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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137 </conditional>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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138 </inputs>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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139
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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140 <outputs>
3
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141 <expand macro="output_pipeline_param" />
0
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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142 </outputs>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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143
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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144 <tests>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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145 <test>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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146 <expand macro="test_input_pipeline_param" />
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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147 <param name="input_object" value="Nuclei" />
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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148 <param name="name_output_image" value="MaskNuclei" />
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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149 <conditional name="con_color_format">
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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150 <param name="color_format" value="Binary (black &amp; white)" />
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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151 </conditional>
3
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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152 <expand macro="test_out_file" file="convert_objects_to_image.cppipe" />
0
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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153 </test>
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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154 </tests>
3
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155
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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156 <help>
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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157 <![CDATA[
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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158 .. class:: infomark
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159
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160 **What it does**
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161
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162 This module allows you to take previously identified objects and convert them into an image according to a colormap you select, which can then be saved with the *SaveImages* module.
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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163
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164 For the *colormap*, you have the following options:
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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165
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166 - *Color*: Allows you to choose a colormap that will produce jumbled colors for your objects.
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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167
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168 - *Binary (black & white)*: All object pixels will be assigned 1 and all background pixels will be assigned 0, creating a binary image.
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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169
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170 - *Grayscale*: Assigns all background pixels to 0 and each object a different number from 1 to 255 (the maximum value that you can put in an 8-bit integer) and numbers all pixels in each object with the object’s number. This creates an image where objects in the top left corner of the image are very dark and where the colors progress to white toward the bottom right corner of the image.
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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171
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172 - *uint16*: Assigns all background pixels to 0 and each object a different number from 1 to 65535 (the maximum value that you can put in a 16-bit integer) and numbers all pixels in each object with the object’s number. This creates an image where objects in the top left corner of the image are very dark and where the colors progress to white toward the bottom right corner of the image (though this can usually only be seen in a scientific image viewer since standard image viewers only handle 8-bit images).
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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173
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174 You can choose Color with a Gray colormap to produce jumbled gray objects.
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175
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176 @COMMON_HELP@
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177 ]]>
2690da374874 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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178 </help>
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d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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179 <expand macro="citations" />
d9fa2e6fae97 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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180 </tool>