annotate auto_threshold.xml @ 6:8bccb36e055a draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit cb3d628f4c91e996e10dcb35b1168332e692293a
author imgteam
date Wed, 13 Mar 2024 06:15:54 +0000
parents 7db4fc31dbee
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1 <tool id="ip_threshold" name="Threshold image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>with scikit-image</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.18.1</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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7 <edam_operations>
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8 <edam_operation>operation_3443</edam_operation>
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9 </edam_operations>
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10 <xrefs>
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11 <xref type="bio.tools">scikit-image</xref>
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12 <xref type="biii">scikit-image</xref>
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13 </xrefs>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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14 <requirements>
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15 <requirement type="package" version="0.18.1">scikit-image</requirement>
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16 <requirement type="package" version="2020.10.1">tifffile</requirement>
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17 </requirements>
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18 <command detect_errors="aggressive">
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19 <![CDATA[
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20 python '$__tool_directory__/auto_threshold.py'
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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21 '$input'
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22 ./out.tif
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23 '$th_method.method_id'
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24 '$th_method.block_size'
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25 '$th_method.threshold'
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26 $invert_output
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27 ]]>
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28 </command>
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29 <inputs>
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30 <param name="input" type="data" format="tiff,png" label="Input image" />
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31 <conditional name="th_method">
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32 <param name="method_id" type="select" label="Thresholding method">
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33 <option value="manual">Manual</option>
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34 <option value="otsu" selected="True">Globally adaptive / Otsu</option>
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35 <option value="li">Globally adaptive / Li's Minimum Cross Entropy</option>
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36 <option value="isodata">Globally adaptive / Isodata</option>
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37 <option value="yen">Globally adaptive / Yen</option>
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38 <option value="loc_gaussian">Locally adaptive / Gaussian</option>
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39 <option value="loc_median">Locally adaptive / Median</option>
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40 <option value="loc_mean">Locally adaptive / Mean</option>
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41 </param>
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42 <when value="manual">
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43 <param name="threshold" type="float" value="0" label="Threshold value" />
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44 <param name="block_size" type="hidden" value="0" />
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45 </when>
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46 <when value="otsu">
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47 <param name="threshold" type="hidden" value="0" />
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48 <param name="block_size" type="hidden" value="0" />
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49 </when>
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50 <when value="li">
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51 <param name="threshold" type="hidden" value="0" />
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52 <param name="block_size" type="hidden" value="0" />
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53 </when>
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54 <when value="isodata">
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55 <param name="threshold" type="hidden" value="0" />
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56 <param name="block_size" type="hidden" value="0" />
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57 </when>
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58 <when value="yen">
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59 <param name="threshold" type="hidden" value="0" />
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60 <param name="block_size" type="hidden" value="0" />
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61 </when>
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62 <when value="loc_gaussian">
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63 <param name="threshold" type="hidden" value="0" />
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64 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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65 </when>
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66 <when value="loc_median">
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67 <param name="threshold" type="hidden" value="0" />
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68 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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69 </when>
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70 <when value="loc_mean">
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71 <param name="threshold" type="hidden" value="0" />
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72 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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73 </when>
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74 </conditional>
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75 <param name="invert_output" type="boolean" checked="false" truevalue="--invert_output" falsevalue="" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
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76 </inputs>
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77 <outputs>
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78 <data format="tiff" name="output" from_work_dir="out.tif" />
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="input" value="sample.tif"/>
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83 <output name="output" value="out.tif" ftype="tiff" compare="sim_size" delta="10"/>
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84 <param name="method_id" value="loc_gaussian"/>
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85 <param name="block_size" value="3"/>
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86 <param name="invert_output" value="False"/>
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87 </test>
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88 <test>
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89 <param name="input" value="sample.tif"/>
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90 <output name="output" value="out2.tif" ftype="tiff" compare="sim_size" delta="10"/>
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91 <param name="method_id" value="otsu"/>
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92 <param name="block_size" value="5"/>
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93 <param name="invert_output" value="False"/>
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94 </test>
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95 <test>
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96 <param name="input" value="sample.tif"/>
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97 <output name="output" value="out3.tif" ftype="tiff" compare="sim_size" delta="10"/>
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98 <param name="method_id" value="manual"/>
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99 <param name="threshold" value="64"/>
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100 <param name="invert_output" value="True"/>
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101 </test>
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102 </tests>
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103 <help>
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104 Applies a standard thresholding algorithm to an image.
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105
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106 The thresholding algorithm automatically determines a threshold value (unless manual thresholding is used).
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107 The input image is then thresholded, by assigning white (pixel value 255) to image regions above the determined threshold,
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108 and black (pixel value 0) to image regions below or equal to the determined threshold.
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109
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110 The assignment of black and white to image regions below and above the threshold is inverted, if the corresponding option is set.
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111 </help>
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112 <citations>
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113 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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114 </citations>
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115 </tool>