Mercurial > repos > imgteam > 2d_auto_threshold

annotate auto_threshold.xml @ 7:e5c8e7e72373 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:23:18 +0000
parents 8bccb36e055a
children 699a5e9146b3
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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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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e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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4 <import>creators.xml</import>
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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5 <import>tests.xml</import>
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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6 <token name="@TOOL_VERSION@">0.18.1</token>
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e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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7 <token name="@VERSION_SUFFIX@">2</token>
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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8 <xml name="inputs/offset">
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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9 <param name="offset" type="float" value="0" label="Offset" help="Offset to be added to the automatically determined threshold value. Positive values will increase the threshold (and thus reduce the amount of values above the threshold)." />
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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10 </xml>
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11 </macros>
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e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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12 <creator>
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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13 <expand macro="creators/bmcv"/>
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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14 </creator>
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15 <edam_operations>
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16 <edam_operation>operation_3443</edam_operation>
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17 </edam_operations>
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18 <xrefs>
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19 <xref type="bio.tools">scikit-image</xref>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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20 <xref type="biii">scikit-image</xref>
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21 </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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22 <requirements>
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23 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
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24 <requirement type="package" version="2020.10.1">tifffile</requirement>
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25 </requirements>
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26 <command detect_errors="aggressive">
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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27 <![CDATA[
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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28 python '$__tool_directory__/auto_threshold.py'
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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29 '$input'
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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30 ./out.tif
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31 '$th_method.method_id'
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32 '$th_method.block_size'
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33 '$th_method.offset'
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34 '$th_method.threshold'
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35 $invert_output
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36 ]]>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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37 </command>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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38 <inputs>
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39 <param name="input" type="data" format="tiff,png" label="Input image" />
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40 <conditional name="th_method">
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41 <param name="method_id" type="select" label="Thresholding method">
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42 <option value="manual">Manual</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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43 <option value="otsu" selected="True">Globally adaptive / Otsu</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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44 <option value="li">Globally adaptive / Li's Minimum Cross Entropy</option>
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45 <option value="isodata">Globally adaptive / Isodata</option>
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46 <option value="yen">Globally adaptive / Yen</option>
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47 <option value="loc_gaussian">Locally adaptive / Gaussian</option>
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48 <option value="loc_median">Locally adaptive / Median</option>
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49 <option value="loc_mean">Locally adaptive / Mean</option>
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50 </param>
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51 <when value="manual">
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52 <param name="threshold" type="float" value="0" label="Threshold value" />
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53 <param name="block_size" type="hidden" value="0" />
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54 <param name="offset" type="hidden" value="0" />
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55 </when>
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56 <when value="otsu">
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57 <param name="threshold" type="hidden" value="0" />
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58 <param name="block_size" type="hidden" value="0" />
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59 <expand macro="inputs/offset" />
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60 </when>
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61 <when value="li">
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62 <param name="threshold" type="hidden" value="0" />
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63 <param name="block_size" type="hidden" value="0" />
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64 <expand macro="inputs/offset" />
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65 </when>
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66 <when value="isodata">
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67 <param name="threshold" type="hidden" value="0" />
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68 <param name="block_size" type="hidden" value="0" />
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69 <expand macro="inputs/offset" />
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70 </when>
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71 <when value="yen">
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72 <param name="threshold" type="hidden" value="0" />
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73 <param name="block_size" type="hidden" value="0" />
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74 <expand macro="inputs/offset" />
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75 </when>
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76 <when value="loc_gaussian">
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77 <param name="threshold" type="hidden" value="0" />
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78 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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79 <expand macro="inputs/offset" />
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80 </when>
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81 <when value="loc_median">
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82 <param name="threshold" type="hidden" value="0" />
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83 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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84 <expand macro="inputs/offset" />
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85 </when>
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86 <when value="loc_mean">
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87 <param name="threshold" type="hidden" value="0" />
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88 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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89 <expand macro="inputs/offset" />
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90 </when>
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91 </conditional>
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92 <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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93 </inputs>
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94 <outputs>
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95 <data format="tiff" name="output" from_work_dir="out.tif" />
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96 </outputs>
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97 <tests>
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98 <!-- Tests for single-channel images -->
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99 <test>
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100 <param name="input" value="sample.tif"/>
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101 <param name="method_id" value="loc_gaussian"/>
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102 <param name="block_size" value="51"/>
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103 <param name="invert_output" value="False"/>
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104 <expand macro="tests/binary_image_diff" name="output" value="out1.tif" ftype="tiff"/>
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105 </test>
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106 <test>
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107 <param name="input" value="sample.tif"/>
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108 <param name="method_id" value="loc_gaussian"/>
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109 <param name="block_size" value="51"/>
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110 <param name="offset" value="1"/>
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111 <param name="invert_output" value="False"/>
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112 <expand macro="tests/binary_image_diff" name="output" value="out2.tif" ftype="tiff"/>
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113 </test>
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114 <test>
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115 <param name="input" value="sample.tif"/>
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116 <param name="method_id" value="otsu"/>
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117 <param name="invert_output" value="False"/>
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118 <expand macro="tests/binary_image_diff" name="output" value="out3.tif" ftype="tiff"/>
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119 </test>
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120 <test>
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121 <param name="input" value="sample.tif"/>
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122 <param name="method_id" value="manual"/>
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123 <param name="threshold" value="64"/>
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124 <param name="invert_output" value="True"/>
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125 <expand macro="tests/binary_image_diff" name="output" value="out4.tif" ftype="tiff"/>
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126 </test>
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127 <!-- Tests for multi-channel images -->
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128 <test expect_failure="true">
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129 <param name="input" value="rgb.png"/>
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130 </test>
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131 </tests>
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132 <help>
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133
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134 **Applies a standard thresholding algorithm to a 2-D single-channel image. Yields a binary image.**
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135
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136 The thresholding algorithm automatically determines a threshold value (unless manual thresholding is used).
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137 The input image is then thresholded, by assigning white (pixel value 255) to image regions above the determined threshold,
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138 and black (pixel value 0) to image regions below or equal to the determined threshold.
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139
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140 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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141
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142 </help>
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143 <citations>
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144 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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145 </citations>
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146 </tool>