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annotate overlay_images.xml @ 5:c1fd8b7c6bbc draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:22:51 +0000
parents 61009b4361c1
children
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61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
imgteam
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1 <tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@" profile="20.05">
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2 <description></description>
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3 <macros>
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4 <import>creators.xml</import>
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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5 <import>tests.xml</import>
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6 <token name="@TOOL_VERSION@">0.0.5</token>
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7 </macros>
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8 <creator>
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9 <expand macro="creators/bmcv"/>
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10 <expand macro="creators/kostrykin"/>
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11 <expand macro="creators/thawn"/>
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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12 </creator>
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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13 <edam_operations>
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14 <edam_operation>operation_3443</edam_operation>
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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15 </edam_operations>
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16 <xrefs>
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17 <xref type="bio.tools">galaxy_image_analysis</xref>
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18 </xrefs>
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19 <requirements>
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20 <requirement type="package" version="0.18.1">scikit-image</requirement>
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21 <requirement type="package" version="3.3.4">matplotlib</requirement>
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22 <requirement type="package" version="2020.10.1">tifffile</requirement>
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eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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23 <requirement type="package" version="1.21">numpy</requirement>
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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24 <requirement type="package" version="10.4.0">pillow</requirement>
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25 <requirement type="package" version="0.1">giatools</requirement>
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26 </requirements>
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27 <command detect_errors="aggressive">
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28 <![CDATA[
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29 python '$__tool_directory__/overlay_images.py'
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30 '$method_option.im1' '$method_option.im2'
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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31 #if $method_option.method == "seg_contour"
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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32 ./output.png
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33 #else
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34 ./output.tiff
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35 #end if
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36 --method $method_option.method
681873a3c047 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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37 #if $method_option.method == "blending"
681873a3c047 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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38 --alpha $method_option.alpha
681873a3c047 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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39 #elif $method_option.method == "seg_contour"
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40 --fp_lower '${method_option.fp_conversion.lower}'
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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41 --fp_upper '${method_option.fp_conversion.upper}'
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42 --thickness $method_option.thickness
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43 --color '$method_option.color'
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44 $method_option.show_label
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45 --label_color '$method_option.label_color'
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46 #end if
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47 ]]>
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48 </command>
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49 <inputs>
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50 <conditional name="method_option">
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51
3
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52 <param name="method" type="select" label="Type of the overlay">
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53 <option value="coloc_vis" selected="True">Colocalization</option>
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54 <option value="blending">Linear blending</option>
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55 <option value="seg_contour">Segmentation contours over image</option>
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56 </param>
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57
0
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58 <when value="coloc_vis">
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59 <param name="im1" type="data" format="tiff,png" label="Image 1 (red channel)"/>
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60 <param name="im2" type="data" format="tiff,png" label="Image 2 (green channel)"/>
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61 </when>
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62
0
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63 <when value="blending">
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64 <param name="im1" type="data" format="tiff,png" label="Image 1"/>
c1fd8b7c6bbc planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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65 <param name="im2" type="data" format="tiff,png" label="Image 2"/>
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66 <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: result = (1 - weight) * image1 + weight * image2."/>
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67 </when>
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68
0
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69 <when value="seg_contour">
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70 <param name="im1" type="data" format="tiff,png" label="Intensity image" />
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71
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72 <section name="fp_conversion" title="Intensity image floating point conversion" expanded="false" help="This is only used if the values of the intensity image have a floating point format. Overlay images are created as PNG files, that do not support floating point values (but only integer values between 0 and 255). Conversion of floating point intensity values to integer values via linear mapping is generally ambiguous and can be adapted here.">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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73 <param name="lower" type="select" label="Lower bound conversion" help="Choose which floating point intensity value will be mapped to 0 (i.e. black if grayscale).">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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74 <option value="0" selected="True">0</option>
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75 <option value="-1">-1</option>
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76 <option value="min">Minimum value of the image</option>
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77 </param>
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78 <param name="upper" type="select" label="Upper bound conversion" help="Choose which floating point intensity value will be mapped to 255 (i.e. white if grayscale).">
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79 <option value="1" selected="True">1</option>
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80 <option value="max">Maximum value of the image</option>
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81 </param>
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82 </section>
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83
3
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84 <param name="im2" type="data" format="tiff,png" label="Label map" />
2
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85 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" />
f42d21fe65d8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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86 <param name="color" type="color" value="#ff0000" label="Contour color"/>
5
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87 <param argument="--show_label" type="boolean" checked="false" truevalue="--show_label" falsevalue="" label="Show labels"/>
2
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88 <param name="label_color" type="color" value="#ffff00" label="Label color"/>
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89 </when>
4
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90
0
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91 </conditional>
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92 </inputs>
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93 <outputs>
4
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94 <data format="tiff" name="out_tiff" from_work_dir="output.tiff" label="${tool.name} on ${on_string} output:tiff">
3
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95 <filter>method_option['method'] != 'seg_contour'</filter>
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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96 </data>
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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97 <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png">
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98 <filter>method_option['method'] == 'seg_contour'</filter>
eb173a1fabc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
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99 </data>
0
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100 </outputs>
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101 <tests>
3
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102 <test expect_num_outputs="1">
4
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103 <conditional name="method_option">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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104 <param name="method" value="coloc_vis"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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105 <param name="im1" value="mask1.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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106 <param name="im2" value="mask1r.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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107 </conditional>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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108 <expand macro="tests/intensity_image_diff" name="out_tiff" value="test1.tiff" ftype="tiff"/>
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109 </test>
3
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110 <test expect_num_outputs="1">
4
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111 <conditional name="method_option">
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112 <param name="method" value="blending"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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113 <param name="im1" value="mask1.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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114 <param name="im2" value="mask1r.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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115 <param name="alpha" value="0.3"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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116 </conditional>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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117 <expand macro="tests/intensity_image_diff" name="out_tiff" value="test2.tiff" ftype="tiff"/>
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118 </test>
3
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119 <test expect_num_outputs="1">
4
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120 <conditional name="method_option">
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121 <param name="method" value="seg_contour"/>
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122 <param name="im1" value="sample1_uint8.tiff"/>
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123 <param name="im2" value="mask1.tiff"/>
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124 <param name="thickness" value="2"/>
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125 <param name="color" value="#ff0000"/>
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126 <param name="label_color" value="#ffff00"/>
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127 <param name="show_label" value="true"/>
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128 </conditional>
3
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129 <expand macro="tests/intensity_image_diff" name="out_png" value="test3.png" ftype="png"/>
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130 </test>
3
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131 <test expect_num_outputs="1"><!-- segmentation overlay, 8bit test -->
4
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132 <conditional name="method_option">
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133 <param name="method" value="seg_contour"/>
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134 <param name="im1" value="sample1_uint8.tiff"/>
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135 <param name="im2" value="mask2.tiff"/>
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136 <param name="thickness" value="2"/>
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137 <param name="color" value="#ff0000"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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138 <param name="label_color" value="#ffff00"/>
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139 </conditional>
3
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140 <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png"/>
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141 </test>
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142 <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test -->
4
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143 <conditional name="method_option">
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144 <param name="method" value="seg_contour"/>
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145 <param name="im1" value="sample1_uint16.tiff"/>
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146 <param name="im2" value="mask2.tiff"/>
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147 <param name="thickness" value="2"/>
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148 <param name="color" value="#ff0000"/>
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149 <param name="label_color" value="#ffff00"/>
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150 </conditional>
3
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151 <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png" eps="1"/>
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152 </test>
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153 <test expect_num_outputs="1"><!-- segmentation overlay, 8bit RGB test -->
4
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154 <conditional name="method_option">
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155 <param name="method" value="seg_contour"/>
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156 <param name="im1" value="sample1_uint8_rgb.png"/>
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157 <param name="im2" value="mask2.tiff"/>
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158 <param name="thickness" value="2"/>
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159 <param name="color" value="#ff0000"/>
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160 <param name="label_color" value="#ffff00"/>
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161 </conditional>
3
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162 <expand macro="tests/intensity_image_diff" name="out_png" value="test5.png" ftype="png"/>
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163 </test>
4
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164 <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test 0/1 -->
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165 <conditional name="method_option">
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166 <param name="method" value="seg_contour"/>
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167 <param name="im1" value="sample2.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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168 <param name="im2" value="mask3.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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169 <param name="thickness" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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170 <param name="color" value="#ff0000"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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171 <param name="label_color" value="#ffff00"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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172 <section name="fp_conversion">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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173 <param name="lower" value="0"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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174 <param name="upper" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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175 </section>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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176 </conditional>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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177 <expand macro="tests/intensity_image_diff" name="out_png" value="test6.png" ftype="png"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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178 </test>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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179 <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test -1/1 -->
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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180 <conditional name="method_option">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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181 <param name="method" value="seg_contour"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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182 <param name="im1" value="sample2.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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183 <param name="im2" value="mask3.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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184 <param name="thickness" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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185 <param name="color" value="#ff0000"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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186 <param name="label_color" value="#ffff00"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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187 <section name="fp_conversion">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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188 <param name="lower" value="-1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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189 <param name="upper" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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190 </section>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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191 </conditional>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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192 <expand macro="tests/intensity_image_diff" name="out_png" value="test7.png" ftype="png"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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193 </test>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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194 <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test min/1 -->
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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195 <conditional name="method_option">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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196 <param name="method" value="seg_contour"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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197 <param name="im1" value="sample2.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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198 <param name="im2" value="mask3.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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199 <param name="thickness" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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200 <param name="color" value="#ff0000"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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201 <param name="label_color" value="#ffff00"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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202 <section name="fp_conversion">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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203 <param name="lower" value="min"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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204 <param name="upper" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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205 </section>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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206 </conditional>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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207 <expand macro="tests/intensity_image_diff" name="out_png" value="test8.png" ftype="png"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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208 </test>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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209 <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test 0/max -->
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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210 <conditional name="method_option">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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211 <param name="method" value="seg_contour"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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212 <param name="im1" value="sample2.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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213 <param name="im2" value="mask3.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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214 <param name="thickness" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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215 <param name="color" value="#ff0000"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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216 <param name="label_color" value="#ffff00"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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217 <section name="fp_conversion">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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218 <param name="lower" value="0"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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219 <param name="upper" value="max"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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220 </section>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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221 </conditional>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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222 <expand macro="tests/intensity_image_diff" name="out_png" value="test9.png" ftype="png"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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223 </test>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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224 <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test min/max -->
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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225 <conditional name="method_option">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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226 <param name="method" value="seg_contour"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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227 <param name="im1" value="sample2.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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228 <param name="im2" value="mask3.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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229 <param name="thickness" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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230 <param name="color" value="#ff0000"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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231 <param name="label_color" value="#ffff00"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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232 <section name="fp_conversion">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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233 <param name="lower" value="min"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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234 <param name="upper" value="max"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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235 </section>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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236 </conditional>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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237 <expand macro="tests/intensity_image_diff" name="out_png" value="test10.png" ftype="png"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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238 </test>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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239 <test expect_failure="true"><!-- segmentation overlay, floating point conversion test with illegal settings -->
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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240 <conditional name="method_option">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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241 <param name="method" value="seg_contour"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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242 <param name="im1" value="sample3.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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243 <param name="im2" value="mask3.tiff"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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244 <param name="thickness" value="1"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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245 <param name="color" value="#ff0000"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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246 <param name="label_color" value="#ffff00"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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247 <section name="fp_conversion">
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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248 <param name="lower" value="0"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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249 <param name="upper" value="max"/>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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250 </section>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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251 </conditional>
61009b4361c1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
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252 <assert_stderr>
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253 <has_text text="Lower bound (0) must be less than upper bound (-10)." />
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254 </assert_stderr>
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255 </test>
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256 </tests>
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257 <help><![CDATA[
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258
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259 **Overlays two images for visualization.**
0
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260
3
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261 This tool overlays two image to visualize *linear image blending*, *colocalization*, or *segmentation contours*
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262 over an intensity image. For *image blending* and *colocalization*, the input images must be single-channel 2-D
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263 images. For *segmentation contours*, the intensity must be a 2-D single-channel or 2-D RGB image.
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264
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265 ]]></help>
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266 <citations>
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267 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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268 </citations>
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269 </tool>