annotate overlay_images.xml @ 4:37662cbf44b8 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
author imgteam
date Fri, 17 Nov 2023 23:34:57 +0000
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1 <tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description></description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.0.4</token>
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5 <token name="@VERSION_SUFFIX@">0</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">galaxy_image_analysis</xref>
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12 </xrefs>
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13 <requirements>
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14 <requirement type="package" version="0.18.1">scikit-image</requirement>
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15 <requirement type="package" version="3.3.4">matplotlib</requirement>
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16 <requirement type="package" version="2020.10.1">tifffile</requirement>
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17 <requirement type="package" version="1.20.2">numpy</requirement>
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18 </requirements>
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19 <command detect_errors="aggressive">
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20 <![CDATA[
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21 python '$__tool_directory__/overlay_images.py'
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22 '$method_option.im1' '$method_option.im2'
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23 #if $method_option.method == "seg_contour"
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24 ./output.png
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25 #else
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26 ./output.tif
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27 #end if
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28 --method $method_option.method
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29 #if $method_option.method == "blending"
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30 --alpha $method_option.alpha
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31 #elif $method_option.method == "seg_contour"
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32 --thickness $method_option.thickness
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33 --color '$method_option.color'
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34 $method_option.show_label
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35 --label_color '$method_option.label_color'
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36 #end if
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37 ]]>
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38 </command>
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39 <inputs>
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40 <conditional name="method_option">
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41 <param name="method" type="select" label="How to visualize the overlay?">
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42 <option value="coloc_vis" selected="True">Colocalization</option>
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43 <option value="blending">Blending</option>
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44 <option value="seg_contour">Segmentation mask over image</option>
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45 </param>
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46 <when value="coloc_vis">
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47 <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" />
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48 <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" />
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49 </when>
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50 <when value="blending">
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51 <param name="im1" type="data" format="tiff,png" label="Image #1" />
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52 <param name="im2" type="data" format="tiff,png" label="Image #2" />
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53 <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/>
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54 </when>
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55 <when value="seg_contour">
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56 <param name="im1" type="data" format="tiff,png" label="Image" />
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57 <param name="im2" type="data" format="tiff,png" label="Label image" />
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58 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" />
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59 <param name="color" type="color" value="#ff0000" label="Contour color"/>
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60 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" />
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61 <param name="label_color" type="color" value="#ffff00" label="Label color"/>
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62 </when>
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63 </conditional>
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64 </inputs>
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65 <outputs>
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66 <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${tool.name} on ${on_string} output:tiff">
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67 <filter>method_option['method'] != 'seg_contour'</filter>
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68 </data>
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69 <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png">
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70 <filter>method_option['method'] == 'seg_contour'</filter>
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71 </data>
0
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72 </outputs>
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73 <tests>
3
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74 <test expect_num_outputs="1">
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75 <param name="im1" value="mask1.tif"/>
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76 <param name="im2" value="mask1r.tif"/>
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77 <param name="method" value="coloc_vis"/>
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78 <output name="out_tiff" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
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79 </test>
3
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80 <test expect_num_outputs="1">
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81 <param name="im1" value="mask1.tif"/>
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82 <param name="im2" value="mask1r.tif"/>
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83 <param name="method" value="blending"/>
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84 <param name="alpha" value="0.3"/>
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85 <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
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86 </test>
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87 <test expect_num_outputs="1">
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88 <param name="im1" value="sample1_uint8.tif"/>
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89 <param name="im2" value="mask1.tif"/>
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90 <param name="method" value="seg_contour"/>
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91 <param name="thickness" value="2"/>
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92 <param name="color" value="#ff0000"/>
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93 <param name="show_label" value="--show_label"/>
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94 <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
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95 </test>
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96 <test expect_num_outputs="1"><!-- segemtation overlay, 8bit test -->
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97 <param name="im1" value="sample1_uint8.tif"/>
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98 <param name="im2" value="mask2.tif"/>
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99 <param name="method" value="seg_contour"/>
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100 <param name="thickness" value="2"/>
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101 <param name="color" value="#ff0000"/>
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102 <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
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103 </test>
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104 <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test -->
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105 <param name="im1" value="sample1_uint16.tif"/>
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106 <param name="im2" value="mask2.tif"/>
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107 <param name="method" value="seg_contour"/>
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108 <param name="thickness" value="2"/>
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109 <param name="color" value="#ff0000"/>
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110 <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
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111 </test>
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112 </tests>
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113 <help>
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114 <![CDATA[
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115 This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image.
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116 ]]>
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117 </help>
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118 <citations>
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119 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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120 </citations>
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121 </tool>