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annotate overlay_images.xml @ 2:b74693340624 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
author imgteam
date Thu, 10 Aug 2023 07:29:34 +0000
parents bf590a9733ed
children 22ff7c705a83
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b74693340624 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 71dae1df58f579b84d4f9d92fb0dd509c02dd48f
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1 <tool id="ip_overlay_images" name="Overlay Images" version="0.0.3" profile="20.05">
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2 <description>for visualization</description>
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3 <requirements>
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4 <requirement type="package" version="0.18.1">scikit-image</requirement>
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5 <requirement type="package" version="3.3.4">matplotlib</requirement>
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6 <requirement type="package" version="2020.10.1">tifffile</requirement>
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7 <requirement type="package" version="1.20.2">numpy</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive">
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10 <![CDATA[
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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11 python '$__tool_directory__/overlay_images.py'
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12 '$method_option.im1' '$method_option.im2' ./output.tif
bf590a9733ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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13 --method $method_option.method
bf590a9733ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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14 #if $method_option.method == "blending"
bf590a9733ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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15 --alpha $method_option.alpha
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16 #elif $method_option.method == "seg_contour"
bf590a9733ed planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit cd63bc5e6eb7254111012209fac9154569355f20
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17 --thickness $method_option.thickness
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18 --color '$method_option.color'
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19 $method_option.show_label
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20 --label_color '$method_option.label_color'
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21 #end if
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22 ]]>
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23 </command>
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24 <inputs>
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25 <conditional name="method_option">
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26 <param name="method" type="select" label="How to visualize the overlay?">
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27 <option value="coloc_vis" selected="True">Colocalization</option>
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28 <option value="blending">Blending</option>
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29 <option value="seg_contour">Segmentation mask over image</option>
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30 </param>
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31 <when value="coloc_vis">
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32 <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" />
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33 <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" />
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34 </when>
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35 <when value="blending">
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36 <param name="im1" type="data" format="tiff,png" label="Image #1" />
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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37 <param name="im2" type="data" format="tiff,png" label="Image #2" />
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38 <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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39 </when>
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40 <when value="seg_contour">
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41 <param name="im1" type="data" format="tiff,png" label="Image" />
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42 <param name="im2" type="data" format="tiff,png" label="Label image" />
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43 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" />
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44 <param name="color" type="color" value="#ff0000" label="Contour color"/>
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45 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" />
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46 <param name="label_color" type="color" value="#ffff00" label="Label color"/>
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data format="tiff" name="out" from_work_dir="output.tif" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="im1" value="mask1.tif"/>
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56 <param name="im2" value="mask1r.tif"/>
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57 <param name="method" value="coloc_vis"/>
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58 <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
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59 </test>
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60 <test>
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61 <param name="im1" value="mask1.tif"/>
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62 <param name="im2" value="mask1r.tif"/>
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63 <param name="method" value="blending"/>
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64 <param name="alpha" value="0.3"/>
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65 <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
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66 </test>
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67 <test>
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68 <param name="im1" value="sample1.tif"/>
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69 <param name="im2" value="mask1.tif"/>
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70 <param name="method" value="seg_contour"/>
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71 <param name="thickness" value="2"/>
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72 <param name="color" value="#ff0000"/>
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73 <param name="show_label" value="--show_label"/>
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74 <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
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75 </test>
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76 <test>
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77 <param name="im1" value="sample1.tif"/>
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78 <param name="im2" value="mask2.tif"/>
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79 <param name="method" value="seg_contour"/>
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80 <param name="thickness" value="2"/>
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81 <param name="color" value="#ff0000"/>
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82 <output name="out" value="test4.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
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83 </test>
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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84 </tests>
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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85 <help>
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86 **What it does**
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87
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88 This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image.
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89 </help>
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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90 <citations>
2
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91 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
0
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92 </citations>
589af0005df5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 736949b5fb325cc7880d0ff0bb13b78115b9f81c"
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93 </tool>