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annotate crop_image.xml @ 1:457514bb6750 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
author imgteam
date Fri, 09 Jan 2026 14:54:49 +0000
parents f8bfa85cac4c
children
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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1 <tool id="ip_crop_image" name="Crop image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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2 <description>with giatools</description>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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3 <macros>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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4 <import>creators.xml</import>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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5 <import>tests.xml</import>
1
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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6 <token name="@TOOL_VERSION@">0.7.3</token>
0
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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7 <token name="@VERSION_SUFFIX@">0</token>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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8 </macros>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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9 <creator>
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10 <expand macro="creators/bmcv"/>
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11 <expand macro="creators/kostrykin"/>
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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12 </creator>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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13 <edam_operations>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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14 <edam_operation>operation_3443</edam_operation>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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15 </edam_operations>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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16 <xrefs>
1
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17 <xref type="bio.tools">galaxy_image_analysis</xref>
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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18 <xref type="bio.tools">giatools</xref>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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19 </xrefs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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20 <requirements>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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21 <requirement type="package" version="@TOOL_VERSION@">giatools</requirement>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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22 </requirements>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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23 <command detect_errors="aggressive"><![CDATA[
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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24
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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25 mkdir ./output &&
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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26 python '$__tool_directory__/crop_image.py'
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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27
1
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28 #if $image.extension == "zarr"
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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29 '$image.extra_files_path/$image.metadata.store_root'
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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30 #else
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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31 '$image'
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32 #end if
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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33
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34 #if $labelmap.extension == "zarr"
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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35 '$labelmap.extra_files_path/$labelmap.metadata.store_root'
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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36 #else
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37 '$labelmap'
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38 #end if
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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39
0
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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40 '$skip_labels'
1
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41
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42 #if str($image.ext).lower() == 'png'
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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43 'png'
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44 #else
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45 'tiff'
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46 #end if
0
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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47
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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48 ./output
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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49
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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50 ]]></command>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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51 <inputs>
1
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52 <param name="image" type="data" format="png,tiff,zarr" label="Image file"
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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53 help="The image to be cropped."/>
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54 <param name="labelmap" type="data" format="png,tiff,zarr" label="Label map"
457514bb6750 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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55 help="Each label identifies an individual region of interest, for which a cropped image is produced."/>
0
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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56 <param name="skip_labels" type="text" label="Skip labels" value="0" optional="true" help="Comma-separated list of labels for which no cropped image shall be produced.">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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57 <validator type="regex">^\d+(,\d+)*$|^$</validator>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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58 </param>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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59 </inputs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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60 <outputs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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61 <collection type="list" name="output" label="Crop ${on_string}" format_source="image">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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62 <discover_datasets directory="output" pattern="__name_and_ext__"/>
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63 </collection>
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64 </outputs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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65 <tests>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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66 <!-- Test 2D TIFF -->
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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67 <test>
1
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68 <param name="image" value="yx_float32.tiff"/>
0
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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69 <param name="labelmap" value="yx_uint8.tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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70 <output_collection name="output" type="list" count="2">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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71 <expand macro="tests/intensity_image_diff/element" name="1" value="yx_float32_uint8_1.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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72 <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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73 </output_collection>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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74 </test>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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75 <!-- Test with `skip_labels` -->
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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76 <test>
1
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77 <param name="image" value="yx_float32.tiff"/>
0
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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78 <param name="labelmap" value="yx_uint8.tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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79 <param name="skip_labels" value="0,1"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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80 <output_collection name="output" type="list" count="1">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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81 <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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82 </output_collection>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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83 </test>
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84 <!-- Test with empty `skip_labels` -->
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85 <test>
1
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86 <param name="image" value="yx_float32.tiff"/>
0
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87 <param name="labelmap" value="yx_uint8.tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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88 <param name="skip_labels" value=""/>
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89 <output_collection name="output" type="list" count="3">
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90 <expand macro="tests/intensity_image_diff/element" name="0" value="yx_float32_uint8_0.tiff" ftype="tiff"/>
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91 <expand macro="tests/intensity_image_diff/element" name="1" value="yx_float32_uint8_1.tiff" ftype="tiff"/>
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92 <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
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93 </output_collection>
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94 </test>
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95 <!-- Test 3D TIFF (multi-frame) -->
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96 <test>
1
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97 <param name="image" value="zyx_uint16.tiff"/>
0
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98 <param name="labelmap" value="yxz_uint8.tiff"/>
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99 <output_collection name="output" type="list" count="1">
1
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100 <expand macro="tests/intensity_image_diff/element" name="1" value="zyx_uint16_uint8_1.tiff" ftype="tiff">
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101 <has_image_width width="5"/>
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102 <has_image_height height="3"/>
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103 <has_image_depth depth="6"/>
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104 </expand>
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105 </output_collection>
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106 </test>
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107 <!-- Test PNG (multi-channel) -->
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108 <test>
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109 <param name="image" value="yxc_uint8.png"/>
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110 <param name="labelmap" value="yxc_uint8_mask.png"/>
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111 <output_collection name="output" type="list" count="1">
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112 <expand macro="tests/intensity_image_diff/element" name="2" value="yxc_uint8_uint8_2.png" ftype="png">
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113 <has_image_width width="10"/>
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114 <has_image_height height="12"/>
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115 <has_image_channels channels="3"/>
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116 </expand>
0
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117 </output_collection>
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118 </test>
1
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119 <!-- Test PNG+Zarr (multi-channel `image` PNG with single-channel `labelmap` Zarr) -->
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120 <test>
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121 <param name="image" value="yxc_uint8.png"/>
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122 <param name="labelmap" value="yx_uint8_mask.zarr"/>
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123 <output_collection name="output" type="list" count="1">
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124 <expand macro="tests/intensity_image_diff/element" name="2" value="yxc_uint8_uint8_2.png" ftype="png">
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125 <has_image_width width="10"/>
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126 <has_image_height height="12"/>
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127 <has_image_channels channels="3"/>
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128 </expand>
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129 </output_collection>
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130 </test>
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131 <!-- Test Zarr+TIFF (multi-channel `image` Zarr with single-channel `labelmap` TIFF) -->
0
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132 <test>
1
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133 <param name="image" value="cyx_uint8.zarr"/>
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134 <param name="labelmap" value="yx_uint8_mask.tiff"/>
0
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135 <output_collection name="output" type="list" count="1">
1
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136 <!--
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137 OME-Zarr requires a specific axes order. For this reason, it is not possible to generally write "any" image as an OME-Zarr.
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138 This would require adapting the axes order, which is do-able, but changes the image. This might be unintended or unexpected
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139 in many cases, which is why it is not happening automatically. We might change this behaviour somehow in the future.
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140 -->
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141 <expand macro="tests/intensity_image_diff/element" name="2" value="cyx_uint8_uint8.tiff" ftype="tiff">
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142 <has_image_width width="10"/>
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143 <has_image_height height="12"/>
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144 <has_image_channels channels="3"/>
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145 </expand>
0
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146 </output_collection>
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147 </test>
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148 </tests>
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149 <help>
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150
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151 **Crops an image using one or more regions of interest.**
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152
1
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153 The image is cropped using a label map that identifies individual regions of interest. The image and the label map must be of
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154 compatible size. The sizes are compatible if they are equal, or, if the label map can be broadcasted to the size of the image
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155 (e.g., if the image is a multi-channel image and the label map is single-channel but has identical width and height).
0
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156
1
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157 This operation preserves the brightness and the range of values of the input image. The file format is also preserved, unless
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158 the input image is a Zarr, for which the output image file format is TIFF.
0
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159
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160 </help>
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161 <citations>
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162 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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163 </citations>
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164 </tool>