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annotate binary2label.xml @ 3:a041e4e9d449 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
author imgteam
date Mon, 12 May 2025 08:15:32 +0000
parents 37b99b904027
children
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3
a041e4e9d449 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
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1 <tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description></description>
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3 <macros>
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4 <import>creators.xml</import>
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5 <token name="@TOOL_VERSION@">0.6</token>
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6 <token name="@VERSION_SUFFIX@">0</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 </creator>
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11 <edam_operations>
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12 <edam_operation>operation_3443</edam_operation>
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13 </edam_operations>
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14 <xrefs>
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15 <xref type="bio.tools">galaxy_image_analysis</xref>
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16 </xrefs>
0
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17 <requirements>
3
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18 <requirement type="package" version="0.4.0">giatools</requirement>
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19 <requirement type="package" version="1.12.0">scipy</requirement>
0
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20 </requirements>
1
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21 <command detect_errors="aggressive">
0
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22 <![CDATA[
3
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23 #if str($mode.mode_selector) == 'cca':
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24 python '$__tool_directory__/binary2label.py' '$input' '$output'
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25 #elif str($mode.mode_selector) == 'watershed':
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26 python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance
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27 #end if
0
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28 ]]>
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29 </command>
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30 <inputs>
3
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31 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary image"/>
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32 <conditional name="mode">
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33 <param name="mode_selector" type="select" label="Mode">
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34 <option value="cca" selected="true">Connected component analysis</option>
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35 <option value="watershed">Watershed transform</option>
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36 </param>
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37 <when value="cca">
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38 </when>
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39 <when value="watershed">
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40 <param name="min_distance" type="integer" min="0" value="5" label="Minimum distance between two objects" />
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41 </when>
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42 </conditional>
0
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43 </inputs>
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44 <outputs>
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45 <data format="tiff" name="output"/>
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46 </outputs>
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47 <tests>
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48 <test>
3
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49 <param name="input" value="galaxyIcon_noText.tiff" />
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50 <conditional name="mode">
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51 <param name="mode_selector" value="cca" />
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52 </conditional>
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53 <output name="output" value="label.tiff" ftype="tiff" compare="image_diff"/>
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54 </test>
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55 <test>
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56 <param name="input" value="in.tiff"/>
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57 <conditional name="mode">
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58 <param name="mode_selector" value="watershed" />
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59 <param name="min_distance" value="10" />
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60 </conditional>
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61 <output name="output" value="out.tiff" ftype="tiff" compare="image_diff"/>
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62 </test>
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63 <test>
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64 <param name="input" value="uint8_z12_x11_y10.tiff"/>
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65 <conditional name="mode">
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66 <param name="mode_selector" value="cca" />
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67 </conditional>
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68 <output name="output" value="uint8_z12_x11_y10-output.tiff" ftype="tiff" compare="image_diff">
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69 <assert_contents>
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70 <has_image_width width="11"/>
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71 <has_image_height height="10"/>
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72 <has_image_depth depth="12"/>
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73 </assert_contents>
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74 </output>
0
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75 </test>
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76 </tests>
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77 <help>
3
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78 This tool assigns each object a unique label.
0
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79
3
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80 Individual objects are determined using connected component analysis, or distance transform and watershed.
0
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81 </help>
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82 <citations>
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83 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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84 </citations>
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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85 </tool>