Mercurial > repos > imgteam > binary2labelimage

comparison binary2label.xml @ 4:984358e43242 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
author imgteam
date Tue, 14 Nov 2023 08:27:27 +0000
parents 9bb446db4a1e
children
comparison
equal deleted inserted replaced
3:9bb446db4a1e 4:984358e43242
1 <tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="0.4-2"> 1 <tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description></description> 2 <description></description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.5</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
3 <edam_operations> 7 <edam_operations>
4 <edam_operation>operation_3443</edam_operation> 8 <edam_operation>operation_3443</edam_operation>
5 </edam_operations> 9 </edam_operations>
6 <xrefs> 10 <xrefs>
7 <xref type="bio.tools">galaxy_image_analysis</xref> 11 <xref type="bio.tools">galaxy_image_analysis</xref>
8 </xrefs> 12 </xrefs>
9 <requirements> 13 <requirements>
10 <requirement type="package" version="0.12.3">scikit-image</requirement> 14 <requirement type="package" version="0.14.2">scikit-image</requirement>
11 <requirement type="package" version="0.15.1">tifffile</requirement> 15 <requirement type="package" version="0.15.1">tifffile</requirement>
16 <requirement type="package" version="1.15.4">numpy</requirement>
17 <requirement type="package" version="5.3.0">pillow</requirement>
18 <requirement type="package" version="1.2.1">scipy</requirement>
12 </requirements> 19 </requirements>
13 <command detect_errors="aggressive"> 20 <command detect_errors="aggressive">
14 <![CDATA[ 21 <![CDATA[
15 python '$__tool_directory__/binary2label.py' '$input' '$output' 22 #if str($mode.mode_selector) == 'cca':
23 python '$__tool_directory__/binary2label.py' '$input' '$output'
24 #elif str($mode.mode_selector) == 'watershed':
25 python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance
26 #end if
16 ]]> 27 ]]>
17 </command> 28 </command>
18 <inputs> 29 <inputs>
19 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/> 30 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary image"/>
31 <conditional name="mode">
32 <param name="mode_selector" type="select" label="Mode">
33 <option value="cca">Connected component analysis</option>
34 <option value="watershed">Watershed transform</option>
35 </param>
36 <when value="cca">
37 </when>
38 <when value="watershed">
39 <param name="min_distance" type="integer" min="0" value="5" label="Minimum distance between two objects" />
40 </when>
41 </conditional>
20 </inputs> 42 </inputs>
21 <outputs> 43 <outputs>
22 <data format="tiff" name="output"/> 44 <data format="tiff" name="output"/>
23 </outputs> 45 </outputs>
24 <tests> 46 <tests>
25 <test> 47 <test>
26 <param name="input" value="galaxyIcon_noText.tif" /> 48 <param name="input" value="galaxyIcon_noText.tif" />
49 <conditional name="mode">
50 <param name="mode_selector" value="cca" />
51 </conditional>
27 <output name="output" value="label.tif" ftype="tiff" compare="sim_size"/> 52 <output name="output" value="label.tif" ftype="tiff" compare="sim_size"/>
53 </test>
54 <test>
55 <param name="input" value="in.tif"/>
56 <conditional name="mode">
57 <param name="mode_selector" value="watershed" />
58 <param name="min_distance" value="10" />
59 </conditional>
60 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
28 </test> 61 </test>
29 </tests> 62 </tests>
30 <help> 63 <help>
31 **What it does** 64 This tool assigns each object a unique label.
32 65
33 This tool assigns every object an own grey value. 66 Individual objects are determined using connected component analysis, or distance transform and watershed.
34 </help> 67 </help>
35 <citations> 68 <citations>
36 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 69 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
37 </citations> 70 </citations>
38 </tool> 71 </tool>