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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
author | imgteam |
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date | Tue, 14 Nov 2023 08:27:27 +0000 |
parents | 9bb446db4a1e |
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<tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description></description> <macros> <token name="@TOOL_VERSION@">0.5</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> <xrefs> <xref type="bio.tools">galaxy_image_analysis</xref> </xrefs> <requirements> <requirement type="package" version="0.14.2">scikit-image</requirement> <requirement type="package" version="0.15.1">tifffile</requirement> <requirement type="package" version="1.15.4">numpy</requirement> <requirement type="package" version="5.3.0">pillow</requirement> <requirement type="package" version="1.2.1">scipy</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ #if str($mode.mode_selector) == 'cca': python '$__tool_directory__/binary2label.py' '$input' '$output' #elif str($mode.mode_selector) == 'watershed': python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance #end if ]]> </command> <inputs> <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary image"/> <conditional name="mode"> <param name="mode_selector" type="select" label="Mode"> <option value="cca">Connected component analysis</option> <option value="watershed">Watershed transform</option> </param> <when value="cca"> </when> <when value="watershed"> <param name="min_distance" type="integer" min="0" value="5" label="Minimum distance between two objects" /> </when> </conditional> </inputs> <outputs> <data format="tiff" name="output"/> </outputs> <tests> <test> <param name="input" value="galaxyIcon_noText.tif" /> <conditional name="mode"> <param name="mode_selector" value="cca" /> </conditional> <output name="output" value="label.tif" ftype="tiff" compare="sim_size"/> </test> <test> <param name="input" value="in.tif"/> <conditional name="mode"> <param name="mode_selector" value="watershed" /> <param name="min_distance" value="10" /> </conditional> <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> </test> </tests> <help> This tool assigns each object a unique label. Individual objects are determined using connected component analysis, or distance transform and watershed. </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> </citations> </tool>