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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 05:00:03 -0400
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1 <tool id="ip_2d_filter_segmentation_by_features" name="Filter segmentation" version="0.0.1">
2 <description>Filter segmentation by rules</description>
3 <requirements>
4 <requirement type="package" version="0.14.2">scikit-image</requirement>
5 <requirement type="package" version="5.3.0">pillow</requirement>
6 <requirement type="package" version="0.23.4">pandas</requirement>
7 <requirement type="package" version="0.15.1">tifffile</requirement>
8 </requirements>
9 <command detect_errors="aggressive">
10 <![CDATA[
11 python '$__tool_directory__/2d_filter_segmentation_by_features.py' '$input' '$output' '$feature_file' '$rule_file'
12 ]]>
13 </command>
14 <inputs>
15 <param name="input" type="data" format="tiff" label="Source file" />
16 <param name="feature_file" type="data" format="tabular" label="Feature file" />
17 <param name="rule_file" type="data" format="tabular" label="Rules file" />
18 </inputs>
19 <outputs>
20 <data format="tiff" name="output" />
21 </outputs>
22 <tests>
23 <test>
24 <param name="input" value="in.tif"/>
25 <param name="feature_file" value="features.tabular"/>
26 <param name="rule_file" value="rules.tabular"/>
27 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
28 </test>
29 </tests>
30 <help>
31 Filter label image by rules (e.g., remove large or deformed objects).
32 Rules file has a specific format (cols: ,f1,2, rows: feature_name, min, max). The features have to be also profived in a specific format (cols: label, f1, f2).
33 </help>
34 <citations>
35 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
36 </citations>
37 </tool>