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comparison filter.xml @ 2:f70b215d155c draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
author imgteam
date Fri, 10 Nov 2023 13:44:57 +0000
parents dba87c4b32d3
children 6c4b22ef2b81
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1:dba87c4b32d3 2:f70b215d155c
1 <tool id="ip_filter_standard" name="Filter Image" version="0.0.3"> 1 <tool id="ip_filter_standard" name="Filter 2D image" version="0.0.3-3">
2 <description>applies a standard filter to an image</description> 2 <description>with scikit-image</description>
3 <edam_operations>
4 <edam_operation>operation_3443</edam_operation>
5 </edam_operations>
6 <xrefs>
7 <xref type="bio.tools">scikit-image</xref>
8 <xref type="biii">scikit-image</xref>
9 </xrefs>
3 <requirements> 10 <requirements>
4 <requirement type="package" version="0.14.2">scikit-image</requirement> 11 <requirement type="package" version="0.14.2">scikit-image</requirement>
5 <requirement type="package" version="1.15.4">numpy</requirement> 12 <requirement type="package" version="1.15.4">numpy</requirement>
6 <requirement type="package" version="5.3.0">pillow</requirement> 13 <requirement type="package" version="5.3.0">pillow</requirement>
7 <requirement type="package" version="0.15.1">tifffile</requirement> 14 <requirement type="package" version="0.15.1">tifffile</requirement>
10 <![CDATA[ 17 <![CDATA[
11 python '$__tool_directory__/filter_image.py' '$input' '$output' $filter_type $radius 18 python '$__tool_directory__/filter_image.py' '$input' '$output' $filter_type $radius
12 ]]> 19 ]]>
13 </command> 20 </command>
14 <inputs> 21 <inputs>
15 <param name="filter_type" type="select" label="Image type"> 22 <param name="filter_type" type="select" label="Filter type">
16 <option value="median" selected="True">Median</option> 23 <option value="median" selected="True">Median</option>
17 <option value="gaussian">Gaussian Blur</option> 24 <option value="gaussian">Gaussian Blur</option>
18 <option value="prewitt">Prewitt</option> 25 <option value="prewitt">Prewitt</option>
19 <option value="sobel">Sobel</option> 26 <option value="sobel">Sobel</option>
20 <option value="scharr">Scharr</option> 27 <option value="scharr">Scharr</option>
22 <param name="radius" type="integer" value="3" label="Radius/Sigma" /> 29 <param name="radius" type="integer" value="3" label="Radius/Sigma" />
23 <param name="input" type="data" format="tiff" label="Source file" /> 30 <param name="input" type="data" format="tiff" label="Source file" />
24 </inputs> 31 </inputs>
25 <outputs> 32 <outputs>
26 <data format="tiff" name="output" /> 33 <data format="tiff" name="output" />
27 </outputs> 34 </outputs>
28 <tests> 35 <tests>
29 <test> 36 <test>
30 <param name="input" value="sample.tif" /> 37 <param name="input" value="sample.tif" />
31 <output name="output" value="res.tif" ftype="tiff" compare="sim_size"/> 38 <output name="output" value="res.tif" ftype="tiff" compare="sim_size"/>
32 <param name="filter_type" value="prewitt" /> 39 <param name="filter_type" value="prewitt" />