annotate histogram_equalization.xml @ 3:b1c2c210813c draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:11:54 +0000
parents 3f3783846dc0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
1 <tool id="ip_histogram_equalization" name="Perform histogram equalization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
2 <description>with scikit-image</description>
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
3 <macros>
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
4 <import>creators.xml</import>
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
5 <import>tests.xml</import>
3
b1c2c210813c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
parents: 2
diff changeset
6 <token name="@TOOL_VERSION@">0.18.1</token>
2
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
7 <token name="@VERSION_SUFFIX@">0</token>
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
8 </macros>
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
9 <creator>
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
10 <expand macro="creators/bmcv" />
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
11 </creator>
1
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
12 <edam_operations>
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
13 <edam_operation>operation_3443</edam_operation>
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
14 </edam_operations>
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
15 <xrefs>
2
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
16 <xref type="bio.tools">scikit-image</xref>
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
17 <xref type="biii">scikit-image</xref>
1
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
18 </xrefs>
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
19 <requirements>
2
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
20 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
3
b1c2c210813c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
parents: 2
diff changeset
21 <requirement type="package" version="1.23.3">numpy</requirement>
b1c2c210813c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
parents: 2
diff changeset
22 <requirement type="package" version="2020.10.1">tifffile</requirement>
b1c2c210813c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
parents: 2
diff changeset
23 <requirement type="package" version="0.1">giatools</requirement>
1
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
24 </requirements>
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
25 <command detect_errors="aggressive">
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
26 <![CDATA[
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
27 python '$__tool_directory__/histogram_equalization.py' '$input' '$output' $h_type
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
28 ]]>
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
29 </command>
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
30 <inputs>
2
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
31 <param name="input" type="data" format="tiff" label="Input image" />
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
32 <param name="h_type" type="select" label="Histogram equalization algorithm">
0
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
33 <option value="default">Stretching</option>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
34 <option value="clahe" selected="True">CLAHE</option>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
35 </param>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
36 </inputs>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
37 <outputs>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
38 <data format="tiff" name="output" />
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
39 </outputs>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
40 <tests>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
41 <test>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
42 <param name="input" value="sample.tif"/>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
43 <param name="h_type" value="default"/>
2
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
44 <expand macro="tests/intensity_image_diff" name="output" value="out.tif" ftype="tiff"/>
0
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
45 </test>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
46 </tests>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
47 <help>
2
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
48
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
49 **Applies histogram equalization to an image.**
3f3783846dc0 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
parents: 1
diff changeset
50
0
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
51 </help>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
52 <citations>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
53 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
54 </citations>
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
55 </tool>