Mercurial > repos > imgteam > 2d_auto_threshold

annotate auto_threshold.xml @ 0:6fc65082d1e6 draft

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/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
author imgteam
date Sat, 09 Feb 2019 14:02:57 -0500
parents
children 7f2962f619e3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
1 <tool id="ip_threshold" name="Auto Threshold" version="0.0.3">
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
2 <description>applies a standard threshold algorithm to an image</description>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
3 <requirements>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
4 <requirement type="package" version="0.14.2">scikit-image</requirement>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
5 <requirement type="package" version="1.15.4">numpy</requirement>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
6 <requirement type="package" version="5.3.0">pillow</requirement>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
7 <requirement type="package" version="0.15.1">tifffile</requirement>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
8 </requirements>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
9 <command detect_errors="aggressive">
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
10 <![CDATA[
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
11 python '$__tool_directory__/auto_threshold.py' '$input' '$output' $thresh_type $dark_background
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
12 ]]>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
13 </command>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
14 <inputs>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
15 <param name="input" type="data" format="tiff" label="Source file" />
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
16 <param name="thresh_type" type="select" label="Threshold Algorithm">
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
17 <option value="otsu" selected="True">Otsu</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
18 <option value="li">Li’s Minimum Cross Entropy</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
19 <option value="isodata">Isodata</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
20 <option value="gaussian_adaptive">Adaptive (Gauss)</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
21 <option value="mean_adaptive">Adaptive (Mean)</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
22 <option value="yen">Yen</option>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
23 </param>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
24 <param name="dark_background" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Dark Background" />
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
25 </inputs>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
26 <outputs>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
27 <data format="tiff" name="output" />
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
28 </outputs>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
29 <tests>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
30 <test>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
31 <param name="input" value="sample.tif"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
32 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
33 <param name="thresh_type" value="gaussian_adaptive"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
34 <param name="dark_backgroud" value="True"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
35 </test>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
36 <test>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
37 <param name="input" value="sample.tif"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
38 <output name="output" value="out2.tif" ftype="tiff" compare="sim_size"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
39 <param name="thresh_type" value="otsu"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
40 <param name="dark_backgroud" value="True"/>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
41 </test>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
42 </tests>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
43 <help>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
44 Applies a standard threshold algorithm to an image.
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
45 </help>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
46 <citations>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
47 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
48 </citations>
6fc65082d1e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit bd6ef77515c4c15901b67f73738afbdd5faadae5
imgteam
parents:
diff changeset
49 </tool>