Mercurial > repos > imgteam > coordinates_of_roi
comparison coordinates_of_roi.xml @ 0:0d30ffea8874 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author | imgteam |
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date | Sat, 09 Feb 2019 14:33:43 -0500 |
parents | |
children | 24d9bd16c953 |
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1 <tool id="ip_coordinates_of_roi" name="Coordinates of ROI" version="0.0.3"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="0.14.2">scikit-image</requirement> | |
5 <requirement type="package" version="0.23.4">pandas</requirement> | |
6 </requirements> | |
7 <command detect_errors="aggressive"> | |
8 <![CDATA[ | |
9 python '$__tool_directory__/coordinates_of_roi.py' | |
10 '$im' | |
11 '$pixel_table' | |
12 $offset_x $offset_y | |
13 $white_obj | |
14 --threshold $threshold | |
15 ]]> | |
16 </command> | |
17 <inputs> | |
18 <param name="im" type="data" format="png" label="Source file" /> | |
19 <param name="white_obj" type="boolean" truevalue="--white_obj" falsevalue="" checked="false" | |
20 label="Set to Yes if object is white and background black, otherwise set to No" /> | |
21 <param name="threshold" type="float" value="0.5" label="Threshold value" /> | |
22 <param name="offset_x" type="integer" value="0" label="Added offset in x direction (=width direction)" /> | |
23 <param name="offset_y" type="integer" value="0" label="Added offset in y direction (=height direction)" /> | |
24 </inputs> | |
25 <outputs> | |
26 <data format="tabular" name="pixel_table" /> | |
27 </outputs> | |
28 <tests> | |
29 <test> | |
30 <param name="im" value="test.png"/> | |
31 <param name="white_obj" value="true"/> | |
32 <output name="pixel_table" value="table.tsv" ftype="tabular"/> | |
33 </test> | |
34 <test> | |
35 <param name="im" value="test.png"/> | |
36 <param name="white_obj" value="true"/> | |
37 <param name="offset_x" value="1"/> | |
38 <param name="offset_y" value="2"/> | |
39 <output name="pixel_table" value="table2.tsv" ftype="tabular"/> | |
40 </test> | |
41 </tests> | |
42 <help> | |
43 **What it does** | |
44 | |
45 This tool creates a table containing the pixelcoordinates of the Region of Interest (ROI). | |
46 </help> | |
47 <citations> | |
48 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | |
49 </citations> | |
50 </tool> |