Mercurial > repos > imgteam > 2d_split_binaryimage_by_watershed

annotate 2d_split_binaryimage_by_watershed.xml @ 1:f8f7987586b7 draft default tip

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_split_binaryimage_by_watershed/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:01:10 -0500
parents 5e21d7342593
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
1 <tool id="ip_2d_split_binaryimage_by_watershed" name="Split objects" version="0.0.1">
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
2 <description>Split binary image by using watershed</description>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
3 <requirements>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
4 <requirement type="package" version="0.14.2">scikit-image</requirement>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
5 <requirement type="package" version="1.15.4">numpy</requirement>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
6 <requirement type="package" version="5.3.0">pillow</requirement>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
7 <requirement type="package" version="0.15.1">tifffile</requirement>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
8 <requirement type="package" version="1.2.1">scipy</requirement>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
9 </requirements>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
10 <command detect_errors="aggressive">
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
11 <![CDATA[
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
12 python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
13 ]]>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
14 </command>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
15 <inputs>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
16 <param name="input" type="data" format="tiff" label="Source file" />
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
17 <param name="min_distance" type="integer" value="5" label="Minimum distance between two objects." />
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
18 </inputs>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
19 <outputs>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
20 <data format="tiff" name="output" />
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
21 </outputs>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
22 <tests>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
23 <test>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
24 <param name="input" value="in.tif"/>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
25 <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
26 <param name="min_distance" value="10"/>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
27 </test>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
28 </tests>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
29 <help>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
30 Split binary image by using distance transform and watershed.
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
31 </help>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
32 <citations>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
33 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
34 </citations>
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
35 </tool>