Mercurial > repos > imgteam > landmark_registration

annotate landmark_registration.xml @ 0:a71239f3543a 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/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
author imgteam
date Tue, 12 Feb 2019 08:35:45 -0500
parents
children 4e089a0983b1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
1 <tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.2">
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
2 <description>Landmark Registration</description>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
3 <requirements>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
4 <requirement type="package" version="0.14.2">scikit-image</requirement>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
5 <requirement type="package" version="0.23.4">pandas</requirement>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
6 <requirement type="package" version="1.15.4">numpy</requirement>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
7 </requirements>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
8 <command><![CDATA[
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
9 python '$__tool_directory__/landmark_registration.py'
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
10 --residual_threshold $residual_threshold
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
11 --max_trials $max_trials
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
12 '$points_file1'
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
13 '$points_file2'
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
14 '$warp_matrix'
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
15 ]]></command>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
16 <inputs>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
17 <param name="points_file1" type="data" format="tabular" label="Path to tab-separated file with src points" />
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
18 <param name="points_file2" type="data" format="tabular" label="Path to tab-separated file with dst points" />
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
19 <param name="residual_threshold" type="float" value="2" label="Maximum distance for a data point to be classified as an inlier." />
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
20 <param name="max_trials" type="integer" value="100" label="Maximum number of iterations for random sample selection." />
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
21 </inputs>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
22 <outputs>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
23 <data format="tabular" name="warp_matrix" />
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
24 </outputs>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
25 <tests>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
26 <test>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
27 <param name="points_file1" value="points1.tsv"/>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
28 <param name="points_file2" value="points2.tsv"/>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
29 <param name="residual_threshold" value="2"/>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
30 <param name="max_trials" value="100"/>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
31 <output name="warp_matrix" value="warp.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
32 </test>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
33 </tests>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
34 <help>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
35 **What it does**
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
36
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
37 This tool estimates the transformation matrix between two sets of 2d points.
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
38 </help>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
39 <citations>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
40 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
41 </citations>
a71239f3543a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ commit d5df0e2f37920d09b5d942a7b128041ee1f0b6f5
imgteam
parents:
diff changeset
42 </tool>