Mercurial > repos > imgteam > landmark_registration

diff landmark_registration.xml @ 0:a71239f3543a draft

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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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/landmark_registration.xml	Tue Feb 12 08:35:45 2019 -0500
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+<tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.2">
+    <description>Landmark Registration</description>
+    <requirements>
+        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="0.23.4">pandas</requirement>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+    </requirements>
+    <command><![CDATA[
+         python '$__tool_directory__/landmark_registration.py'
+         --residual_threshold $residual_threshold
+         --max_trials $max_trials
+         '$points_file1'
+         '$points_file2'
+         '$warp_matrix'
+]]></command>
+    <inputs>
+          <param name="points_file1" type="data" format="tabular" label="Path to tab-separated file with src points" />
+          <param name="points_file2" type="data" format="tabular" label="Path to tab-separated file with dst points" />
+          <param name="residual_threshold" type="float" value="2" label="Maximum distance for a data point to be classified as an inlier." />
+        <param name="max_trials" type="integer" value="100" label="Maximum number of iterations for random sample selection." />
+    </inputs>
+    <outputs>
+       <data format="tabular" name="warp_matrix" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="points_file1" value="points1.tsv"/>
+            <param name="points_file2" value="points2.tsv"/>
+            <param name="residual_threshold" value="2"/>
+            <param name="max_trials" value="100"/>
+            <output name="warp_matrix" value="warp.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    This tool estimates the transformation matrix between two sets of 2d points.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>