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comparison projective_transformation_points.xml @ 5:c88235457379 draft default tip

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c4424f5dd4110c92ae39815ebfe2ea8c1010be9c"
author imgteam
date Wed, 26 Jan 2022 15:25:08 +0000
parents b9121ff67280
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4:b9121ff67280 5:c88235457379
1 <tool id="ip_projective_transformation_points" name="Projective Transformation" version="0.1.0"> 1 <tool id="ip_projective_transformation_points" name="Projective Transformation" license="MIT" version="0.1.1" profile="20.05">
2 <description>of input points</description> 2 <description>of ROIs defined by pixel (point) coordinates</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.14.2">scikit-image</requirement> 4 <requirement type="package" version="0.14.2">scikit-image</requirement>
5 <requirement type="package" version="1.2.1">scipy</requirement> 5 <requirement type="package" version="1.2.1">scipy</requirement>
6 <requirement type="package" version="0.23.4">pandas</requirement> 6 <requirement type="package" version="0.23.4">pandas</requirement>
7 <requirement type="package" version="1.15.2">numpy</requirement> 7 <requirement type="package" version="1.15.2">numpy</requirement>
8 <requirement type="package" version="0.15.1">tifffile</requirement> 8 <requirement type="package" version="0.15.1">tifffile</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command detect_errors="aggressive">
11 <![CDATA[ 11 <![CDATA[
12 python '$__tool_directory__/projective_transformation_points.py' 12 python '$__tool_directory__/projective_transformation_points.py'
13 '$moving_points' 13 '$input'
14 '$warp_matrix' 14 '$tmat'
15 '$out' 15 '$output'
16 ]]> 16 ]]>
17 </command> 17 </command>
18 <inputs> 18 <inputs>
19 <param name="moving_points" type="data" format="tabular" label="Moving Points" /> 19 <param name="input" type="data" format="tabular" label="ROIs (pixel coordinates) to be transformed (TSV file)" />
20 <param name="warp_matrix" type= "data" format="tabular" label="Warp Matrix" /> 20 <param name="tmat" type= "data" format="tabular" label="Transformation matrix (TSV file)" />
21 </inputs> 21 </inputs>
22 <outputs> 22 <outputs>
23 <data format="tabular" name="out" /> 23 <data format="tabular" name="output" />
24 </outputs> 24 </outputs>
25 <tests> 25 <tests>
26 <test> 26 <test>
27 <param name="moving_points" value="points_tsv.tsv" /> 27 <param name="input" value="in.tabular" />
28 <param name="warp_matrix" value="warp_matrix.tsv" /> 28 <param name="tmat" value="tmat.tabular" />
29 <output name="out" value="out.tsv" ftype="tabular" /> 29 <output name="output" value="out.tabular" ftype="tabular" compare="diff" />
30 </test> 30 </test>
31 </tests> 31 </tests>
32 <help> 32 <help>
33 **What it does** 33 **What it does**
34 34
35 This tool performs a projective transformation of the input (moving) points (with/without labels). 35 This tool performs a projective transformation of regions of interest (ROIs) defined by pixel (point) coordinates with/without labels.
36
37 About the format of point coordinates (and labels) in the input TSV table:
38 1st column: x-coordinate;
39 2nd column: y-coordinate;
40 (optional) more column(s): point label(s) (numerical or categorical).
41 The top row of the table will be regarded as column headers.
42
36 </help> 43 </help>
37 <citations> 44 <citations>
38 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 45 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
39 </citations> 46 </citations>
40 </tool> 47 </tool>