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comparison projective_transformation.xml @ 6:2f504e075496 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:07 +0000
parents f5744f0e5a81
children 6a8ae8cd7167
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5:f5744f0e5a81 6:2f504e075496
1 <tool id="ip_projective_transformation" name="Performs projective transformation with/without labels" version="0.1.2-2" profile="20.05"> 1 <tool id="ip_projective_transformation" name="Perform projective transformation of an image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description></description> 2 <description></description>
3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">0.1.2</token>
7 <token name="@VERSION_SUFFIX@">3</token>
8 </macros>
9 <creator>
10 <expand macro="creators/bmcv"/>
11 </creator>
3 <edam_operations> 12 <edam_operations>
4 <edam_operation>operation_3443</edam_operation> 13 <edam_operation>operation_3443</edam_operation>
5 </edam_operations> 14 </edam_operations>
6 <xrefs> 15 <xrefs>
7 <xref type="bio.tools">galaxy_image_analysis</xref> 16 <xref type="bio.tools">galaxy_image_analysis</xref>
8 </xrefs> 17 </xrefs>
9 <requirements> 18 <requirements>
10 <requirement type="package" version="0.18.1">scikit-image</requirement> 19 <requirement type="package" version="0.18.3">scikit-image</requirement>
11 <requirement type="package" version="1.2.4">pandas</requirement> 20 <requirement type="package" version="1.2.4">pandas</requirement>
12 <requirement type="package" version="1.20.2">numpy</requirement> 21 <requirement type="package" version="1.24.4">numpy</requirement>
13 <requirement type="package" version="1.6.2">scipy</requirement> 22 <requirement type="package" version="1.10.1">scipy</requirement>
14 <requirement type="package" version="2020.10.1">tifffile</requirement> 23 <requirement type="package" version="2021.7.2">tifffile</requirement>
15 </requirements> 24 </requirements>
16 <command detect_errors="aggressive"> 25 <command detect_errors="aggressive">
17 <![CDATA[ 26 <![CDATA[
18 ln -s '$moving' ./in.${moving.ext} && 27 ln -s '$moving' ./in.${moving.ext} &&
19 python '$__tool_directory__/projective_transformation.py' 28 python '$__tool_directory__/projective_transformation.py'
23 ./out.${moving.ext} 32 ./out.${moving.ext}
24 && mv ./out.${moving.ext} ./result_image 33 && mv ./out.${moving.ext} ./result_image
25 ]]> 34 ]]>
26 </command> 35 </command>
27 <inputs> 36 <inputs>
28 <param name="moving" type="data" format="tiff,png" label="Moving image (to be transformed)" /> 37 <param name="moving" type="data" format="tiff,png" label="Moving image" help="The image to be transformed." />
29 <param name="fixed" type="data" format="tiff,png" label="Fixed image (the reference)" /> 38 <param name="fixed" type="data" format="tiff,png" label="Fixed image" help="The reference image." />
30 <param name="tmat" type="data" format="tabular" label="Transformation matrix" /> 39 <param name="tmat" type="data" format="tabular" label="Transformation matrix" help="Homogeneous transformation matrix (3⨉3)." />
31 </inputs> 40 </inputs>
32 <outputs> 41 <outputs>
33 <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" /> 42 <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" />
34 </outputs> 43 </outputs>
35 <tests> 44 <tests>
36 <test> 45 <test>
37 <param name="fixed" value="fixed.png"/> 46 <param name="fixed" value="fixed.png"/>
38 <param name="moving" value="moving.png"/> 47 <param name="moving" value="moving.png"/>
39 <param name="tmat" value="tmat.tsv"/> 48 <param name="tmat" value="tmat.tsv"/>
40 <output name="warped" value="moving_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" /> 49 <expand macro="tests/intensity_image_diff" name="warped" value="moving_warped.png" ftype="png"/>
41 </test> 50 </test>
42 <test> 51 <test>
43 <param name="fixed" value="fixed_rgb.png"/> 52 <param name="fixed" value="fixed_rgb.png"/>
44 <param name="moving" value="moving_rgb.png"/> 53 <param name="moving" value="moving_rgb.png"/>
45 <param name="tmat" value="tmat.tsv"/> 54 <param name="tmat" value="tmat.tsv"/>
46 <output name="warped" value="moving_rgb_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" /> 55 <expand macro="tests/intensity_image_diff" name="warped" value="moving_rgb_warped.png" ftype="png"/>
47 </test> 56 </test>
48 <test> 57 <test>
49 <param name="fixed" value="multi_f.tif"/> 58 <param name="fixed" value="multi_f.tif"/>
50 <param name="moving" value="multi_m.tif"/> 59 <param name="moving" value="multi_m.tif"/>
51 <param name="tmat" value="tmat.tsv"/> 60 <param name="tmat" value="tmat.tsv"/>
52 <output name="warped" value="multi_m_warped.tif" ftype="tiff" compare="sim_size" delta_frac="0.1" /> 61 <expand macro="tests/intensity_image_diff" name="warped" value="multi_m_warped.tif" ftype="tiff"/>
53 </test> 62 </test>
54 </tests> 63 </tests>
55 <help> 64 <help>
56 65
57 **What it does** 66 **Performs projective transformation.**
58 67
59 This tool performs a projective transformation of the moving 2D image so that it fits the fixed 2D image. 68 This tool performs a projective transformation of 2-D image into the coordinate system of another 2-D image.
60 Multi-channel and RGB images are supported. 69 Multi-channel images are supported (e.g., RGB).
70
61 </help> 71 </help>
62 <citations> 72 <citations>
63 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 73 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
64 </citations> 74 </citations>
65 </tool> 75 </tool>