Mercurial > repos > imgteam > points2binaryimage
comparison points2binaryimage.xml @ 1:54b8c8bceb32 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2994366afa0a1c537c0edf6c4578bda079494b2f
author | imgteam |
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date | Wed, 26 Jun 2024 08:35:48 +0000 |
parents | c2dcc029a23b |
children | 380b628a2213 |
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0:c2dcc029a23b | 1:54b8c8bceb32 |
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1 <tool id="ip_points_to_binaryimage" name="Points to Binary Image" version="0.1"> | 1 <tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
2 <description>Converts points to a binary image</description> | 2 <description></description> |
3 <macros> | |
4 <import>creators.xml</import> | |
5 <token name="@TOOL_VERSION@">0.2</token> | |
6 <token name="@VERSION_SUFFIX@">3</token> | |
7 </macros> | |
8 <creator> | |
9 <expand macro="creators/bmcv" /> | |
10 </creator> | |
11 <edam_operations> | |
12 <edam_operation>operation_3443</edam_operation> | |
13 </edam_operations> | |
14 <xrefs> | |
15 <xref type="bio.tools">galaxy_image_analysis</xref> | |
16 </xrefs> | |
3 <requirements> | 17 <requirements> |
4 <requirement type="package" version="0.14.2">scikit-image</requirement> | 18 <requirement type="package" version="0.14.2">scikit-image</requirement> |
5 <requirement type="package" version="1.15.4">numpy</requirement> | 19 <requirement type="package" version="1.15.4">numpy</requirement> |
6 <requirement type="package" version="0.23.4">pandas</requirement> | 20 <requirement type="package" version="0.23.4">pandas</requirement> |
7 <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed--> | 21 <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed--> |
8 <requirement type="package" version="2.4.1">dateutil</requirement> | 22 <requirement type="package" version="2.5.2">python-dateutil</requirement> |
23 <requirement type="package" version="0.15.1">tifffile</requirement> | |
9 </requirements> | 24 </requirements> |
10 <command> | 25 <command detect_errors="aggressive"> |
11 <![CDATA[ | 26 <![CDATA[ |
12 python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy | 27 python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy |
13 ]]> | 28 ]]> |
14 </command> | 29 </command> |
15 <inputs> | 30 <inputs> |
31 <param name="invert_xy" value="true" /> | 46 <param name="invert_xy" value="true" /> |
32 <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/> | 47 <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/> |
33 </test> | 48 </test> |
34 </tests> | 49 </tests> |
35 <help> | 50 <help> |
36 **What it does** | |
37 | 51 |
38 Converts CSV point file to binary image. | 52 This tool converts a CSV list of points to a binary image by rasterizing the point coordinates. |
53 | |
54 The created image is a single-channel image with 16 bits per pixel (unsigned integer). | |
55 The points are rasterized with value 32767 (white). | |
56 Pixels not corresponding to any points in the CSV are assigned the value 0 (black). | |
57 | |
39 </help> | 58 </help> |
40 <citations> | 59 <citations> |
41 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | 60 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
42 </citations> | 61 </citations> |
43 </tool> | 62 </tool> |