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
date Wed, 26 Jun 2024 08:35:48 +0000
parents c2dcc029a23b
children 380b628a2213
comparison
equal deleted inserted replaced
0:c2dcc029a23b 1:54b8c8bceb32
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>