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comparison points2binaryimage.xml @ 2:2ad6350df85b draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
author imgteam
date Thu, 14 Mar 2024 15:12:23 +0000
parents 90385ec28b34
children a80f92ec6f89
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1:90385ec28b34 2:2ad6350df85b
1 <tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="0.2-1"> 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></description> 2 <description></description>
3 <macros>
4 <import>bmcv.xml</import>
5 <token name="@TOOL_VERSION@">0.2</token>
6 <token name="@VERSION_SUFFIX@">2</token>
7 </macros>
8 <creator>
9 <expand macro="creators/bmcv" />
10 </creator>
3 <edam_operations> 11 <edam_operations>
4 <edam_operation>operation_3443</edam_operation> 12 <edam_operation>operation_3443</edam_operation>
5 </edam_operations> 13 </edam_operations>
6 <xrefs> 14 <xrefs>
7 <xref type="bio.tools">galaxy_image_analysis</xref> 15 <xref type="bio.tools">galaxy_image_analysis</xref>
9 <requirements> 17 <requirements>
10 <requirement type="package" version="0.14.2">scikit-image</requirement> 18 <requirement type="package" version="0.14.2">scikit-image</requirement>
11 <requirement type="package" version="1.15.4">numpy</requirement> 19 <requirement type="package" version="1.15.4">numpy</requirement>
12 <requirement type="package" version="0.23.4">pandas</requirement> 20 <requirement type="package" version="0.23.4">pandas</requirement>
13 <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-->
14 <requirement type="package" version="2.4.1">dateutil</requirement> 22 <requirement type="package" version="2.5.2">python-dateutil</requirement>
15 <requirement type="package" version="0.15.1">tifffile</requirement> 23 <requirement type="package" version="0.15.1">tifffile</requirement>
16 </requirements> 24 </requirements>
17 <command detect_errors="aggressive"> 25 <command detect_errors="aggressive">
18 <![CDATA[ 26 <![CDATA[
19 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
38 <param name="invert_xy" value="true" /> 46 <param name="invert_xy" value="true" />
39 <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/> 47 <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/>
40 </test> 48 </test>
41 </tests> 49 </tests>
42 <help> 50 <help>
43 **What it does**
44 51
45 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
46 </help> 58 </help>
47 <citations> 59 <citations>
48 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 60 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
49 </citations> 61 </citations>
50 </tool> 62 </tool>