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Fix points2binaryimage tool #116

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merged 6 commits into from
Mar 14, 2024
Merged

Fix points2binaryimage tool #116

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e975032
Fix requirements
kostrykin Mar 14, 2024
f9ecd89
Update help
kostrykin Mar 14, 2024
8453a6f
Add creators
kostrykin Mar 14, 2024
53ab3de
Fix creators
kostrykin Mar 14, 2024
53ddd7f
Update creators
kostrykin Mar 14, 2024
403ec07
Add `<yield/>` tag
kostrykin Mar 14, 2024
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5 changes: 5 additions & 0 deletions macros/creators/bmcv.xml
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<macros>
<xml name="creator">
<organization name="Biomedical Computer Vision Group" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
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probably good to have a yield here.

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Hm I have looked into yield but I do no see in what way you mean to use it here?

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yield will just allow us to add more organisations, creators on the per tool bases still inheriting this one. Think about it a substantial contribution from someone else that wants to be listed next to you.
A yield also does not hurt if you don't use it.

</xml>
</macros>
1 change: 1 addition & 0 deletions tools/points2binaryimage/bmcv.xml
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../../macros/creators/bmcv.xml
17 changes: 13 additions & 4 deletions tools/points2binaryimage/points2binaryimage.xml
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<tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="0.2-1">
<tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
<description></description>
<macros>
<import>bmcv.xml</import>
<token name="@TOOL_VERSION@">0.2</token>
<token name="@VERSION_SUFFIX@">2</token>
</macros>
<edam_operations>
<edam_operation>operation_3443</edam_operation>
</edam_operations>
Expand All @@ -11,7 +16,7 @@
<requirement type="package" version="1.15.4">numpy</requirement>
<requirement type="package" version="0.23.4">pandas</requirement>
<requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed-->
<requirement type="package" version="2.4.1">dateutil</requirement>
<requirement type="package" version="2.5.2">python-dateutil</requirement>
<requirement type="package" version="0.15.1">tifffile</requirement>
</requirements>
<command detect_errors="aggressive">
Expand Down Expand Up @@ -40,9 +45,13 @@
</test>
</tests>
<help>
**What it does**

Converts CSV point file to binary image.
This tool converts a CSV list of points to a binary image by rasterizing the point coordinates.

The created image is a single-channel image with 16 bits per pixel (unsigned integer).
The points are rasterized with value 32767 (white).
Pixels not corresponding to any points in the CSV are assigned the value 0 (black).

</help>
<citations>
<citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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