Mercurial > repos > imgteam > points2binaryimage

changeset 2:2ad6350df85b draft default tip

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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
files bmcv.xml points2binaryimage.xml
diffstat 2 files changed, 22 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bmcv.xml	Thu Mar 14 15:12:23 2024 +0000
@@ -0,0 +1,6 @@
+<macros>
+    <xml name="creators/bmcv">
+        <organization name="Biomedical Computer Vision Group" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
+        <yield />
+    </xml>
+</macros>
--- a/points2binaryimage.xml	Mon Nov 13 22:11:42 2023 +0000
+++ b/points2binaryimage.xml	Thu Mar 14 15:12:23 2024 +0000
@@ -1,5 +1,13 @@
-<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>
+    <creator>
+        <expand macro="creators/bmcv" />
+    </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
@@ -11,7 +19,7 @@
         <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">
@@ -40,9 +48,13 @@
         </test>
     </tests>
     <help>
-    **What it does**
+
+        This tool converts a CSV list of points to a binary image by rasterizing the point coordinates.
 
-    Converts CSV point file to binary image.
+        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>