changeset 3:e07bfdcb1d26 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065

--- a/README.md	Tue Jan 06 01:29:49 2026 +0000
+++ b/README.md	Tue Jan 06 11:26:30 2026 +0000
@@ -10,7 +10,7 @@
 ```bash
 --gpus all -e NVIDIA_VISIBLE_DEVICES=all -e NVIDIA_DRIVER_CAPABILITIES=graphics,compute
 ```
-Otherwise, the tool runs with software rendering, whuch is much slower.
+Otherwise, the tool runs with software rendering, which is much slower.
 
 When using `planemo test`, the full command line is:
 ```bash

--- a/render.py	Tue Jan 06 01:29:49 2026 +0000
+++ b/render.py	Tue Jan 06 11:26:30 2026 +0000
@@ -126,12 +126,15 @@
             mode.cmap(tool.args.params['colormap'], **cmap_kwargs)
 
         # Render
+        colorbars = list()
+        if tool.args.params['colorbar']:
+            colorbars.append(mode.cmap.bar(intensities_volume))
         html = libcarna.imshow(
             libcarna.animate(
                 libcarna.animate.rotate_local(camera),
                 n_frames=tool.args.params['video']['frames'],
             ).render(r, camera),
-            mode.cmap.bar(intensities_volume),
+            *colorbars,
             fps=tool.args.params['video']['fps'],
         )
 

--- a/render.xml	Tue Jan 06 01:29:49 2026 +0000
+++ b/render.xml	Tue Jan 06 11:26:30 2026 +0000
@@ -19,7 +19,7 @@
         <xml name="params/builtin_cmap">
             <conditional name="ramp">
                 <param name="enabled" type="select" label="Ramp function"
-                       help="Use a piecewise linear ramp function for the alpha channel of the colormap.">
+                       help="Use a piecewise linear ramp function for the alpha channel of the color map.">
                     <option value="false" selected="true">Disabled</option>
                     <option value="true">Enabled</option>
                 </param>
@@ -77,7 +77,7 @@
         <container type="docker">docker.io/kostrykin/libcarna-python:@TOOL_VERSION@-0</container>
     </requirements>
     <required_files>
-        <include type="literal" path="clip_image.py"/>
+        <include type="literal" path="render.py"/>
         <exclude type="literal" path="README.md"/>
     </required_files>
     <command detect_errors="aggressive"><![CDATA[
@@ -129,6 +129,7 @@
                 },
 
                 "colormap": "$colormap.name",
+                "colorbar": $colorbar,
 
                 #if str($colormap.name) != "custom"
                     "ramp": {
@@ -197,12 +198,13 @@
                 <expand macro="option/builtin_cmap_list"/>
             </param>
             <when value="custom">
-                <param name="custom" type="data" format="tabular" label="Custom colormap">
-                    <validator type="dataset_metadata_in_range" metadata_name="columns" min="3" message="Colormap needs to have at least 3 columns."/>
+                <param name="custom" type="data" format="tabular" label="Custom color map">
+                    <validator type="dataset_metadata_in_range" metadata_name="columns" min="3" message="Color map needs to have at least 3 columns."/>
                 </param>
             </when>
             <expand macro="when/builtin_cmap_list"/>
         </conditional>
+        <param name="colorbar" type="boolean" checked="true" label="Add a color bar"/>
         <section name="camera" title="Camera parameters" expanded="true">
             <param name="fov" type="float" min="10" max="170" value="90" label="Field of view (in degrees)"/>
             <param name="distance" type="float" min="1" value="200" label="Distance"
@@ -316,11 +318,11 @@
   :width: 438px
   :scale: 100%
 
-An overview of the available colormaps is available at `matplotlib.org`_.
+An overview of the available color maps is available at `matplotlib.org`_.
 
 .. _matplotlib.org: https://matplotlib.org/stable/users/explain/colors/colormaps.html
 
-When using custom colormaps, a tabular file with at least 3 columns must be used (`intensity`, `type`, `color`). Each pair of consecutive rows defines a linear segment of the colormap. The `intensity` values can be given either as absolute intensity values, or as relative values where 0 and 1 correspond to the minimum and maximum intensities of the image data, respectively. The `type` column indicates whether the corresponding `intensity` value is `absolute` or `relative`. The `color` must be given in hexadecimal notation with a ``#`` prefix and must be either 6 or 8 digits long (6 for RGB and 8 for RGBA). An example is given below.
+When using custom color maps, a tabular file with at least 3 columns must be used (`intensity`, `type`, `color`). Each pair of consecutive rows defines a linear segment of the color map. The `intensity` values can be given either as absolute intensity values, or as relative values where 0 and 1 correspond to the minimum and maximum intensities of the image data, respectively. The `type` column indicates whether the corresponding `intensity` value is `absolute` or `relative`. The `color` must be given in hexadecimal notation with a ``#`` prefix and must be either 6 or 8 digits long (6 for RGB and 8 for RGBA). An example is given below.
 
 +-----------+------------+----------+
 | color     | intensity  | type     |