Mercurial > repos > imgteam > libcarna_render
comparison render.xml @ 4:a9f10dceb17e draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
| author | imgteam |
|---|---|
| date | Tue, 13 Jan 2026 12:21:55 +0000 |
| parents | 31a2e1909ae5 |
| children |
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| 3:31a2e1909ae5 | 4:a9f10dceb17e |
|---|---|
| 3 <macros> | 3 <macros> |
| 4 <import>creators.xml</import> | 4 <import>creators.xml</import> |
| 5 <import>validators.xml</import> | 5 <import>validators.xml</import> |
| 6 <import>colormaps.xml</import> | 6 <import>colormaps.xml</import> |
| 7 <token name="@TOOL_VERSION@">0.2.0</token> | 7 <token name="@TOOL_VERSION@">0.2.0</token> |
| 8 <token name="@VERSION_SUFFIX@">1</token> | 8 <token name="@VERSION_SUFFIX@">2</token> |
| 9 <xml name="params/intensity" tokens="name,label,value"> | 9 <xml name="params/intensity" tokens="name,label,value,help" token_help=""> |
| 10 <section name="@NAME@" title="@LABEL@" expanded="true"> | 10 <section name="@NAME@" title="@LABEL@" expanded="true" help="@HELP@"> |
| 11 <param name="type" type="select" label="@LABEL@" | 11 <param name="type" type="select" label="Type of the intensity value" |
| 12 help="For relative intensity values, 0 is the minimum intensity of the image, and 1 is the maximum intensity."> | 12 help="For relative intensity values, 0 is the minimum intensity of the image, and 1 is the maximum intensity."> |
| 13 <option value="absolute">Absolute intensity value</option> | 13 <option value="absolute">Absolute intensity value</option> |
| 14 <option value="relative" selected="true">Relative intensity value</option> | 14 <option value="relative" selected="true">Relative intensity value</option> |
| 15 </param> | 15 </param> |
| 16 <param name="value" type="float" value="@VALUE@" label="Intensity value"/> | 16 <param name="value" type="float" value="@VALUE@" label="Intensity value"/> |
| 22 help="Use a piecewise linear ramp function for the alpha channel of the color map."> | 22 help="Use a piecewise linear ramp function for the alpha channel of the color map."> |
| 23 <option value="false" selected="true">Disabled</option> | 23 <option value="false" selected="true">Disabled</option> |
| 24 <option value="true">Enabled</option> | 24 <option value="true">Enabled</option> |
| 25 </param> | 25 </param> |
| 26 <when value="true"> | 26 <when value="true"> |
| 27 <expand macro="params/intensity" name="start" value="0" label="Ramp start"/> | 27 <expand macro="params/intensity" name="start" value="0" label="Ramp start" |
| 28 <expand macro="params/intensity" name="end" value="0.5" label="Ramp end"/> | 28 help="Image voxels with this intensity and below will be invisible."/> |
| 29 <expand macro="params/intensity" name="end" value="0.5" label="Ramp end" | |
| 30 help="Image voxels with this intensity and above will have full visibility."/> | |
| 29 </when> | 31 </when> |
| 30 <when value="false"/> | 32 <when value="false"/> |
| 31 </conditional> | 33 </conditional> |
| 32 </xml> | 34 </xml> |
| 33 <xml name="when/builtin_cmap" tokens="value"> | 35 <xml name="when/builtin_cmap" tokens="value"> |
| 114 #if int($sample_rate_override) > 0 | 116 #if int($sample_rate_override) > 0 |
| 115 #set $sample_rate = int($sample_rate_override) | 117 #set $sample_rate = int($sample_rate_override) |
| 116 #end if | 118 #end if |
| 117 | 119 |
| 118 "sample_rate": $sample_rate, | 120 "sample_rate": $sample_rate, |
| 121 "units": "$units", | |
| 119 "axes": "$axes", | 122 "axes": "$axes", |
| 120 "width": $width, | 123 "width": $width, |
| 121 "height": $height, | 124 "height": $height, |
| 122 "mode": "$mode.name", | 125 "mode": "$mode.name", |
| 123 | 126 |
| 168 <inputs> | 171 <inputs> |
| 169 <param name="intensities" type="data" format="tiff,zarr" label="Input image (3-D)"> | 172 <param name="intensities" type="data" format="tiff,zarr" label="Input image (3-D)"> |
| 170 <expand macro="validators/is_single_channel"/> | 173 <expand macro="validators/is_single_channel"/> |
| 171 <expand macro="validators/is_single_frame"/> | 174 <expand macro="validators/is_single_frame"/> |
| 172 <expand macro="validators/is_3d"/> | 175 <expand macro="validators/is_3d"/> |
| 176 </param> | |
| 177 <param name="units" type="select" label="Unit of the intensity values"> | |
| 178 <option value="raw" selected="true">No unit</option> | |
| 179 <option value="hu">Hounsfield</option> | |
| 173 </param> | 180 </param> |
| 174 <param name="axes" type="select" label="Coordinate system"> | 181 <param name="axes" type="select" label="Coordinate system"> |
| 175 <option value="XZY" selected="true">Point Z to the top</option> | 182 <option value="XZY" selected="true">Point Z to the top</option> |
| 176 <option value="XYZ">Point Y to the top</option> | 183 <option value="XYZ">Point Y to the top</option> |
| 177 </param> | 184 </param> |