comparison render.xml @ 3:e07bfdcb1d26 draft

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

2:7188234ae8f6

            </section>
        </xml>
        <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.">
                    <option value="false" selected="true">Disabled</option>
                    <option value="true">Enabled</option>
                </param>
                <when value="true">
                    <expand macro="params/intensity" name="start" value="0" label="Ramp start"/>

        See https://github.com/kostrykin/LibCarna-Python-Docker for details of the image.
        -->
        <container type="docker">docker.io/kostrykin/libcarna-python:@TOOL_VERSION@-0</container>
    </requirements>
    <required_files>
        <include type="literal" path="clip_image.py"/>
        <exclude type="literal" path="README.md"/>
    </required_files>
    <command detect_errors="aggressive"><![CDATA[

        python '$__tool_directory__/render.py'

                        "diffuse": $mode.diffuse
                    #end if
                },

                "colormap": "$colormap.name",

                #if str($colormap.name) != "custom"
                    "ramp": {
                        #if str($colormap.ramp.enabled) == "true"
                            "start_type": "$colormap.ramp.start.type",

            <param name="name" type="select" label="Color map">
                <option value="custom">Custom</option>
                <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>
            </when>
            <expand macro="when/builtin_cmap_list"/>
        </conditional>
        <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"
                   help="Distance between the camera and the center of the 3-D image."/>
            <param name="z_near" type="float" min="0.01" value="10" label="Near clipping plane"

.. image:: dvr.gif
  :width: 438px
  :scale: 100%

An overview of the available colormaps 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.

+-----------+------------+----------+
| color     | intensity  | type     |
+-----------+------------+----------+
| #ff00007f | 0          | absolute |

3:e07bfdcb1d26

            </section>
        </xml>
        <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 color map.">
                    <option value="false" selected="true">Disabled</option>
                    <option value="true">Enabled</option>
                </param>
                <when value="true">
                    <expand macro="params/intensity" name="start" value="0" label="Ramp start"/>

        See https://github.com/kostrykin/LibCarna-Python-Docker for details of the image.
        -->
        <container type="docker">docker.io/kostrykin/libcarna-python:@TOOL_VERSION@-0</container>
    </requirements>
    <required_files>
        <include type="literal" path="render.py"/>
        <exclude type="literal" path="README.md"/>
    </required_files>
    <command detect_errors="aggressive"><![CDATA[

        python '$__tool_directory__/render.py'

                        "diffuse": $mode.diffuse
                    #end if
                },

                "colormap": "$colormap.name",
                "colorbar": $colorbar,

                #if str($colormap.name) != "custom"
                    "ramp": {
                        #if str($colormap.ramp.enabled) == "true"
                            "start_type": "$colormap.ramp.start.type",

            <param name="name" type="select" label="Color map">
                <option value="custom">Custom</option>
                <expand macro="option/builtin_cmap_list"/>
            </param>
            <when value="custom">
                <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"
                   help="Distance between the camera and the center of the 3-D image."/>
            <param name="z_near" type="float" min="0.01" value="10" label="Near clipping plane"

.. image:: dvr.gif
  :width: 438px
  :scale: 100%

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 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     |
+-----------+------------+----------+
| #ff00007f | 0          | absolute |