annotate imagej2_create_image.xml @ 2:666af1279007 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

<tool id="imagej2_create_image" name="Create new image" version="@WRAPPER_VERSION@.1">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">imagej</xref>
        <xref type="biii">imagej2</xref>
    </xrefs>
    <expand macro="fiji_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#set output_log = '$output_log.txt'
#set output_name = '.'.join(['new_image', str($output_datatype)])
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_create_image_jython_script.py'
'$image_title'
$width
$height
$depth
'$image_type'
'$output_name'
&>'$output_log';
if [[ $? -ne 0 ]]; then
    cat '$output_log' >&2;
else
    mv '$output_name' '$output';
fi
]]></command>
    <inputs>
        <expand macro="image_type"/>
        <param name="image_title" type="text" label="Image title" help="Leave blank for no title"/>
        <param name="width" type="integer" value="512" min="1" label="Image width in pixels"/>
        <param name="height" type="integer" value="512" min="1" label="Image height in pixels"/>
        <param name="depth" type="integer" value="1" min="1" label="Image depth" help="Specifies the number of stack slices"/>
        <param name="output_datatype" type="select" label="Save as format">
            <expand macro="image_datatypes"/>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="jpg">
            <actions>
                <action type="format">
                    <option type="from_param" name="output_datatype"/>
                 </action>
           </actions>
       </data>
    </outputs>
    <tests>
        <test>
            <param name="image_type" value="8-bit_ramp"/>
            <param name="image_title" value="MyTitle"/>
            <param name="width" value="256"/>
            <param name="height" value="256"/>
            <param name="depth" value="1"/>
            <param name="output_datatype" value="jpg"/>
            <output name="output" file="create_image1.jpg" ftype="jpg"/>
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Creates a new image based on the following entries.

- **Type** specifies the image type "8-bit", "16-bit", "32-bit" or "RGB" with options
- **Title** is associated with the image, but not displayed in the image
- **Width** specifies the width of the image in pixels
- **Height** specifies the height of the image in pixels
- **Depth** specifies the number of stack slices
- **Format** specifies the image format "jpg", "png", etc
]]>

    </help>
    <expand macro="fiji_headless_citations"/>
</tool>