comparison imagej2_create_image.xml @ 1:1a7c29d5fc11 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"

0:dc3935a0165a

<?xml version='1.0' encoding='UTF-8'?>
<tool id="imagej2_create_image" name="Create new image" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <expand macro="fiji_requirements" />
    <command>
<![CDATA[
    python $__tool_directory__/imagej2_create_image.py
    --width $width
    --height $height
    --depth $depth
    --image_type $image_type
    --image_title "$image_title"
    --jython_script $__tool_directory__/imagej2_create_image_jython_script.py
    --output_datatype $output_datatype
    --out_fname "$output"
]]>
    </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**

- **Depth** specifies the number of stack slices
- **Format** specifies the image format "jpg", "png", etc
]]>

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

1:1a7c29d5fc11

<tool id="imagej2_create_image" name="Create new image" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <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**

- **Depth** specifies the number of stack slices
- **Format** specifies the image format "jpg", "png", etc
]]>

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