view clip_image.xml @ 1:eb5a84e77beb draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14

<tool id="clip_image" name="Clip image intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1">
    <description>with giatools</description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">0.7.3</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <xml name="bound" tokens="name,label,help">
            <param name="@NAME@" type="float" optional="true" label="@LABEL@" help="@HELP@"/>
        </xml>
    </macros>
    <creator>
        <expand macro="creators/bmcv"/>
        <expand macro="creators/kostrykin"/>
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
        <xref type="bio.tools">giatools</xref>
        <xref type="bio.tools">numpy</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">giatools</requirement>
        <requirement type="package" version="0.12.2">ome-zarr</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="clip_image.py"/>
    </required_files>
    <command detect_errors="aggressive"><![CDATA[

        python '$__tool_directory__/clip_image.py'

        #if $input.extension == "zarr"
            --input '$input.extra_files_path/$input.metadata.store_root'
        #else
            --input '$input'
        #end if

        --output 'output.tiff'
        --params '$params'
        --verbose

    ]]></command>
    <configfiles>
        <configfile name="params"><![CDATA[
            {

            #if str($lower_bound) != ""
                "lower_bound": $lower_bound,
            #end if

            #if str($upper_bound) != ""
                "upper_bound": $upper_bound,
            #end if

                "": null
            }
        ]]></configfile>
    </configfiles>
    <inputs>
        <param name="input" type="data" format="tiff,zarr,png,jpg" label="Input image"/>
        <expand macro="bound" name="lower_bound" label="Lower bound"
                help="Image intensities below this value will be set to this value."/>
        <expand macro="bound" name="upper_bound" label="Upper bound"
                help="Image intensities above this value will be set to this value."/>
    </inputs>
    <outputs>
        <data format="tiff" name="output" from_work_dir="output.tiff"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="input/input4_float16.tiff"/>
            <param name="lower_bound" value="0.5"/>
            <expand macro="tests/intensity_image_diff" name="output" value="output/input4.tiff" ftype="tiff"/>
            <assert_stdout>
                <has_line line="[input] Input image axes: ZYX"/>
                <has_line line="[input] Input image shape: (10, 15, 18)"/>
                <has_line line="[input] Input image dtype: float16"/>
                <has_line line="[input] Input image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
                <has_line line="Applying clipping: [0.5, inf]"/>
                <has_line line="[output] Output image axes: ZYX"/>
                <has_line line="[output] Output image shape: (10, 15, 18)"/>
                <has_line line="[output] Output image dtype: float16"/>
                <has_line line="[output] Output image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
            </assert_stdout>
        </test>
        <test>
            <param name="input" value="input/input5.jpg"/>
            <param name="upper_bound" value="100.5"/>
            <expand macro="tests/intensity_image_diff" name="output" value="output/input5.tiff" ftype="tiff"/>
            <assert_stdout>
                <has_line line="[input] Input image axes: YXC"/>
                <has_line line="[input] Input image shape: (10, 10, 3)"/>
                <has_line line="[input] Input image dtype: uint8"/>
                <has_line line="Applying clipping: [-inf, 100.5]"/>
                <has_line line="[output] Output image axes: YXC"/>
                <has_line line="[output] Output image shape: (10, 10, 3)"/>
                <has_line line="[output] Output image dtype: uint8"/>
            </assert_stdout>
        </test>
        <test expect_failure="true">
            <param name="input" value="input/input5.jpg"/>
            <param name="lower_bound" value="60"/>
            <param name="upper_bound" value="50"/>
            <assert_stderr>
                <has_line line="Lower bound (60) must be less or equal compared to the upper bound (50)."/>
            </assert_stderr>
        </test>
        <test>
            <param name="input" value="input/input6_yx.zarr"/>
            <param name="lower_bound" value="-21.5"/>
            <param name="upper_bound" value="101.5"/>
            <expand macro="tests/intensity_image_diff" name="output" value="output/input6.tiff" ftype="tiff"/>
            <assert_stdout>
                <has_line line="[input] Input image axes: YX"/>
                <has_line line="[input] Input image shape: (200, 200)"/>
                <has_line line="[input] Input image dtype: float64"/>
                <has_line line="[input] Input image resolution=(1.0, 1.0), unit='um'"/>
                <has_line line="Applying clipping: [-21.5, 101.5]"/>
                <has_line line="[output] Output image axes: YX"/>
                <has_line line="[output] Output image shape: (200, 200)"/>
                <has_line line="[output] Output image dtype: float64"/>
                <has_line line="[output] Output image resolution=(1.0, 1.0), unit='um'"/>
            </assert_stdout>
        </test>
        <test>
            <param name="input" value="input/input4_float16.tiff"/>
            <expand macro="tests/intensity_image_diff" name="output" value="input/input4_float16.tiff" ftype="tiff"/>
            <assert_stdout>
                <has_line line="[input] Input image axes: ZYX"/>
                <has_line line="[input] Input image shape: (10, 15, 18)"/>
                <has_line line="[input] Input image dtype: float16"/>
                <has_line line="[input] Input image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
                <has_line line="Applying clipping: [-inf, inf]"/>
                <has_line line="[output] Output image axes: ZYX"/>
                <has_line line="[output] Output image shape: (10, 15, 18)"/>
                <has_line line="[output] Output image dtype: float16"/>
                <has_line line="[output] Output image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
            </assert_stdout>
        </test>
    </tests>
    <help>

**Applies intensity clipping to an image.**

Supports 2-D and 3-D images, single-channel and multi-channel images, and arbitrary series of images (e.g., temporal image sequences).

This tool preserves the image pixel data type and—subject to clipping—the image brightness and the range of values.

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>