comparison dicom2text.xml @ 0:199de6887566 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce

0:199de6887566

<tool id="highdicom_dicom2text" name="Export DICOM metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.01">
    <expand macro="description"/>
    <macros>
        <import>macros.xml</import>
        <import>creators.xml</import>
    </macros>
    <creator>
        <expand macro="creators/bmcv"/>
        <expand macro="creators/kostrykin"/>
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command><![CDATA[

    python '$__tool_directory__/dicom2text.py'
    '$input'

    #if $export_to == "json"
        ./output.json
    #elif $export_to == "yaml"
        ./output.yaml
    #end if

    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="binary" label="DICOM dataset"/>
        <param name="export_to" type="select" label="Export to">
            <option value="json" selected="true">JSON</option>
            <option value="yaml">YAML</option>
        </param>
    </inputs>
    <outputs>
        <data format="json" name="output_json" from_work_dir="output.json" label="${tool.name} on ${on_string} (JSON)">
            <filter>export_to == 'json'</filter>
        </data>
        <data format="yaml" name="output_yaml" from_work_dir="output.yaml" label="${tool.name} on ${on_string} (YAML)">
            <filter>export_to == 'yaml'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="highdicom/ct_image.dcm"/>
            <param name="export_to" value="json"/>
            <output name="output_json" ftype="json">
                <assert_contents>
                    <has_json_property_with_value property="00080080" value='{"vr": "LO", "Value": ["JFK IMAGING CENTER"]}'/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input" value="highdicom/sm_image.dcm"/>
            <param name="export_to" value="yaml"/>
            <output name="output_yaml" ftype="yaml">
                <assert_contents>
                    <has_text_matching expression="00080104:\n +Value:\n +- Brightfield illumination\n"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

        **Exports the metadata of a DICOM dataset as JSON or YAML.**

        @DICOM_INTRO@

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