Tomo/tomo_reduce.xml at master · CHESSComputing/Tomo · GitHub

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<tool id="tomo_reduce" name="Tomo Reduce" version="1.0.0" python_template_version="3.9">
    <description>Reduce tomography images</description>
    <macros>
        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
            mkdir tomo_reduce_plots;
            $__tool_directory__/tomo_reduce.py
            --input_file "$input_file"
            --output_file "output.nex"
            --galaxy_flag
            #if str($station.type_selector) == "id3b"
                #if str($station.img_bounds.type_selector) == "enter_range"
                    --img_x_bounds $station.img_bounds.low $station.img_bounds.upp
                #end if
            #end if
            -l "$log"
        ]]>
    </command>
    <inputs>
        <param name="input_file" type="data" optional="false" label="Input file"/>
        <conditional name="station">
            <param name="type_selector" type="select" display="radio" label="Choose station">
                <option value="id3a" selected="true">id3a (SMB)</option>
                <option value="id3b">id3b (FMB)</option>
            </param>
            <when value="id3a"/>
            <when value="id3b">
                <conditional name="img_bounds">
                    <param name="type_selector" type="select" display="radio" label="Choose image range for data reduction">
                        <option value="enter_range" selected="true">Manually enter the image range</option>
                        <option value="full_range">Use the full image range</option>
                    </param>
                    <when value="enter_range">
                        <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in vertical direction"/>
                        <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in vertical direction"/>
                    </when>
                    <when value="full_range"/>
                </conditional>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="common_outputs"/>
        <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
            <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
        </collection>
        <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
    </outputs>
    <help>
        <![CDATA[
            Reduce tomography images.
        ]]>
    </help>
    <expand macro="citations"/>
</tool>