Merge branch 'move-refl1d-to-dev' into 'dev'

<tool id="neutrons_reflectometry_refl1d" tool_type="interactive" name="Refl1D" profile="22.05" version="0.1.0">

  <description></description>

    <requirements>

        <container type="docker" shell="/bin/bash">code.ornl.gov:4567/ndip/tool-sources/reflectometry/refl1d:0.2.9</container>

    </requirements>

    <entry_points>

        <entry_point name="Refl1D" label="refl1d" requires_domain="False" requires_path_in_url="True">

            <port>8081</port>

        </entry_point>

    </entry_points>

    <environment_variables>

        <environment_variable name="EP_PATH" inject="entry_point_path_for_label">refl1d</environment_variable>

    </environment_variables>

    <command strict="false"><![CDATA[

        bash /prepare_nginx.sh &&

        mkdir -p /data/inputs &&

        mkdir -p /data/outputs &&

        ln -s /data/outputs ./outputs &&

        #for $i, $s in enumerate($datasets)

            #set $name = os.path.basename(str($s.input.element_identifier))

            ln -sf '${s.input}' '/data/inputs/${name}' &&

        #end for

        python -m refl1d.webview.server --port 8080 --external --path /data

        > >(tee -a $output_console) 2>&1;

        exit 0

    ]]>

    </command>

    <inputs>

         <repeat name="datasets" title="Datasets">

            <param name="input" type="data" label="Dataset"/>

        </repeat>

    </inputs>

    <outputs>

        <collection type="list" name="output" label="Refl1D Output Files">

                <discover_datasets pattern="__designation__" directory="outputs" />

        </collection>

        <data name="output_console" auto_format="true" label="Ref1D Console Output"/>

    </outputs>

    <help>

        1-D reflectometry allows material scientists to understand the structure of thin films, providing composition and 

        density information as a function of depth. With polarized neutron measurements, scientists can study the sub-surface 

        structure of magnetic samples. The Refl1D modeling program supports a mixture of slabs, freeform and specialized layer 

        types such as models for the density distribution of polymer brushes. More information on Refl1D can be found at

        https://refl1d.readthedocs.io/en/latest/index.html

        Any tool input files will be made available in the /data/inputs directory. Any files placed in the /data/outputs

        directory will be returned to the history in a dataset collection when the tool finishes.

    </help>

</tool>