<tool id="neper_meshing" name="Neper Meshing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
    <description>scalar and raster tessellations</description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
        <xml name="meshing">
            <section name="meshing" expanded="false" title="Meshing Options">
                <param argument="-elttype" type="select" optional="true" label="Set element type">
                    <help>Default value: tetrahedral in 3D and triangular in 2D</help>
                    <option value="tri">triangular</option>
                    <option value="quad">quadrangular</option>
                    <option value="quad9">9-node quadrangular</option>
                    <option value="tet">tetrahedral</option>
                    <option value="hex">hexahedral</option>
                </param>
                <!-- cl,rcl -->
                <param argument="-dim" type="select" multiple="true" optional="true" label="Set the meshing dimension">
                    <help>Default value: inputdim</help>
                    <option value="inputdim">inputdim</option>
                    <option value="all">all</option>
                    <option value="none">none</option>
                    <option value="0">0</option>
                    <option value="1">1</option>
                    <option value="2">2</option>
                    <option value="3">3</option>
                </param>
                <param argument="-order" type="select" optional="true" label="Set the mesh order">
                    <help>Default value: 1
                          A value of 1 corresponds to 2-node linear elements, 3-node triangular elements, 
                          4-node quadrangular elements, 4-node tetrahedral elements and 8-node hexahedral elements, 
                          A value of 2 corresponds to 3-node linear elements, 6-node triangular elements, 
                          8-node or 9-node quadrangular elements, 10-node tetrahedral elements 
                          and 20-node hexahedral elements.
                    </help>
                    <option value="1">1 - 2-node linear...</option>
                    <option value="2">2 - 3-node linear...</option>
                </param>

                <!--
                <expand macro="set_ny" name="elttype" label="Set element typescale">
                    <expand macro="tx3d" label="scale" lx="x factor" ly="y factor" lz="z factor"/>
                </expand>
                -->
            </section>
        </xml>
        <token name="@MESHING@">
        #if $meshing.elttype
            -elttype $meshing.elttype
        #end if
        #if $meshing.dim
            -dim $meshing.dim
        #end if
        #if $meshing.order
            -order $meshing.order
        #end if
        </token>

        <xml name="meshing_output">
            <section name="meshing_output" expanded="false" title="Meshing Output Options">
                <param argument="-nset" type="text" value="" optional="true" label="Specify the node sets">
                    <option value="faces">faces</option>
                    <option value="edges">edges</option>
                    <option value="vertices">vertices</option>
                    <option value="facebodies">facebodies</option>
                    <option value="edgebodies">edgebodies</option>
                    <option value="all">all</option>
                    <option value="none">none</option>
                    <!--
                    <validator type="regex" message="">^all|none|(faces|edges|vertices|facebodies|edgebodies)*|([x-z][01]|[x-z][01][x-z][01]|[x-z][01][x-z][01][x-z][01]|z[0,1]f[1-9][0-9]*|f[1-9][0-9]*)*$</validator>
                    -->
                </param>
                <param argument="-faset" type="text" value="" optional="true" label="Specify the element surface meshes">
                    <option value="faces">faces</option>
                    <option value="internal">internal</option>
                    <!--
                    <validator type="regex" message="">^(faces|internal|([x-z][01]|[x-z][01][x-z][01]|[x-z][01][x-z][01][x-z][01]|z[0,1]f[1-9][0-9]*|f[1-9][0-9]*)?$</validator>
                    -->
                </param>
            </section>
        </xml>
        <token name="@MESHING_OUTPUT@">
        #if $meshing_output.nset
            -nset "$meshing_output.nset"
        #end if
        #if $meshing_output.faset
            -faset "$meshing_output.faset"
        #end if
        </token>

    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        neper -M 
        '$input'
        @MESHING@
        @MESHING_OUTPUT@
        @TRANSFORM@
        -format "$format"
        -part "\${GALAXY_SLOTS:-4}"
        -o output
        | grep -v '%$' | tee 'neper.log'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="neper.tesr,neper.tess,gmsh.msh" label="Input tessellation or mesh file"/>
        <expand macro="meshing"/>
        <expand macro="meshing_output"/>
        <expand macro="transform"/>
        <param name="format" argument="-format" type="select" multiple="true" optional="false" label="Output formats">
            <option value="msh" selected="true">Gmsh-style msh ascii</option>
            <option value="msh:binary">Gmsh-style msh binary</option>
            <option value="msh4">Gmsh v4</option>
            <option value="vtk">VTK</option>
        </param>
    </inputs>
    <outputs>
        <data name="log" format="txt" label="${tool.name} on ${on_string} log" from_work_dir="neper.log"/>
        <data name="output_msh" format="gmsh.msh" label="${tool.name} on ${on_string} msh" from_work_dir="output.msh">
            <filter>'msh' in format.split(',') or 'mshi:binary' in format.split(',')</filter>
        </data>
        <data name="output_msh4" format="gmsh.msh" label="${tool.name} on ${on_string} msh4" from_work_dir="output.tesr">
            <filter>'msh4' in format</filter>
        </data>
        <data name="output_vtk" format="vtkascii" label="${tool.name} on ${on_string} vtk" from_work_dir="output.vtk">
            <filter>'vtk' in format</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test-1  neper -M defaults -->
        <test>
            <param name="input" ftype="neper.tess" value="neper.tess"/>
            <output name="log">
                <assert_contents>
                    <has_text text="Wrote file `output.msh'." />
                </assert_contents>
            </output>
            <output name="output_msh">
                <assert_contents>
                    <has_text text="$MeshFormat" />
                    <has_text text="2.2" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**Neper Meshing**

@NEPER_HELP@

Neper Mesahing Module *-M* is the module for meshing scalar and raster tessellations. The two meshing strategies are: 

  (i) Free (or unstructured) meshing creates a conforming mesh into tetrahedral elements (triangular in 2D).
  (ii) Mapped (or structured) meshing generates a non-conforming mesh into regular hexahedral elements (quadrangular in 2D).

 The output is a Gmsh msh format and/or VTK format. 

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