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annotate neper_meshing.xml @ 0:03bbcfd3d708 draft default tip

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
author ximgchess
date Thu, 07 Jul 2022 12:31:10 +0000
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03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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1 <tool id="neper_meshing" name="Neper Meshing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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2 <description>scalar and raster tessellations</description>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <xml name="meshing">
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7 <section name="meshing" expanded="false" title="Meshing Options">
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8 <param argument="-elttype" type="select" optional="true" label="Set element type">
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9 <help>Default value: tetrahedral in 3D and triangular in 2D</help>
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10 <option value="tri">triangular</option>
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11 <option value="quad">quadrangular</option>
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12 <option value="quad9">9-node quadrangular</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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13 <option value="tet">tetrahedral</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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14 <option value="hex">hexahedral</option>
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15 </param>
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16 <!-- cl,rcl -->
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17 <param argument="-dim" type="select" multiple="true" optional="true" label="Set the meshing dimension">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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18 <help>Default value: inputdim</help>
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19 <option value="inputdim">inputdim</option>
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20 <option value="all">all</option>
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21 <option value="none">none</option>
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22 <option value="0">0</option>
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23 <option value="1">1</option>
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24 <option value="2">2</option>
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25 <option value="3">3</option>
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26 </param>
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27 <param argument="-order" type="select" optional="true" label="Set the mesh order">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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28 <help>Default value: 1
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29 A value of 1 corresponds to 2-node linear elements, 3-node triangular elements,
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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30 4-node quadrangular elements, 4-node tetrahedral elements and 8-node hexahedral elements,
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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31 A value of 2 corresponds to 3-node linear elements, 6-node triangular elements,
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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32 8-node or 9-node quadrangular elements, 10-node tetrahedral elements
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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33 and 20-node hexahedral elements.
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34 </help>
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35 <option value="1">1 - 2-node linear...</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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36 <option value="2">2 - 3-node linear...</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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37 </param>
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38
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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39 <!--
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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40 <expand macro="set_ny" name="elttype" label="Set element typescale">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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41 <expand macro="tx3d" label="scale" lx="x factor" ly="y factor" lz="z factor"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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42 </expand>
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43 -->
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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44 </section>
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45 </xml>
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46 <token name="@MESHING@">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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47 #if $meshing.elttype
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48 -elttype $meshing.elttype
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49 #end if
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50 #if $meshing.dim
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51 -dim $meshing.dim
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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52 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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53 #if $meshing.order
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54 -order $meshing.order
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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55 #end if
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56 </token>
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57
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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58 <xml name="meshing_output">
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59 <section name="meshing_output" expanded="false" title="Meshing Output Options">
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60 <param argument="-nset" type="text" value="" optional="true" label="Specify the node sets">
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61 <option value="faces">faces</option>
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62 <option value="edges">edges</option>
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63 <option value="vertices">vertices</option>
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64 <option value="facebodies">facebodies</option>
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65 <option value="edgebodies">edgebodies</option>
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66 <option value="all">all</option>
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67 <option value="none">none</option>
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68 <!--
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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69 <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>
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70 -->
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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71 </param>
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72 <param argument="-faset" type="text" value="" optional="true" label="Specify the element surface meshes">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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73 <option value="faces">faces</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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74 <option value="internal">internal</option>
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75 <!--
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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76 <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>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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77 -->
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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78 </param>
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79 </section>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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80 </xml>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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81 <token name="@MESHING_OUTPUT@">
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82 #if $meshing_output.nset
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83 -nset "$meshing_output.nset"
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84 #end if
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85 #if $meshing_output.faset
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86 -faset "$meshing_output.faset"
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87 #end if
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88 </token>
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89
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90 </macros>
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91 <expand macro="requirements" />
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92 <expand macro="version_command" />
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93 <command detect_errors="exit_code"><![CDATA[
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94 neper -M
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95 '$input'
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96 @MESHING@
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97 @MESHING_OUTPUT@
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98 @TRANSFORM@
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99 -format "$format"
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100 -part "\${GALAXY_SLOTS:-4}"
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101 -o output
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102 | grep -v '%$' | tee 'neper.log'
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103 ]]></command>
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104 <inputs>
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105 <param name="input" type="data" format="neper.tesr,neper.tess,gmsh.msh" label="Input tessellation or mesh file"/>
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106 <expand macro="meshing"/>
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107 <expand macro="meshing_output"/>
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108 <expand macro="transform"/>
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109 <param name="format" argument="-format" type="select" multiple="true" optional="false" label="Output formats">
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110 <option value="msh" selected="true">Gmsh-style msh ascii</option>
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111 <option value="msh:binary">Gmsh-style msh binary</option>
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112 <option value="msh4">Gmsh v4</option>
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113 <option value="vtk">VTK</option>
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114 </param>
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115 </inputs>
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116 <outputs>
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117 <data name="log" format="txt" label="${tool.name} on ${on_string} log" from_work_dir="neper.log"/>
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118 <data name="output_msh" format="gmsh.msh" label="${tool.name} on ${on_string} msh" from_work_dir="output.msh">
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119 <filter>'msh' in format.split(',') or 'mshi:binary' in format.split(',')</filter>
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120 </data>
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121 <data name="output_msh4" format="gmsh.msh" label="${tool.name} on ${on_string} msh4" from_work_dir="output.tesr">
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122 <filter>'msh4' in format</filter>
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123 </data>
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124 <data name="output_vtk" format="vtkascii" label="${tool.name} on ${on_string} vtk" from_work_dir="output.vtk">
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125 <filter>'vtk' in format</filter>
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126 </data>
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127 </outputs>
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128 <tests>
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129 <!-- Test-1 neper -M defaults -->
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130 <test>
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131 <param name="input" ftype="neper.tess" value="neper.tess"/>
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132 <output name="log">
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133 <assert_contents>
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134 <has_text text="Wrote file `output.msh'." />
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135 </assert_contents>
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136 </output>
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137 <output name="output_msh">
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138 <assert_contents>
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139 <has_text text="$MeshFormat" />
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140 <has_text text="2.2" />
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141 </assert_contents>
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142 </output>
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143 </test>
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144 </tests>
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145 <help><![CDATA[
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146 **Neper Meshing**
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147
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148 @NEPER_HELP@
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149
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150 Neper Mesahing Module *-M* is the module for meshing scalar and raster tessellations. The two meshing strategies are:
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151
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152 (i) Free (or unstructured) meshing creates a conforming mesh into tetrahedral elements (triangular in 2D).
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153 (ii) Mapped (or structured) meshing generates a non-conforming mesh into regular hexahedral elements (quadrangular in 2D).
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154
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155 The output is a Gmsh msh format and/or VTK format.
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156
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157 ]]></help>
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158 <expand macro="citations" />
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159 </tool>