Mercurial > repos > ximgchess > neper
changeset 0:03bbcfd3d708 draft default tip
"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 |
| parents | |
| children | |
| files | color_macros.xml macros.xml neper_meshing.xml neper_tessellation.xml neper_visualization.xml test-data/gmsh.msh test-data/neper.tess |
| diffstat | 7 files changed, 6748 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/color_macros.xml Thu Jul 07 12:31:10 2022 +0000 @@ -0,0 +1,149 @@ + <macros> + <xml name="color_options"> + <option value="black">black</option> + <option value="red">red</option> + <option value="green">green</option> + <option value="yellow">yellow</option> + <option value="cyan">cyan</option> + <option value="blue">blue</option> + <option value="magenta">magenta</option> + <option value="white">white</option> + <option value="maroon">maroon</option> + <option value="chartreuse">chartreuse</option> + <option value="olive">olive</option> + <option value="teal">teal</option> + <option value="deepskyblue">deepskyblue</option> + <option value="darkgray">darkgray</option> + <option value="silver">silver</option> + <option value="darkred">darkred</option> + <option value="darkorange">darkorange</option> + <option value="ghostwhite">ghostwhite</option> + <option value="mediumblue">mediumblue</option> + <option value="mintcream">mintcream</option> + <option value="lightcoral">lightcoral</option> + <option value="coral">coral</option> + <option value="floralwhite">floralwhite</option> + <option value="lemonchiffon">lemonchiffon</option> + <option value="darkgreen">darkgreen</option> + <option value="aliceblue">aliceblue</option> + <option value="lightyellow">lightyellow</option> + <option value="darkcyan">darkcyan</option> + <option value="steelblue">steelblue</option> + <option value="seashell">seashell</option> + <option value="darkslateblue">darkslateblue</option> + <option value="lightsalmon">lightsalmon</option> + <option value="lightskyblue">lightskyblue</option> + <option value="honeydew">honeydew</option> + <option value="peachpuff">peachpuff</option> + <option value="tomato">tomato</option> + <option value="hotpink">hotpink</option> + <option value="blanchedalmond">blanchedalmond</option> + <option value="moccasin">moccasin</option> + <option value="mediumseagreen">mediumseagreen</option> + <option value="violet">violet</option> + <option value="papayawhip">papayawhip</option> + <option value="rosybrown">rosybrown</option> + <option value="saddlebrown">saddlebrown</option> + <option value="dodgerblue">dodgerblue</option> + <option value="burlywood">burlywood</option> + <option value="linen">linen</option> + <option value="turquoise">turquoise</option> + <option value="mediumturquoise">mediumturquoise</option> + <option value="mistyrose">mistyrose</option> + <option value="antiquewhite">antiquewhite</option> + <option value="limegreen">limegreen</option> + <option value="lightsteelblue">lightsteelblue</option> + <option value="palegreen">palegreen</option> + <option value="wheat">wheat</option> + <option value="lavender">lavender</option> + <option value="lightgreen">lightgreen</option> + <option value="darkslategray">darkslategray</option> + <option value="seagreen">seagreen</option> + <option value="blueviolet">blueviolet</option> + <option value="navy">navy</option> + <option value="springgreen">springgreen</option> + <option value="purple">purple</option> + <option value="gray">gray</option> + <option value="lawngreen">lawngreen</option> + <option value="orangered">orangered</option> + <option value="snow">snow</option> + <option value="darkblue">darkblue</option> + <option value="azure">azure</option> + <option value="ivory">ivory</option> + <option value="lightpink">lightpink</option> + <option value="indigo">indigo</option> + <option value="pink">pink</option> + <option value="salmon">salmon</option> + <option value="aquamarine">aquamarine</option> + <option value="gold">gold</option> + <option value="orange">orange</option> + <option value="lightcyan">lightcyan</option> + <option value="darkmagenta">darkmagenta</option> + <option value="peru">peru</option> + <option value="lavenderblush">lavenderblush</option> + <option value="mediumspringgreen">mediumspringgreen</option> + <option value="darkgoldenrod">darkgoldenrod</option> + <option value="bisque">bisque</option> + <option value="lightgoldenrodyellow">lightgoldenrodyellow</option> + <option value="cornsilk">cornsilk</option> + <option value="whitesmoke">whitesmoke</option> + <option value="slategray">slategray</option> + <option value="oldlace">oldlace</option> + <option value="darkkhaki">darkkhaki</option> + <option value="darkturquoise">darkturquoise</option> + <option value="mediumvioletred">mediumvioletred</option> + <option value="greenyellow">greenyellow</option> + <option value="darkseagreen">darkseagreen</option> + <option value="deeppink">deeppink</option> + <option value="darkviolet">darkviolet</option> + <option value="lightslategray">lightslategray</option> + <option value="navajowhite">navajowhite</option> + <option value="mediumslateblue">mediumslateblue</option> + <option value="skyblue">skyblue</option> + <option value="beige">beige</option> + <option value="tan">tan</option> + <option value="thistle">thistle</option> + <option value="darksalmon">darksalmon</option> + <option value="royalblue">royalblue</option> + <option value="crimson">crimson</option> + <option value="mediumorchid">mediumorchid</option> + <option value="khaki">khaki</option> + <option value="paleturquoise">paleturquoise</option> + <option value="darkorchid">darkorchid</option> + <option value="yellowgreen">yellowgreen</option> + <option value="palevioletred">palevioletred</option> + <option value="olivedrab">olivedrab</option> + <option value="sandybrown">sandybrown</option> + <option value="mediumaquamarine">mediumaquamarine</option> + <option value="palegoldenrod">palegoldenrod</option> + <option value="midnightblue">midnightblue</option> + <option value="lightgray">lightgray</option> + <option value="cornflowerblue">cornflowerblue</option> + <option value="firebrick">firebrick</option> + <option value="indianred">indianred</option> + <option value="lightblue">lightblue</option> + <option value="brown">brown</option> + <option value="gainsboro">gainsboro</option> + <option value="cadetblue">cadetblue</option> + <option value="mediumpurple">mediumpurple</option> + <option value="darkolivegreen">darkolivegreen</option> + <option value="slateblue">slateblue</option> + <option value="forestgreen">forestgreen</option> + <option value="lightseagreen">lightseagreen</option> + <option value="orchid">orchid</option> + <option value="sienna">sienna</option> + <option value="powderblue">powderblue</option> + <option value="dimgray">dimgray</option> + <option value="chocolate">chocolate</option> + <option value="goldenrod">goldenrod</option> + <option value="plum">plum</option> + </xml> + <token name="@COLOR_REGEX@">([0-9]|[1-9][0-9]|1[0-9][0-9]|2[0-4][0-9]|25[0-5])</token> + <xml name="color_selector" token_name="imagebackground" token_label="Color"> + <param name="@NAME@" type="text" value="" optional="true" label="@LABEL@"> + <help>A color name or RGB, e.g. yellow or 255,255,0 </help> + <expand macro="color_options"/> + <validator type="regex" message="color name or numbers between 0 and 255" >^([a-z]+|@COLOR_REGEX@,@COLOR_REGEX@,@COLOR_REGEX@)$</validator> + </param> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jul 07 12:31:10 2022 +0000 @@ -0,0 +1,148 @@ +<macros> + <token name="@TOOL_VERSION@">4.1.2</token> + <token name="@PROFILE@">22.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">neper</requirement> + <requirement type="package" version="4.8.4">gmsh</requirement> + <requirement type="package" version="3.7.0.8">povray</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.cma.2011.01.002</citation> + <citation type="doi">10.1016/j.cma.2017.10.029</citation> + <citation type="doi">10.1107/S1600576718009019</citation> + <yield /> + </citations> + </xml> + <xml name="version_command"> + <version_command>neper --version</version_command> + </xml> + + <xml name="optional_yn" token_arg="-x" token_label="Show" token_help=""> + <param argument="@ARG@" type="select" optional="true" label="@LABEL@" help="@HELP@"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + </xml> + + <xml name="coords2d" token_label="Set" token_x="1.0" token_y="1.0"> + <param name="x" type="float" value="@X@" label="@LABEL@ x"/> + <param name="y" type="float" value="@Y@" label="@LABEL@ y"/> + </xml> + <xml name="coords3d" token_label="Set" token_x="1.0" token_y="1.0" token_z="1.0"> + <param name="x" type="float" value="@X@" label="@LABEL@ x"/> + <param name="y" type="float" value="@Y@" label="@LABEL@ y"/> + <param name="z" type="float" value="@Z@" label="@LABEL@ z"/> + </xml> + + <xml name="size2d" token_label="Set" token_xl="x" token_yl="y" token_x="1" token_y="1"> + <param name="x" type="integer" value="@X@" min="0" label="@LABEL@ @XL@"/> + <param name="y" type="integer" value="@Y@" min="0" label="@LABEL@ @YL@"/> + </xml> + <xml name="size3d" token_label="Set" token_xl="x" token_yl="y" token_zl="z" token_x="1" token_y="1" token_z="1"> + <param name="x" type="integer" value="@X@" min="0" label="@LABEL@ @XL@"/> + <param name="y" type="integer" value="@Y@" min="0" label="@LABEL@ @YL@"/> + <param name="z" type="integer" value="@Z@" min="0" label="@LABEL@ @ZL@"/> + </xml> + + <xml name="tx2d" token_label="Set" token_xl="x" token_yl="y" token_x="1" token_y="1"> + <param name="x" type="float" value="@X@" label="@LABEL@ @XL@"/> + <param name="y" type="float" value="@Y@" label="@LABEL@ @YL@"/> + <yield/> + </xml> + <xml name="tx3d" token_label="Set" token_xl="x" token_yl="y" token_zl="z" token_x="1" token_y="1" token_z="1"> + <expand macro="tx2d" label="@LABEL@" xl="@XL@" yl="@YL@" x="@X@" y="@Y@"> + <param name="z" type="float" value="@Z@" label="@LABEL@ @ZL@"/> + </expand> + </xml> + <xml name="tx4d" token_label="Set" token_xl="x" token_yl="y" token_zl="z" token_al="a" token_x="1" token_y="1" token_z="1" token_a="1"> + <expand macro="tx3d" label="@LABEL@" xl="@XL@" yl="@YL@" zl="@ZL@" x="@X@" y="@Y@" z="@Z@"> + <param name="a" type="float" value="@A@" label="@LABEL@ @AL@"/> + </expand> + </xml> + <xml name="set_ny" token_name="scale" token_label="Scale"> + <conditional name="@NAME@"> + <param name="set_@NAME@" type="select" label="@LABEL@"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <yield/> + </when> + </conditional> + </xml> + <xml name="set_nv" token_name="option" token_label="Option"> + <conditional name="@NAME@"> + <param name="set_@NAME@" type="select" label="@LABEL@"> + <option value="no">No</option> + <option value="by_value">by value </option> + </param> + <when value="no"/> + <when value="by_value"> + <yield/> + </when> + </conditional> + </xml> + <xml name="set_nve" token_name="option" token_label="Option"> + <conditional name="@NAME@"> + <param name="set_@NAME@" type="select" label="@LABEL@"> + <option value="no">No</option> + <option value="by_value">by value </option> + <option value="by_expr">by expression</option> + </param> + <when value="no"/> + <when value="by_value"> + <yield/> + </when> + <when value="by_expr"> + <yield/> + </when> + </conditional> + </xml> + + <xml name="transform"> + <section name="transform" expanded="false" title="Set Transforms"> + <expand macro="set_ny" name="scale" label="Set scale"> + <expand macro="tx3d" label="scale" lx="x factor" ly="y factor" lz="z factor"/> + </expand> + <expand macro="set_ny" name="rotate" label="Set rotate"> + <expand macro="tx4d" label="rotate" lx="x axis" ly="y axis" lz="z axis" la="angle"/> + </expand> + <expand macro="set_ny" name="translate" label="Set translate"> + <expand macro="tx3d" label="translate" lx="x distance" ly="y distance" lz="z distance"/> + </expand> + </section> + </xml> + <token name="@TRANSFORM@"> +#set $transforms = [] +#if $transform.scale.set_scale == 'yes' +#silent $transforms.append('scale(' + str($transform.scale.x) + ',' + str($transform.scale.y) + ',' + str($transform.scale.z) + ')') +#end if +#if $transform.rotate.set_rotate == 'yes' +#silent $transforms.append('rotate(' + str($transform.rotate.x) + ',' + str($transform.rotate.y) + ',' + str($transform.rotate.z) + ',' + str($transform.rotate.a) + ')') +#end if +#if $transform.translate.set_translate == 'yes' +#silent $transforms.append('translate(' + str($transform.translate.x) + ',' + str($transform.translate.y) + ',' + str($transform.translate.z) + ')') +#end if +#if $transforms + #set $txargs = ','.join($transforms) + -transform "$txargs" +#end if +</token> + + <token name="@NEPER_HELP@"> +Neper_ is a software package for polycrystal generation and meshing. The polycrystals can be 2D or 3D. +See the neper user manual for a complete description: https://neper.info/docs/neper.pdf + +*Only a small number of the neper options are currently implemented in this galaxy tool. +If there is an option you need, please create an issue at:* https://github.com/ximg-chess/galaxytools/issues + + +.. _Neper: https://github.com/rquey/neper + + </token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/neper_meshing.xml Thu Jul 07 12:31:10 2022 +0000 @@ -0,0 +1,159 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/neper_tessellation.xml Thu Jul 07 12:31:10 2022 +0000 @@ -0,0 +1,301 @@ +<tool id="neper_tessellation" name="Neper Tessellation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5"> + <description>generates polycrystals as tessellations</description> + <macros> + <import>macros.xml</import> + <token name="@VERSION_SUFFIX@">0</token> + + <xml name="cells"> + <conditional name="cells"> + <param name="format" argument="-n" type="select" label="Specify cells by"> + <option value="number">number</option> + <option value="from_morpho">from_morpho</option> + <option value="expression"></option> + </param> + <when value="number"> + <param name="number_of_cells" argument="-n" type="integer" value="10" min="1" label="the number of cells of the tessellation"/> + </when> + <when value="from_morpho"> + </when> + <when value="expression"> + </when> + </conditional> + </xml> + <token name="@CELLS@"> + #if $cells.format == 'number' + -n $cells.number_of_cells + #elif $cells.format == 'from_morpho' + -n from_morpho + #end if + </token> + + <xml name="tessellation"> + <conditional name="tessellation"> + <param name="dim" argument="-dim" type="select" label="Dimensions"> + <option value="3" selected="true">3D</option> + <option value="2">2D</option> + </param> + <when value="3"> + <conditional name="domain"> + <param name="shape" argument="-domain" type="select" label="Domain"> + <option value="cube">cube</option> + <option value="cylinder">cylinder</option> + <option value="sphere">sphere</option> + </param> + <when value="cube"> + <param name="size_x" type="float" value="1.0" min="0.0" label="size x"/> + <param name="size_y" type="float" value="1.0" min="0.0" label="size y"/> + <param name="size_z" type="float" value="1.0" min="0.0" label="size z"/> + </when> + <when value="cylinder"> + <param name="height" type="float" value="1.0" min="0.0" label="height"/> + <param name="diameter" type="float" value="1.0" min="0.0" label="diameter"/> + </when> + <when value="sphere"> + <param name="diameter" type="float" value="1.0" min="0.0" label="diameter"/> + </when> + </conditional> + </when> + <when value="2"> + <conditional name="domain"> + <param name="shape" argument="-domain" type="select" label="Domain"> + <option value="square">square</option> + <option value="circle">circle</option> + </param> + <when value="square"> + <param name="size_x" type="float" value="1.0" min="0.0" label="size x"/> + <param name="size_y" type="float" value="1.0" min="0.0" label="size y"/> + </when> + <when value="circle"> + <param name="diameter" type="float" value="1.0" min="0.0" label="diameter"/> + </when> + </conditional> + </when> + </conditional> + </xml> + <token name="@TESSELLATION@"> + -dim $tessellation.dim + #if $tessellation.domain.shape == 'cube' + -domain "${tessellation.domain.shape}($tessellation.domain.size_x,$tessellation.domain.size_y,$tessellation.domain.size_z)" + #elif $tessellation.domain.shape == 'cylinder' + -domain "${tessellation.domain.shape}($tessellation.domain.height,$tessellation.domain.diameter)" + #elif $tessellation.domain.shape == 'sphere' + -domain "${tessellation.domain.shape}($tessellation.domain.diameter)" + #elif $tessellation.domain.shape == 'square' + -domain "${tessellation.domain.shape}($tessellation.domain.size_x,$tessellation.domain.size_y)" + #elif $tessellation.domain.shape == 'circle' + -domain "${tessellation.domain.shape}($tessellation.domain.diameter)" + #end if + </token> + + <xml name="morpho"> + <conditional name="morpho"> + <param name="morpho_type" argument="-morpho" type="select" label="Morphology"> + <option value="voronoi" selected="true">voronoi</option> + <option value="tesr">tesr file</option> + <option value="gg">graingrowth</option> + </param> + <when value="voronoi"> + </when> + <when value="tesr"> + <param name="tesr_file" type="data" format="neper.tesr" label="tesr file" help="Use -n from_morpho"/> + <param name="pts_region" type="select" optional="true" label="control points region"> + <option value="surf">surface voxels</option> + <option value="all">all voxels</option> + </param> + <param name="pts_res" type="float" value="" min="1.0" optional="true" label="control points resolution" help="average number of control points along a direction of a grain"/> + </when> + <when value="gg"> + </when> + </conditional> + </xml> + <token name="@MORPHO@"> + #if $morpho.morpho_type == 'tesr' + -morpho "tesr:file($morpho.tesr_file)" + #set $pts = [] + #if $morpho.pts_region + #silent $pts.append('region=' + str($morpho.pts_region)) + #end if + #if $morpho.pts_res + #silent $pts.append('res=' + str($morpho.pts_res)) + #end if + #if $pts + #set $args = ','.join($pts) + -morphooptiobj "tesr:pts($args)" + #end if + #end if + </token> + + <xml name="morphooptistop"> + <section name="morphooptistop" expanded="false" title="Set Optimization Stop Criteria"> + <param argument="-eps" type="float" value="" optional="true" label="Absolute error on objective function"/> + <param argument="-reps" type="float" value="" optional="true" label="Relative error on objective function"/> + <param argument="-xeps" type="float" value="" optional="true" label="Absolute error on components of the solution vector"/> + <param argument="-xreps" type="float" value="" optional="true" label="Relative error on components of the solution vector"/> + <param argument="-itermax" type="integer" value="" min="1" optional="true" label="After n iterations"/> + <param argument="-loopmax" type="integer" value="" min="1" optional="true" label="After n iteration loops"/> + <param argument="-time" type="float" value="" optional="true" label="After n seconds"/> + </section> + </xml> + <token name="@MORPHOOPTISTOP@"> + #set $stops = [] + #if $morphooptistop.eps + #silent $stops.append('eps=' + str($morphooptistop.eps)) + #end if + #if $morphooptistop.reps + #silent $stops.append('reps=' + str($morphooptistop.reps)) + #end if + #if $morphooptistop.xeps + #silent $stops.append('xeps=' + str($morphooptistop.xeps)) + #end if + #if $morphooptistop.xreps + #silent $stops.append('xreps=' + str($morphooptistop.xreps)) + #end if + #if $morphooptistop.itermax + #silent $stops.append('itermax=' + str($morphooptistop.itermax)) + #end if + #if $morphooptistop.loopmax + #silent $stops.append('loopmax=' + str($morphooptistop.loopmax)) + #end if + #if $morphooptistop.time + #silent $stops.append('time=' + str($morphooptistop.time)) + #end if + #if $stops + #set $stopargs = ','.join($stops) + -morphooptistop "$stopargs" + #end if + </token> + + <xml name="regularization"> + <conditional name="regularization"> + <param name="regularize" argument="-regularization" type="select" label="Regularize tessellation"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + <when value="0"/> + <when value="1"> + <param name="fmax" argument="-fmax" type="float" value="20.0" min="0.0" max="180.0" label="face flatness fault (in degrees)" + help="The flatness fault is the maxi- mum angle between the normals at two locations on a face."/> + <param name="mloop" argument="-mloop" type="integer" value="2" min="1" label="maximum number of regularization loops"/> + </when> + </conditional> + </xml> + <token name="@REGULARIZATION@"> + -reg $regularization.regularize + #if $regularization.regularize == '1' + -fmax $regularization.fmax + -mloop $regularization.mloop + #end if + </token> + + <xml name="output_options"> + <section name="output_options" expanded="false" title="Output_options"> + <param name="tesrformat" argument="-tesrformat" type="select" optional="true" label="TESR format"> + <option value="ascii">ASCII</option> + <option value="binary8">8-bit binary / unsigned char-type</option> + <option value="binary16">16-bit binary / short-type little endian</option> + <option value="binary16_big">16-bit binary / short-type big endian</option> + <option value="binary32">32-bit binary / int-type little endian</option> + <option value="binary32_big">32-bit binary / int-type big endian</option> + </param> + <param name="tesrsize" argument="-tesrsize" type="text" value="" optional="true" label="TESR size"> + <help><![CDATA[ + Specify the number of points of a raster tessellation along a direction of the domain. In case of a domain of different lengths along the different directions, the argument stands for the geometrical average of the number of points along the different directions, so that the raster points are as close to cubic as possible. To specify different values along the x, y and z directions, combine the values with ‘:’. Default value: 20 + ]]></help> + <validator type="regex" message="integer sizes">[1-9]\d(:[1-9]\d+){,2}</validator> + </param> + <!-- macro for oridescriptor --> + </section> + </xml> + <token name="@OUTPUT_OPTIONS@"> + #if 'tesr' in $format + #if $output_options.tesrformat: + -tesrformat '$output_options.tesrformat' + #end if + #if $output_options.tesrsize: + -tesrsize '$output_options.tesrsize' + #end if + #end if + </token> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + neper -T + @CELLS@ + @TESSELLATION@ + @MORPHO@ + @MORPHOOPTISTOP@ + @TRANSFORM@ + @REGULARIZATION@ + @OUTPUT_OPTIONS@ + -format "$format" + -o output + | grep -v '%$' | tee 'neper.log' + ]]></command> + <inputs> + <expand macro="cells"/> + <expand macro="tessellation"/> + <expand macro="morpho"/> + <expand macro="morphooptistop"/> + <expand macro="transform"/> + <expand macro="regularization"/> + <expand macro="output_options"/> + <param name="format" argument="-format" type="select" multiple="true" optional="false" label="Output format"> + <option value="tess" selected="true">Neper scalar tessellation file (.tess)</option> + <option value="tesr">Neper raster tessellation file (.tesr)</option> + <option value="vtk">VTK raster file (.vtk)</option> + <option value="geo">Gmsh geometry file (.geo)</option> + <option value="ply">Polygon File Format file (.ply)</option> + </param> + </inputs> + <outputs> + <data name="log" format="txt" label="${tool.name} on ${on_string} log" from_work_dir="neper.log"/> + <data name="output_tess" format="neper.tess" label="${tool.name} on ${on_string} tess" from_work_dir="output.tess"> + <filter>'tess' in format</filter> + </data> + <data name="output_tesr" format="neper.tesr" label="${tool.name} on ${on_string} tesr" from_work_dir="output.tesr"> + <filter>'tesr' in format</filter> + </data> + <data name="output_vtk" format="vtkbinary" label="${tool.name} on ${on_string} vtk" from_work_dir="output.vtk"> + <filter>'vtk' in format</filter> + </data> + <data name="output_ply" format="plyascii" label="${tool.name} on ${on_string} ply" from_work_dir="output.ply"> + <filter>'ply' in format</filter> + </data> + <data name="output_geo" format="gmsh.geo" label="${tool.name} on ${on_string} geo" from_work_dir="output.geo"> + <filter>'geo' in format</filter> + </data> + </outputs> + <tests> + <!-- Test-1 neper -T -n 4 --> + <test> + <conditional name="cells"> + <param name="format" value="number"/> + <param name="number_of_cells" value="4"/> + </conditional> + <output name="output_tess"> + <assert_contents> + <has_text text="***tess" /> + <has_text_matching expression="[*][*]cell\n 4\n [*]id\n 1 2 3 4\n"/> + </assert_contents> + </output> + </test> + <!-- Test neper -T -n from_morpho -domain "cube(0.5,0.5,0.5)" -morpho "tesr:file(example_tesr.tesr)" -morphooptiobj "tesr:pts(region=surf,res=7)" -morphooptistop itermax=30 -reg 1 --> + </tests> + <help><![CDATA[ +**Neper Tessellation** + +@NEPER_HELP@ + +Neper Tessellation Module *-T* generates polycrystals as tessellations. The two main capabilities are: + + (i) the generation of tessellations from cell properties (e.g. a size distribution) + (ii) the genera- tion of multiscale tessellations (i.e. including cell subdivisions). + +These capabilities can also be used together. Tessellations are Laguerre (or Voronoi) tessellations and are therefore composed of convex cells. Once generated, the tessellations can be “regularized” by removing their smallest features (edges and faces), which then enables good-quality meshing with module -M. Periodicity conditions can be prescribed. Crystal orientations are pro- vided for the cells. + + The output is a tessellation file written at a scalar (vectorial) or raster format. Scalar tessellations are intended to be passed to modules -M and -V while raster tessellations can be used by FFT solvers. + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/neper_visualization.xml Thu Jul 07 12:31:10 2022 +0000 @@ -0,0 +1,482 @@ +<tool id="neper_visualization" name="Neper Visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5"> + <description></description> + <macros> + <import>macros.xml</import> + <import>color_macros.xml</import> + <token name="@VERSION_SUFFIX@">0</token> + +<!-- Mesh Keys +id#identifier#node, @var{n}D elt, @var{n}D elset +x#x coordinate#node, @var{n}D elt, @var{n}D elset +y#y coordinate#node, @var{n}D elt, @var{n}D elset +z#z coordinate#node, @var{n}D elt, @var{n}D elset +coo#x, y and z coordinates#node, @var{n}D elt, @var{n}D elset +dim#dimension (= lowest parent elt dimension)#node +elset0d#0D elset#0D elt +elset1d#1D elset#1D elt +elset2d#2D elset#2D elt +elset3d#3D elset#3D elt +part#partition#@var{n}D elt, node +group#group#@var{n}D elt, @var{n}D elset +cyl#whether or not is used to describe the circular part of a cylinder domain#1D elt, 1D elset +vol#volume#3D elt, 3D elset +area#surface area#2D elt +diameq#equivalent diameter@footnote{Equivalent diameter = diameter of the circle of equivalent area/volume in 2D/3D.#2D elt, 3D elt, 2D elset, 3D elset +radeq#equivalent radius@footnote{Equivalent radius = radius of the circle of equivalent area/volume in 2D/3D.}#2D elt, 3D elt, 2D elset, 3D elset +length#average edge length#@math{n}D elt, 1D elset +lengths#edge lengths#2D elt, 3D elt +elsetvol#elset volume#3D elt +elsetarea#elset area#2D elt +elsetlength#elset length#1D elt +rr#radius ratio#3D elt +rrav}, @code{rrmin}, @code{rrmax} +#average, min and max radius ratios @tab 3D elset +Osize#Osize#3D elset +eltnb#number of elements#@var{n}D elset +true#true level#@var{n}D elt, @var{n}D elset +body#body level#@var{n}D elt, @var{n}D elset +domtype#type of domain (0 if on a domain vertex, 1 if on a domain edge and 2 if on a domain face)#@w{2D elset}, @w{1D elset}, @w{0D elset}, @w{2D elt}, @w{1D elt}, @w{0D elt} +2dmeshp#coordinates of the closest point of the 2D mesh#node, 3D elt +2dmeshd#distance to @samp{2dmeshp}#node, 3D elt +2dmeshv#vector to @samp{2dmeshp}#node, 3D elt +2dmeshn#outgoing normal vector of the 2D mesh at @samp{2dmeshp#node, 3D elt +per#periodic (1 if periodic, 0 otherwise)#0D elt, 1D elt, 2D elt (in 3D), 0D elset, 1D elset, 2D elset (in 3D) +col_rodrigues#color according to the Rodrigues vector color convention@footnote{Applies to a mesh of Rodrigues space.}#node +col_stdtriangle#color according to the stereographic triangle (IPF) color convention@footnote{Applies to a mesh of the stereographic triangle.}#node +--> + + <xml name="set_elt" token_name="option"> + <conditional name="@NAME@"> + <param name="set_@NAME@" type="select" label="Set @NAME@"> + <option value="default">use default</option> + <option value="by_value">by value </option> + <option value="from_file">from file</option> + </param> + <when value="default"/> + <when value="by_value"> + <param name="@NAME@" argument="-@NAME@" type="text" label="@NAME@"> + <option value="all">all</option> + <option value="none">none</option> + <yield/> + </param> + </when> + <when value="from_file"> + <param name="elements_file" argument="-@NAME@" type="data" format="txt" label="Elements file"/> + </when> + </conditional> + </xml> + + <xml name="elt_elset"> + <param name="by_set" type="boolean" truevalue="elset" falsevalue="elt" checked="false" label="apply to element set"/> + </xml> + <xml name="set_el_color" token_name="option"> + <conditional name="@NAME@"> + <param name="set_@NAME@" type="select" label="Set @NAME@ by"> + <option value="default" selected="true">Use default</option> + <option value="data_value">data value</option> + <option value="color">color</option> + <option value="from_file">from file</option> + </param> + <when value="default"/> + <when value="data_value"> + <param argument="-@NAME@" type="text" label="Set @NAME@ by element or element set"> + <yield/> + </param> + <expand macro="elt_elset"/> + </when> + <when value="color"> + <expand macro="color_selector" argument="-@NAME@" label="Set @NAME@ color"/> + <expand macro="elt_elset"/> + </when> + <when value="from_file"> + <param name="color_file" argument="-@NAME@" type="data" format="txt" label="Color file"/> + </when> + </conditional> + </xml> + + <xml name="tess_data"> + <section name="tess" expanded="false" title="Tessellation Rendering"> + <conditional name="datacellcol"> + <param name="set_datacellcol" argument="-datacellcol" type="select" label="Set datacell color"> + <option value="none">None</option> + <option value="id" selected="true">id</option> + <option value="mode">mode</option> + <option value="by_value">By value</option> + </param> + <when value="none"/> + <when value="id"/> + <when value="mode"/> + <when value="by_value"> + <expand macro="color_selector" name="datacellcolor" label="Select datacell color"/> + </when> + <when value="by_value"> + </when> + </conditional> + </section> + </xml> + <token name="@TESS_DATA@"> + #if $tess.datacellcol.set_datacellcol in ['id','mode'] + -datacellcol $tess.datacellcol.set_datacellcol + #elif $tess.datacellcol.set_datacellcol == 'by_value' + -datacellcol $tess.datacellcol.datacellcolor + #end if + </token> + +<!-- +neper -V example_mesh.msh -showelt1d all -dataelset3dcol id -dataelt1drad 0.0025 -dataelt3dedgerad 0.0025 +--> + + <xml name="mesh_data"> + <section name="mesh_data" expanded="false" title="Mesh Data Loading"> + <!-- NOTE: elt or elset --> + <!-- datanodecoo --> + <!-- datanodecoofact --> + <!-- datanoderad --> + <!-- datanodecol --> + <!-- datanodecolscheme --> + <!-- datanodescale --> + <!-- datanodescaletitle --> + </section> + </xml> + <token name="@MESH_DATA@"> + </token> + + <xml name="mesh_color"> + <section name="mesh_color" expanded="false" title="Mesh Data Rendering"> + <!-- NOTE: elt or elset --> + <!-- dataelt3dcol --> + <expand macro="set_el_color" name="dataelt3dcol"> + </expand> + <!-- dataelt3dcolscheme --> + <!-- dataelt3dcolscale --> + <!-- dataelt3dcolscaletitle --> + <!-- dataelt3dedgerad --> + <param argument="-dataelt3dedgerad" type="float" value="" min="0.0" optional="true" label="data element 3d edge radius"/> + <!-- dataelt3dedgecol --> + + <!-- dataelt2dcol --> + <expand macro="set_el_color" name="dataelt2dcol"> + </expand> + <!-- dataelt2dcolscheme --> + <!-- dataelt2dcolscale --> + <!-- dataelt2dcolscaletitle --> + <!-- dataelt2dedgerad --> + <param argument="-dataelt2dedgerad" type="float" value="" min="0.0" optional="true" label="data element 2d edge radius"/> + <!-- dataelt2dedgecol --> + + <!-- dataelt1dcol --> + <expand macro="set_el_color" name="dataelt1dcol"> + </expand> + <!-- dataelt1dcolscheme --> + <!-- dataelt1dcolscale --> + <!-- dataelt1dcolscaletitle --> + <!-- dataelt1drad --> + <param argument="-dataelt1drad" type="float" value="" min="0.0" optional="true" label="data element 1d radius"/> + + <!-- dataelt0dcol --> + <expand macro="set_el_color" name="dataelt0dcol"> + </expand> + <!-- dataelt0dcolscheme --> + <!-- dataelt0dcolscale --> + <!-- dataelt0dcolscaletitle --> + <!-- dataelt0drad --> + <param argument="-dataelt0drad" type="float" value="" min="0.0" optional="true" label="data element 1d radius"/> + </section> + </xml> + <token name="@MESH_COLOR@"> + #if $mesh_color.dataelt3dcol.set_dataelt3dcol == 'from_file' + #pass + #elif $mesh_color.dataelt3dcol.set_dataelt3dcol != 'default' + #set opt = '-dataelt3dcol'.replace('elt',str($mesh_color.dataelt3dcol.by_set)) + $opt '$mesh_color.dataelt3dcol.dataelt3dcol' + #end if + #if $mesh_color.dataelt2dcol.set_dataelt2dcol == 'from_file' + #pass + #elif $mesh_color.dataelt2dcol.set_dataelt2dcol != 'default' + #set opt = '-dataelt2dcol'.replace('elt',str($mesh_color.dataelt2dcol.by_set)) + $opt '$mesh_color.dataelt2dcol.dataelt2dcol' + #end if + #if $mesh_color.dataelt1dcol.set_dataelt1dcol == 'from_file' + #pass + #elif $mesh_color.dataelt1dcol.set_dataelt1dcol != 'default' + #set opt = '-dataelt1dcol'.replace('elt',str($mesh_color.dataelt1dcol.by_set)) + $opt '$mesh_color.dataelt1dcol.dataelt1dcol' + #end if + #if $mesh_color.dataelt0dcol.set_dataelt0dcol == 'from_file' + #pass + #elif $mesh_color.dataelt0dcol.set_dataelt0dcol != 'default' + #set opt = '-dataelt0dcol'.replace('elt',str($mesh_color.dataelt0dcol.by_set)) + $opt '$mesh_color.dataelt0dcol.dataelt3dcol' + #end if + + #if $mesh_color.dataelt3dedgerad + -dataelt3dedgerad $mesh_color.dataelt3dedgerad + #end if + #if $mesh_color.dataelt2dedgerad + -dataelt2dedgerad $mesh_color.dataelt2dedgerad + #end if + #if $mesh_color.dataelt1drad + -dataelt1drad $mesh_color.dataelt1drad + #end if + #if $mesh_color.dataelt0drad + -dataelt0drad $mesh_color.dataelt0drad + #end if + </token> + + <xml name="show_settings"> + <section name="show" expanded="false" title="Show Settings"> + <expand macro="optional_yn" arg="-showtess" label="Show tess" help="test"/> + <expand macro="optional_yn" arg="-showtesr" label="Show tesr" help="test"/> + <expand macro="optional_yn" arg="-showmesh" label="Show mesh" help="test"/> + <expand macro="optional_yn" arg="-showmeshslice" label="Show mesh slice" help="test"/> + <!-- showpoint --> + </section> + </xml> + <token name="@SHOW_SETTINGS@"> + #if $show.showtess + -showtess $show.showtess + #end if + #if $show.showtesr + -showtesr $show.showtesr + #end if + #if $show.showmesh + -showmesh $show.showmesh + #end if + #if $show.showmeshslice + -showmeshslice $show.showmeshslice + #end if + ## -showpoint + </token> + + <xml name="show_tess_settings"> + <section name="show_tess" expanded="false" title="Show Tessellation Settings"> + <!-- showcell --> + <!-- showpoly --> + <!-- showface --> + <!-- showedge --> + <!-- showver --> + <!-- showseed --> + <!-- showfaceinter --> + <expand macro="optional_yn" arg="-showfaceinter" label="Show the interpolations of the tessellation faces" help=""/> + <!-- RASTER tesr --> + <!-- showvoidvox --> + </section> + </xml> + <token name="@SHOW_TESS_SETTINGS@"> + #if $show_tess.showfaceinter + -showfaceinter $show_tess.showfaceinter + #end if + </token> + + <xml name="show_mesh_settings"> + <section name="show_mesh" expanded="false" title="Show Mesh Settings"> + <expand macro="set_elt" name="showelt3d"/> + <expand macro="set_elt" name="showelt2d"> + <option value="elt3d_shown">elt3d_shown</option> + </expand> + <expand macro="set_elt" name="showelt1d"> + <option value="elt2d_shown">elt2d_shown</option> + <option value="elt3d_shown">elt3d_shown</option> + </expand> + <expand macro="set_elt" name="showelt0d"> + <option value="elt1d_shown">elt1d_shown</option> + <option value="elt2d_shown">elt2d_shown</option> + <option value="elt3d_shown">elt3d_shown</option> + </expand> + <!-- shownode --> + <expand macro="optional_yn" arg="-showcys" label="Show the coordinate system" help=""/> + <expand macro="optional_yn" arg="-showshadow" label="Show the shadows" help=""/> + </section> + </xml> + <token name="@SHOW_MESH_SETTINGS@"> + #if $show_mesh.showelt3d.set_showelt3d == 'by_value' + -showelt3d '$show_mesh.showelt3d.showelt3d' + #elif $show_mesh.showelt3d.set_showelt3d == 'from_file' + -showelt3d 'file($show_mesh.showelt3d.elements_file)' + #end if + #if $show_mesh.showelt2d.set_showelt2d == 'by_value' + -showelt2d '$show_mesh.showelt2d.showelt2d' + #elif $show_mesh.showelt2d.set_showelt2d == 'from_file' + -showelt2d 'file($show_mesh.showelt2d.elements_file)' + #end if + #if $show_mesh.showelt1d.set_showelt1d == 'by_value' + -showelt1d '$show_mesh.showelt1d.showelt1d' + #elif $show_mesh.showelt1d.set_showelt1d == 'from_file' + -showelt1d 'file($show_mesh.showelt1d.elements_file)' + #end if + #if $show_mesh.showelt0d.set_showelt0d == 'by_value' + -showelt0d '$show_mesh.showelt0d.showelt0d' + #elif $show_mesh.showelt0d.set_showelt0d == 'from_file' + -showelt0d 'file($show_mesh.showelt0d.elements_file)' + #end if + ## shownode + #if $show_mesh.showcys + -showcys $show_mesh.showcys + #end if + #if $show_mesh.showshadow + -showshadow $show_mesh.showshadow + #end if + </token> + + <xml name="camera_settings"> + <section name="camera" expanded="false" title="Camera Settings"> + <expand macro="set_nv" name="cameracoo" label="Specify the camera coordinates"> + <expand macro="tx3d" label="Camera position" lx="x" ly="y" lz="z"/> + </expand> + <expand macro="set_nv" name="cameralookat" label="Specify the camera look-at point"> + <expand macro="tx3d" label="Camera lookat" lx="x" ly="y" lz="z"/> + </expand> + <param name="cameraangle" type="float" value="" min="1" max="179" optional="true" label="Set the opening angle of the camera along the horizontal direction (in degrees)"/> + <expand macro="set_nv" name="camerasky" label="Specify the sky vector of the camera (vertical direction)"> + <expand macro="tx3d" label="Camera Sky vector" lx="x" ly="y" lz="z" x="0" y="0" z="1"/> + </expand> + <param name="cameraprojection" type="select" optional="true" label="Camera Projection"> + <help>Default value: perspective for 3D and orthographic for 2D</help> + <option value="perspective">perspective</option> + <option value="orthographic">orthographic</option> + </param> + </section> + </xml> + <token name="@CAMERA_SETTINGS@"> + #if $camera.cameracoo.set_cameracoo == 'by_value' + -cameracoo "${camera.cameracoo.x}:${camera.cameracoo.y}:${camera.cameracoo.z}" + #end if + #if $camera.cameralookat.set_cameralookat == 'by_value' + -cameralookat "${camera.cameralookat.x}:${camera.cameralookat.y}:${camera.cameralookat.z}" + #end if + #if $camera.cameraangle + -cameraangle $camera.cameraangle + #end if + #if $camera.camerasky.set_camerasky == 'by_value' + -camerasky "${camera.camerasky.x}:${camera.camerasky.y}:${camera.camerasky.z}" + #end if + #if $camera.cameraprojection + -cameraprojection $camera.cameraprojection + #end if + </token> + + <xml name="image_settings"> + <section name="image" expanded="false" title="Image Settings"> + <expand macro="set_ny" name="imagesize" label="Set the image size"> + <expand macro="size2d" label="Image size" lx="width" ly="height"/> + </expand> + <expand macro="color_selector" name="imagebackground" label="Image background color"/> + <param name="imageantialias" type="boolean" truevalue="" falsevalue="-imageantialias 0" checked="true" label="Use antialiasing" + help="Use antialiasing to produce a smoother image. Switch antialiasing off for faster image gener- ation or smaller image file"/> + </section> + </xml> + <token name="@IMAGE_SETTINGS@"> + #if $image.imagesize.set_imagesize == 'yes' + -imagesize "${image.imagesize.x}:${image.imagesize.y}" + #end if + #if $image.imagebackground + -imagebackground "$image.imagebackground" + #end if + $image.imageantialias + </token> + + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + #* + #set $tessfiles = [] + #set $mshfiles = [] + #for $input in $inputs + #if $input.is_of_type('neper.msh') + #silent $mshfiles.append(str($input)) + #else + #silent $tessfiles.append(str($input)) + #end if + #end for + #set $ds = ','.join($tessfiles + $mshfiles) + neper -V + '$ds' + *# + neper -V + '$inputs' + @TESS_DATA@ + @TRANSFORM@ + @MESH_COLOR@ + @SHOW_SETTINGS@ + @SHOW_TESS_SETTINGS@ + @SHOW_MESH_SETTINGS@ + @CAMERA_SETTINGS@ + @IMAGE_SETTINGS@ + -imageformat "$imageformat" + -print output + | grep -v '%$' | tee 'neper.log' + #if 'png' in $imageformat + && test -s output.png + #end if + #if 'vtk' in $imageformat + && test -s output.vtk + #end if + ]]></command> + <inputs> + <param name="inputs" type="data" format="neper.tesr,neper.tess,gmsh.msh" multiple="true" label="Input to visualize"/> + <expand macro="tess_data"/> + <expand macro="transform"/> + <expand macro="mesh_color"/> + <expand macro="show_settings"/> + <expand macro="show_tess_settings"/> + <expand macro="show_mesh_settings"/> + <expand macro="camera_settings"/> + <expand macro="image_settings"/> + <param name="imageformat" argument="-imageformat" type="select" multiple="true" optional="false" label="Image formats"> + <option value="png" selected="true">PNG</option> + <option value="vtk">VTK</option> + <option value="pov">POV</option> + </param> + </inputs> + <outputs> + <data name="log" format="txt" label="${tool.name} on ${on_string} log" from_work_dir="neper.log"/> + <data name="output_png" format="png" label="${tool.name} on ${on_string} png" from_work_dir="output.png"> + <filter>'png' in imageformat</filter> + </data> + <data name="output_vtk" format="vtkascii" label="${tool.name} on ${on_string} vtk" from_work_dir="output.vtk"> + <filter>'vtk' in imageformat</filter> + </data> + <data name="output_pov" format="pov" label="${tool.name} on ${on_string} pov" from_work_dir="output.pov"> + <filter>'pov' in imageformat</filter> + </data> + </outputs> + <tests> + <!-- Test-1 neper -V neper.tess -datacellcol id -imageformat "png" --> + <test> + <param name="inputs" ftype="neper.tess" value="neper.tess"/> + <output name="log"> + <assert_contents> + <has_text text="Wrote file `output.png'." /> + </assert_contents> + </output> + </test> + <!-- Test-2 neper -V gmsh.msh -datacellcol id -imageformat "png,vtk" --> + <test> + <param name="inputs" ftype="neper.tess" value="gmsh.msh"/> + <param name="imageformat" value="png,vtk"/> + <output name="log"> + <assert_contents> + <has_text text="Wrote file `output.png'." /> + <has_text text="Wrote file `output.vtk'." /> + </assert_contents> + </output> + <output name="output_vtk"> + <assert_contents> + <has_text text="vtk DataFile" /> + <has_text text="DATASET UNSTRUCTURED_GRID" /> + </assert_contents> + </output> + </test> + + </tests> + <help><![CDATA[ +**Neper Visualization** + +@NEPER_HELP@ + +Module -V is the module for visualizing tessellations, meshes and simulation results as publication-quality PNG images1 or as VTK files, for interactive visualization. Results can be defined from internal data, data loaded from external files or a simulation directory as generated by module -S. For the PNG images, it is possible to set different attributes of the tessellations and meshes such as the node coordinates, or the colors and transparencies of the different entities. Point data can also be represented, using symbols of specified sizes and colors. Slice views can also be generated. + + ]]></help> + <expand macro="citations" /> +</tool>
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