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comparison 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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-1:000000000000 0:03bbcfd3d708
1 <tool id="neper_meshing" name="Neper Meshing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
2 <description>scalar and raster tessellations</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <xml name="meshing">
7 <section name="meshing" expanded="false" title="Meshing Options">
8 <param argument="-elttype" type="select" optional="true" label="Set element type">
9 <help>Default value: tetrahedral in 3D and triangular in 2D</help>
10 <option value="tri">triangular</option>
11 <option value="quad">quadrangular</option>
12 <option value="quad9">9-node quadrangular</option>
13 <option value="tet">tetrahedral</option>
14 <option value="hex">hexahedral</option>
15 </param>
16 <!-- cl,rcl -->
17 <param argument="-dim" type="select" multiple="true" optional="true" label="Set the meshing dimension">
18 <help>Default value: inputdim</help>
19 <option value="inputdim">inputdim</option>
20 <option value="all">all</option>
21 <option value="none">none</option>
22 <option value="0">0</option>
23 <option value="1">1</option>
24 <option value="2">2</option>
25 <option value="3">3</option>
26 </param>
27 <param argument="-order" type="select" optional="true" label="Set the mesh order">
28 <help>Default value: 1
29 A value of 1 corresponds to 2-node linear elements, 3-node triangular elements,
30 4-node quadrangular elements, 4-node tetrahedral elements and 8-node hexahedral elements,
31 A value of 2 corresponds to 3-node linear elements, 6-node triangular elements,
32 8-node or 9-node quadrangular elements, 10-node tetrahedral elements
33 and 20-node hexahedral elements.
34 </help>
35 <option value="1">1 - 2-node linear...</option>
36 <option value="2">2 - 3-node linear...</option>
37 </param>
38
39 <!--
40 <expand macro="set_ny" name="elttype" label="Set element typescale">
41 <expand macro="tx3d" label="scale" lx="x factor" ly="y factor" lz="z factor"/>
42 </expand>
43 -->
44 </section>
45 </xml>
46 <token name="@MESHING@">
47 #if $meshing.elttype
48 -elttype $meshing.elttype
49 #end if
50 #if $meshing.dim
51 -dim $meshing.dim
52 #end if
53 #if $meshing.order
54 -order $meshing.order
55 #end if
56 </token>
57
58 <xml name="meshing_output">
59 <section name="meshing_output" expanded="false" title="Meshing Output Options">
60 <param argument="-nset" type="text" value="" optional="true" label="Specify the node sets">
61 <option value="faces">faces</option>
62 <option value="edges">edges</option>
63 <option value="vertices">vertices</option>
64 <option value="facebodies">facebodies</option>
65 <option value="edgebodies">edgebodies</option>
66 <option value="all">all</option>
67 <option value="none">none</option>
68 <!--
69 <validator type="regex" message="">^all|none|(faces|edges|vertices|facebodies|edgebodies)*|([x-z][01]|[x-z][01][x-z][01]|[x-z][01][x-z][01][x-z][01]|z[0,1]f[1-9][0-9]*|f[1-9][0-9]*)*$</validator>
70 -->
71 </param>
72 <param argument="-faset" type="text" value="" optional="true" label="Specify the element surface meshes">
73 <option value="faces">faces</option>
74 <option value="internal">internal</option>
75 <!--
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>
77 -->
78 </param>
79 </section>
80 </xml>
81 <token name="@MESHING_OUTPUT@">
82 #if $meshing_output.nset
83 -nset "$meshing_output.nset"
84 #end if
85 #if $meshing_output.faset
86 -faset "$meshing_output.faset"
87 #end if
88 </token>
89
90 </macros>
91 <expand macro="requirements" />
92 <expand macro="version_command" />
93 <command detect_errors="exit_code"><![CDATA[
94 neper -M
95 '$input'
96 @MESHING@
97 @MESHING_OUTPUT@
98 @TRANSFORM@
99 -format "$format"
100 -part "\${GALAXY_SLOTS:-4}"
101 -o output
102 | grep -v '%$' | tee 'neper.log'
103 ]]></command>
104 <inputs>
105 <param name="input" type="data" format="neper.tesr,neper.tess,gmsh.msh" label="Input tessellation or mesh file"/>
106 <expand macro="meshing"/>
107 <expand macro="meshing_output"/>
108 <expand macro="transform"/>
109 <param name="format" argument="-format" type="select" multiple="true" optional="false" label="Output formats">
110 <option value="msh" selected="true">Gmsh-style msh ascii</option>
111 <option value="msh:binary">Gmsh-style msh binary</option>
112 <option value="msh4">Gmsh v4</option>
113 <option value="vtk">VTK</option>
114 </param>
115 </inputs>
116 <outputs>
117 <data name="log" format="txt" label="${tool.name} on ${on_string} log" from_work_dir="neper.log"/>
118 <data name="output_msh" format="gmsh.msh" label="${tool.name} on ${on_string} msh" from_work_dir="output.msh">
119 <filter>'msh' in format.split(',') or 'mshi:binary' in format.split(',')</filter>
120 </data>
121 <data name="output_msh4" format="gmsh.msh" label="${tool.name} on ${on_string} msh4" from_work_dir="output.tesr">
122 <filter>'msh4' in format</filter>
123 </data>
124 <data name="output_vtk" format="vtkascii" label="${tool.name} on ${on_string} vtk" from_work_dir="output.vtk">
125 <filter>'vtk' in format</filter>
126 </data>
127 </outputs>
128 <tests>
129 <!-- Test-1 neper -M defaults -->
130 <test>
131 <param name="input" ftype="neper.tess" value="neper.tess"/>
132 <output name="log">
133 <assert_contents>
134 <has_text text="Wrote file `output.msh'." />
135 </assert_contents>
136 </output>
137 <output name="output_msh">
138 <assert_contents>
139 <has_text text="$MeshFormat" />
140 <has_text text="2.2" />
141 </assert_contents>
142 </output>
143 </test>
144 </tests>
145 <help><![CDATA[
146 **Neper Meshing**
147
148 @NEPER_HELP@
149
150 Neper Mesahing Module *-M* is the module for meshing scalar and raster tessellations. The two meshing strategies are:
151
152 (i) Free (or unstructured) meshing creates a conforming mesh into tetrahedral elements (triangular in 2D).
153 (ii) Mapped (or structured) meshing generates a non-conforming mesh into regular hexahedral elements (quadrangular in 2D).
154
155 The output is a Gmsh msh format and/or VTK format.
156
157 ]]></help>
158 <expand macro="citations" />
159 </tool>