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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/ commit 8d522c2d14b28a4df096a5a13cd800bbf086f09f
author ufz
date Thu, 06 Mar 2025 17:29:28 +0000
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1 <tool id="ogs_generatestructuredmesh" name="OGS generateStructuredMesh" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 Generation of simple meshes
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 <token name="@VERSION_SUFFIX@">0</token>
8 </macros>
9 <requirements>
10 <expand macro="ogs_requirement"/>
11 </requirements>
12 <expand macro="creator"/>
13 <command detect_errors="exit_code"><![CDATA[
14 generateStructuredMesh
15 -o output.$output_ext
16 -e $element_type
17 #if str($length_x) != "":
18 --lx $length_x
19 #end if
20 #if str($length_y) != "":
21 --ly $length_y
22 #end if
23 #if str($length_z) != "":
24 --lz $length_z
25 #end if
26 #if str($subdiv_x) != "":
27 --nx $subdiv_x
28 #end if
29 #if str($subdiv_y) != "":
30 --ny $subdiv_y
31 #end if
32 #if str($subdiv_z) != "":
33 --nz $subdiv_z
34 #end if
35 #if str($element_length_x) != "":
36 --dx0 $element_length_x
37 #end if
38 #if str($element_length_y) != "":
39 --dy0 $element_length_y
40 #end if
41 #if str($element_length_z) != "":
42 --dz0 $element_length_z
43 #end if
44 #if str($max_element_length_x) != "":
45 --dx-max $max_element_length_x
46 #end if
47 #if str($max_element_length_y) != "":
48 --dy-max $max_element_length_y
49 #end if
50 #if str($max_element_length_z) != "":
51 --dz-max $max_element_length_z
52 #end if
53 #if str($multiplier_x) != "":
54 --mx $multiplier_x
55 #end if
56 #if str($multiplier_y) != "":
57 --my $multiplier_y
58 #end if
59 #if str($multiplier_z) != "":
60 --mz $multiplier_z
61 #end if
62 && mv output.$output_ext '$output'
63
64 ]]></command>
65 <inputs>
66 <param name="output_ext" type="select" label="Output File Format" argument="-o">
67 <option value="vtu">VTK Unstructured Grid</option>
68 <option value="msh">GMSH</option>
69 </param>
70 <param name="element_type" type="select" label="Element Type" argument="-e">
71 <option value="line">Line</option>
72 <option value="tri">Triangle</option>
73 <option value="quad">Quadrilateral</option>
74 <option value="hex">Hexahedron</option>
75 <option value="prism">Prism</option>
76 <option value="tet">Tetrahedron</option>
77 <option value="pyramid">Pyramid</option>
78 </param>
79 <param name="length_x" type="float" min="0" optional="true" label="Length in X" help="Length of the domain in the X direction.">
80 <validator type="in_range" min="0" exclude_min="true"/>
81 </param>
82 <param name="length_y" type="float" min="0" optional="true" label="Length in Y" help="Length of the domain in the Y direction.">
83 <validator type="in_range" min="0" exclude_min="true"/>
84 </param>
85 <param name="length_z" type="float" min="0" optional="true" label="Length in Z" help="Length of the domain in the Z direction.">
86 <validator type="in_range" min="0" exclude_min="true"/>
87 </param>
88 <param name="subdiv_x" type="integer" min="1" optional="true" label="Subdivisions in X" help="Number of subdivisions in the X direction. Overrides element length argument."/>
89 <param name="subdiv_y" type="integer" min="1" optional="true" label="Subdivisions in Y" help="Number of subdivisions in the Y direction. Overrides element length argument."/>
90 <param name="subdiv_z" type="integer" min="1" optional="true" label="Subdivisions in Z" help="Number of subdivisions in the Z direction. Overrides element length argument."/>
91 <param name="element_length_x" type="float" min="0" optional="true" label="Initial Element Length X" help="Initial element length in the X direction. If the value of this parameter is smaller than subdivions or maximum length parameters it gets overridden.">
92 <validator type="in_range" min="0" exclude_min="true"/>
93 </param>
94 <param name="element_length_y" type="float" min="0" optional="true" label="Initial Element Length Y" help="Initial element length in the Y direction. If the value of this parameter is smaller than subdivions or maximum length parameters it gets overridden.">
95 <validator type="in_range" min="0" exclude_min="true"/>
96 </param>
97 <param name="element_length_z" type="float" min="0" optional="true" label="Initial Element Length Z" help="Initial element length in the Z direction. If the value of this parameter is smaller than subdivions or maximum length parameters it gets overridden.">
98 <validator type="in_range" min="0" exclude_min="true"/>
99 </param>
100 <param name="max_element_length_x" type="float" min="0" optional="true" label="Maximum Element Length X" help="Maximum element length in the X direction. Overrides element length argument.">
101 <validator type="in_range" min="0" exclude_min="true"/>
102 </param>
103 <param name="max_element_length_y" type="float" min="0" optional="true" label="Maximum Element Length Y" help="Maximum element length in the Y direction. Overrides element length argument.">
104 <validator type="in_range" min="0" exclude_min="true"/>
105 </param>
106 <param name="max_element_length_z" type="float" min="0" optional="true" label="Maximum Element Length Z" help="Maximum element length in the Z direction. Overrides element length argument.">
107 <validator type="in_range" min="0" exclude_min="true"/>
108 </param>
109 <param name="multiplier_x" type="float" min="0" optional="true" label="Multiplier X" help="Multiplier for element lengths in the X direction.">
110 <validator type="in_range" min="0" exclude_min="true"/>
111 </param>
112 <param name="multiplier_y" type="float" min="0" optional="true" label="Multiplier Y" help="Multiplier for element lengths in the Y direction.">
113 <validator type="in_range" min="0" exclude_min="true"/>
114 </param>
115 <param name="multiplier_z" type="float" min="0" optional="true" label="Multiplier Z" help="Multiplier for element lengths in the Z direction.">
116 <validator type="in_range" min="0" exclude_min="true"/>
117 </param>
118 </inputs>
119 <outputs>
120 <data format="vtkxml" name="output">
121 <change_format>
122 <when input="output_ext" value="msh" format="gmsh.msh"/>
123 </change_format>
124 </data>
125 </outputs>
126 <tests>
127 <test>
128 <param name="output_ext" value="vtu"/>
129 <param name="element_type" value="quad"/>
130 <param name="length_x" value="3"/>
131 <param name="length_y" value="4"/>
132 <output name="output" value="quad_3x4.vtu" ftype="vtkxml"/>
133 </test>
134 <test>
135 <param name="output_ext" value="msh"/>
136 <param name="element_type" value="hex"/>
137 <param name="length_x" value="4"/>
138 <param name="length_y" value="5"/>
139 <param name="length_z" value="6"/>
140 <param name="multiplier_x" value="0.8"/>
141 <param name="multiplier_y" value="1.1"/>
142 <param name="multiplier_z" value="2"/>
143 <param name="max_element_length_z" value="1"/>
144 <param name="element_length_y" value="0.1"/>
145 <param name="element_length_z" value="0.1"/>
146 <output name="output" value="hex_4x5x6.msh"/>
147 </test>
148 </tests>
149 <help><![CDATA[
150
151 **Overview:**
152 This tool generates structured meshes using the OpenGeoSys Mesh Generator.
153 Users can define the element type, dimensions, subdivisions, and other parameters to create a customized mesh.
154 Output data is written in the specified format (VTU/ VTK Unstructured Grid or GMSH).
155
156 **Inputs:**
157 1. **Output Format:** The format of the output file (.vtu or .msh)
158 2. **Element Type:** The type of element to create (e.g., line, triangle, quadrilateral, etc.).
159 3. **Length (X, Y, Z):** The length of the mesh domain in the X, Y, and Z directions.
160 4. **Subdivisions (X, Y, Z):** Number of subdivisions in each direction to define mesh resolution.
161 5. **Initial Element Length (X, Y, Z):** Initial size of the elements in the X, Y, and Z directions.
162 6. **Maximum Element Length (X, Y, Z):** Maximum size of elements for gradual refinement.
163 7. **Multiplier (X, Y, Z):** Refinement multiplier for element lengths in each direction.
164
165 **Outputs:**
166
167 **Output Mesh File:** The generated structured mesh saved as a file in the specified format.
168 ]]></help>
169 <expand macro="ogs_citation"/>
170 </tool>