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Commit message:
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogstools commit 406e30ee3cd2ab7762f1195328c06d547516690f |
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added:
macros.xml msh2vtu.xml test-data/circle.shp test-data/geolayers_2d.msh test-data/input_file_boundary.vtu test-data/input_file_domain.vtu test-data/input_file_physical_group_Bottom.vtu test-data/input_file_physical_group_Left.vtu test-data/input_file_physical_group_Right.vtu test-data/input_file_physical_group_RockBed.vtu test-data/input_file_physical_group_SedimentLayer1.vtu test-data/input_file_physical_group_SedimentLayer2.vtu test-data/input_file_physical_group_SedimentLayer3.vtu test-data/input_file_physical_group_Top.vtu test-data/output.vtu test-data/output2.vtu |
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| diff -r 000000000000 -r be04ecda594e macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 06 16:53:19 2025 +0000 |
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| @@ -0,0 +1,24 @@ +<macros> + <token name="@TOOL_VERSION@">0.4.0</token> + <token name="@PROFILE@">23.0</token> + <token name="@VERSION_SUFFIX@">0</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ogstools</requirement> + <yield/> + </requirements> + </xml> + + <xml name="ogs_citation"> + <citations> + <citation type="doi">10.1007/s12665-012-1546-x</citation> + </citations> + </xml> + + <xml name="creator"> + <creator> + <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Informatics" url ="https://www.ufz.de/index.php?en=34216"/> + </creator> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r be04ecda594e msh2vtu.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msh2vtu.xml Thu Mar 06 16:53:19 2025 +0000 |
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| @@ -0,0 +1,97 @@ + +<tool id="msh2vtu" name="OGSTools msh2vtu" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description> + Convert msh to UnstructuredGrid (vtk) + </description> + <macros> + <import>macros.xml</import> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <expand macro="creator"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_file' input_file.msh && + msh2vtu input_file.msh + -d '$dim' + $delz $swapxy $reindex $keep_ids $ascii + -l '$log_level' + ]]></command> + <inputs> + <param name="input_file" type="data" format="gmsh.msh" label="Input GMSH File"/> + <param name="dim" type="select" label="Set dimensionality of the mesh" argument="-d"> + <option value="1">1D</option> + <option value="2">2D</option> + <option value="3">3D</option> + </param> + <param name="delz" type="boolean" value="false" truevalue="-z" falsevalue="" label="Delete Z Coordinate" optional="true" argument="-z"/> + <param name="swapxy" type="boolean" value="false" truevalue="-s" falsevalue="" label="Swap XY Coordinates" optional="true" argument="-s"/> + <param name="reindex" type="boolean" value="false" truevalue="-r" falsevalue="" label="Reindex" optional="true" argument="-r"/> + <param name="keep_ids" type="boolean" value="false" truevalue="-k" falsevalue="" label="Keep IDs" optional="true" argument="-k"/> + <param name="ascii" type="boolean" value="false" truevalue="-a" falsevalue="" label="ASCII Output" optional="true" argument="-a"/> + <param name="log_level" type="select" label="Log Level" argument="-l"> + <option value="ERROR" selected="true">ERROR</option> + <option value="DEBUG">DEBUG</option> + <option value="INFO">INFO</option> + <option value="WARNING">WARNING</option> + </param> + </inputs> + <outputs> + <data name="boundary" format="xml" label="${tool.name} on ${on_string}: boundary" from_work_dir="input_file_boundary.vtu" /> + <data name="domain" format="xml" label="${tool.name} on ${on_string}: domain" from_work_dir="input_file_domain.vtu" /> + <data name="physical_group_Bottom" format="xml" label="${tool.name} on ${on_string}: physical_group_Bottom" from_work_dir="input_file_physical_group_Bottom.vtu" /> + <data name="physical_group_Left" format="xml" label="${tool.name} on ${on_string}: physical_group_Left" from_work_dir="input_file_physical_group_Left.vtu" /> + <data name="physical_group_Right" format="xml" label="${tool.name} on ${on_string}: physical_group_Right" from_work_dir="input_file_physical_group_Right.vtu" /> + <data name="physical_group_RockBed" format="xml" label="${tool.name} on ${on_string}: physical_group_RockBed" from_work_dir="input_file_physical_group_RockBed.vtu" /> + <data name="physical_group_SedimentLayer1" format="xml" label="${tool.name} on ${on_string}: physical_group_SedimentLayer1" from_work_dir="input_file_physical_group_SedimentLayer1.vtu" /> + <data name="physical_group_SedimentLayer2" format="xml" label="${tool.name} on ${on_string}: physical_group_SedimentLayer2" from_work_dir="input_file_physical_group_SedimentLayer2.vtu" /> + <data name="physical_group_SedimentLayer3" format="xml" label="${tool.name} on ${on_string}: physical_group_SedimentLayer3" from_work_dir="input_file_physical_group_SedimentLayer3.vtu" /> + <data name="physical_group_Top" format="xml" label="${tool.name} on ${on_string}: physical_group_Top" from_work_dir="input_file_physical_group_Top.vtu" /> + </outputs> + <tests> + <test> + <param name="input_file" value="geolayers_2d.msh"/> + <param name="dim" value="2"/> + <param name="delz" value="True"/> + <param name="swapxy" value="True"/> + <param name="reindex" value="True"/> + <param name="keep_ids" value="True"/> + <param name="ascii" value="True"/> + <param name="log_level" value="DEBUG"/> + <output name="boundary" file="input_file_boundary.vtu"/> + <output name="domain" file="input_file_domain.vtu"/> + <output name="physical_group_Bottom" file="input_file_physical_group_Bottom.vtu"/> + <output name="physical_group_Left" file="input_file_physical_group_Left.vtu"/> + <output name="physical_group_Right" file="input_file_physical_group_Right.vtu"/> + <output name="physical_group_RockBed" file="input_file_physical_group_RockBed.vtu"/> + <output name="physical_group_SedimentLayer1" file="input_file_physical_group_SedimentLayer1.vtu"/> + <output name="physical_group_SedimentLayer2" file="input_file_physical_group_SedimentLayer2.vtu"/> + <output name="physical_group_SedimentLayer3" file="input_file_physical_group_SedimentLayer3.vtu"/> + <output name="physical_group_Top" file="input_file_physical_group_Top.vtu"/> + </test> + </tests> + <help><![CDATA[ + **Overview:** + + msh2vtu is a application that converts a Gmsh (.msh) file for use in OGS by extracting domain-, boundary- and physical group-submeshes and saves them in a set of files in the vtu format. + Supported element types: + - lines (linear and quadratic) in 1D + - triangles and quadrilaterals (linear and quadratic) in 2D + - tetra- and hexahedrons (linear and quadratic) in 3D + + **Inputs:** + + 1. **Input GMSH File:** The GMSH (.msh) file to be converted. + 2. **Mesh Dimension (dim):** Select the desired mesh dimension (1, 2, or 3). + 3. **Delete Z Coordinate (delz):** Boolean flag to remove the Z coordinate from the mesh (for 2D meshes with z=0). + 4. **Swap XY Coordinates (swapxy):** Boolean flag to swap the X and Y coordinates. + 5. **Reindex (reindex):** Renumber physical group / region / Material IDs to be renumbered beginning with zero. + 6. **Keep IDs (keep_ids):** By default, rename gmsh:physical to MaterialIDs and change type of corresponding cell data to INT32. If True, this is skipped. + 7. **ASCII Output (ascii):** Boolean flag to output the file in ASCII format instead of binary. + 8. **Log Level (log_level):** Set the level of logging details (DEBUG, INFO, WARNING, ERROR). + + **Outputs:** + + **Output VTU Files:** The converted mesh file as a set of files with VTU format. + ]]></help> + <expand macro="ogs_citation"/> +</tool> |
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| diff -r 000000000000 -r be04ecda594e test-data/circle.shp |
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| Binary file test-data/circle.shp has changed |
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| diff -r 000000000000 -r be04ecda594e test-data/geolayers_2d.msh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/geolayers_2d.msh Thu Mar 06 16:53:19 2025 +0000 |
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| diff -r 000000000000 -r be04ecda594e test-data/input_file_boundary.vtu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_file_boundary.vtu Thu Mar 06 16:53:19 2025 +0000 |
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| diff -r 000000000000 -r be04ecda594e test-data/input_file_physical_group_Bottom.vtu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_file_physical_group_Bottom.vtu Thu Mar 06 16:53:19 2025 +0000 |
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| @@ -0,0 +1,119 @@ +<?xml version="1.0"?> +<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian"> +<!--This file was created by meshio v5.3.5--> +<UnstructuredGrid> +<Piece NumberOfPoints="9" NumberOfCells="8"> +<Points> +<DataArray type="Float64" Name="Points" NumberOfComponents="3" format="ascii"> +0.00000000000e+00 +6.00000000000e+04 +0.00000000000e+00 +-7.50000000000e+03 +6.00000000000e+04 +0.00000000000e+00 +-9.37500000000e+02 +6.00000000000e+04 +0.00000000000e+00 +-1.87500000000e+03 +6.00000000000e+04 +0.00000000000e+00 +-2.81250000000e+03 +6.00000000000e+04 +0.00000000000e+00 +-3.74999999999e+03 +6.00000000000e+04 +0.00000000000e+00 +-4.68749999999e+03 +6.00000000000e+04 +0.00000000000e+00 +-5.62500000000e+03 +6.00000000000e+04 +0.00000000000e+00 +-6.56250000000e+03 +6.00000000000e+04 +0.00000000000e+00 + +</DataArray> +</Points> +<Cells> +<DataArray type="Int64" Name="connectivity" format="ascii"> +0 +2 +2 +3 +3 +4 +4 +5 +5 +6 +6 +7 +7 +8 +8 +1 + +</DataArray> +<DataArray type="Int64" Name="offsets" format="ascii"> +2 +4 +6 +8 +10 +12 +14 +16 + +</DataArray> +<DataArray type="Int64" Name="types" format="ascii"> +3 +3 +3 +3 +3 +3 +3 +3 + +</DataArray> +</Cells> +<PointData> +<DataArray type="Int64" Name="gmsh:dim_tags" NumberOfComponents="2" format="ascii"> +0 +2 +0 +3 +1 +2 +1 +2 +1 +2 +1 +2 +1 +2 +1 +2 +1 +2 + +</DataArray> +</PointData> +<CellData> +<DataArray type="Int64" Name="gmsh:physical" format="ascii"> +1 +1 +1 +1 +1 +1 +1 +1 + +</DataArray> +</CellData> +</Piece> +</UnstructuredGrid> +</VTKFile> |
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| @@ -0,0 +1,119 @@ +<?xml version="1.0"?> +<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian"> +<!--This file was created by meshio v5.3.5--> +<UnstructuredGrid> +<Piece NumberOfPoints="9" NumberOfCells="8"> +<Points> +<DataArray type="Float64" Name="Points" NumberOfComponents="3" format="ascii"> +0.00000000000e+00 +-6.00000000000e+04 +0.00000000000e+00 +-7.50000000000e+03 +-6.00000000000e+04 +0.00000000000e+00 +-6.56250000000e+03 +-6.00000000000e+04 +0.00000000000e+00 +-5.62500000000e+03 +-6.00000000000e+04 +0.00000000000e+00 +-4.68750000000e+03 +-6.00000000000e+04 +0.00000000000e+00 +-3.75000000001e+03 +-6.00000000000e+04 +0.00000000000e+00 +-2.81250000001e+03 +-6.00000000000e+04 +0.00000000000e+00 +-1.87500000000e+03 +-6.00000000000e+04 +0.00000000000e+00 +-9.37500000002e+02 +-6.00000000000e+04 +0.00000000000e+00 + +</DataArray> +</Points> +<Cells> +<DataArray type="Int64" Name="connectivity" format="ascii"> +1 +2 +2 +3 +3 +4 +4 +5 +5 +6 +6 +7 +7 +8 +8 +0 + +</DataArray> +<DataArray type="Int64" Name="offsets" format="ascii"> +2 +4 +6 +8 +10 +12 +14 +16 + +</DataArray> +<DataArray type="Int64" Name="types" format="ascii"> +3 +3 +3 +3 +3 +3 +3 +3 + +</DataArray> +</Cells> +<PointData> +<DataArray type="Int64" Name="gmsh:dim_tags" NumberOfComponents="2" format="ascii"> +0 +1 +0 +4 +1 +4 +1 +4 +1 +4 +1 +4 +1 +4 +1 +4 +1 +4 + +</DataArray> +</PointData> +<CellData> +<DataArray type="Int64" Name="gmsh:physical" format="ascii"> +3 +3 +3 +3 +3 +3 +3 +3 + +</DataArray> +</CellData> +</Piece> +</UnstructuredGrid> +</VTKFile> |
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| diff -r 000000000000 -r be04ecda594e test-data/input_file_physical_group_SedimentLayer1.vtu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_file_physical_group_SedimentLayer1.vtu Thu Mar 06 16:53:19 2025 +0000 |
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| diff -r 000000000000 -r be04ecda594e test-data/input_file_physical_group_SedimentLayer2.vtu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_file_physical_group_SedimentLayer2.vtu Thu Mar 06 16:53:19 2025 +0000 |
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| diff -r 000000000000 -r be04ecda594e test-data/input_file_physical_group_SedimentLayer3.vtu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_file_physical_group_SedimentLayer3.vtu Thu Mar 06 16:53:19 2025 +0000 |
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| b |
| diff -r 000000000000 -r be04ecda594e test-data/output.vtu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.vtu Thu Mar 06 16:53:19 2025 +0000 |
| b |
| b'@@ -0,0 +1,35 @@\n+<?xml version="1.0"?>\n+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">\n+ <UnstructuredGrid>\n+ <Piece NumberOfPoints="9154" NumberOfCells="17985">\n+ <PointData>\n+ </PointData>\n+ <CellData>\n+ </CellData>\n+ <Points>\n+ <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="5537669.868882086" RangeMax="5577719.22892691">\n+ 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\n+ </DataArray>\n+ <DataArray type="UInt8" Name="types" format="binary" RangeMin="5" RangeMax="5">\n+ AQAAAACAAABBRgAAKQAAAA==eJztwTENAAAAw6Cr/i1PxxKgAAAAAAAAAAAAAAAAAAAAAAC4NNBQX1U=\n+ </DataArray>\n+ </Cells>\n+ </Piece>\n+ </UnstructuredGrid>\n+</VTKFile>\n' |
| b |
| diff -r 000000000000 -r be04ecda594e test-data/output2.vtu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output2.vtu Thu Mar 06 16:53:19 2025 +0000 |
| b |
| b'@@ -0,0 +1,35 @@\n+<?xml version="1.0"?>\n+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">\n+ <UnstructuredGrid>\n+ <Piece NumberOfPoints="13550" NumberOfCells="26738">\n+ <PointData>\n+ </PointData>\n+ <CellData>\n+ </CellData>\n+ <Points>\n+ <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="5537690.567656288" RangeMax="5577698.433421741">\n+ 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</DataArray>\n+ <DataArray type="UInt8" Name="types" format="binary" RangeMin="5" RangeMax="5">\n+ AQAAAACAAAByaAAAMgAAAA==eJztwSEBAAAAwyC1/pVf4wIoAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAODfALraClk=\n+ </DataArray>\n+ </Cells>\n+ </Piece>\n+ </UnstructuredGrid>\n+</VTKFile>\n' |