| Previous changeset 2:136ed45d1ea9 (2023-02-03) Next changeset 4:8af5948994b0 (2024-07-18) |
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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim commit 70a4d37ecdf5d586703cfc509922311e95d3205c |
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modified:
muspinsim.xml |
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added:
muon_macros.xml |
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| diff -r 136ed45d1ea9 -r e002cee8f707 muon_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muon_macros.xml Tue Jul 18 13:25:55 2023 +0000 |
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| @@ -0,0 +1,29 @@ +<macros> + <xml name="dftb_set"> + <param type="select" name="dftb_set" value="3ob-3-1" display="radio" label="DFTB parameter set" help="The parameter set to use for DFTB+. Currently supported are: 3ob-3-1 and pbc-0-3. See help section at the bottom of the page for details."> + <option value="3ob-3-1">3ob-3-1</option> + <option value="pbc-0-3">pbc-0-3</option> + </param> + </xml> + <xml name="dftb+"> + <expand macro="dftb_set"/> + <param type="boolean" name="dftb_pbc" label="Use periodic boundary conditions" help="Whether to turn on periodic boundary conditions in DFTB+." checked="true"/> + </xml> + <xml name="dftb_optionals"> + <param type="text" argument="dftb_optionals" value="[]" optional="true" label="DFTB optional files" help="Additional optional json files to activate for DFTBArgs (for example, dftd3.json will use DFTD3 dispersion forces for 3ob-3-1 if DFTB+ has been compiled to support them)."/> + </xml> + <xml name="k_points_grid"> + <param type="text" argument="k_points_grid" value="[1,1,1]" label="K-points grid" help="List of three integer k-points. Default is [1,1,1]."> + <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> + </param> + </xml> + <!-- version of underlying tool (PEP 440) --> + <!-- citation should be updated with every underlying tool version --> + <!-- concept is not updated, and should only be used for referencing the idea of the software --> + <token name="@MUSPINSIM_VERSION@">2.2.1</token> + <token name="@MUSPINSIM_CITATION@">10.5281/zenodo.7733979</token> + <token name="@MUSPINSIM_CONCEPT@">10.5281/zenodo.6517626</token> + <token name="@PYMUONSUITE_VERSION@">0.3.0</token> + <token name="@PYMUONSUITE_CITATION@">10.5281/zenodo.8026711</token> + <token name="@PYMUONSUITE_CONCEPT@">10.5281/zenodo.7025643</token> +</macros> \ No newline at end of file |
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| diff -r 136ed45d1ea9 -r e002cee8f707 muspinsim.xml --- a/muspinsim.xml Fri Feb 03 15:39:01 2023 +0000 +++ b/muspinsim.xml Tue Jul 18 13:25:55 2023 +0000 |
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| @@ -1,24 +1,9 @@ -<tool id="muspinsim" name="MuSpinSim Simulate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> +<tool id="muspinsim" name="MuSpinSim Simulate" version="@MUSPINSIM_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> <description>perform spin dynamics calculations for muon science experiments</description> <macros> - <!-- version of underlying tool (PEP 440) --> - <token name="@TOOL_VERSION@">2.0.2</token> <!-- version of this tool wrapper (integer) --> <token name="@WRAPPER_VERSION@">0</token> - <!-- citation should be updated with every underlying tool version --> - <!-- typical fields to update are version, month, year, and doi --> - <token name="@TOOL_CITATION@"> - @software{muspinsim, - author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and Davies, Joel and Wilkinson, John and {Muon Spectroscopy Computational Project}}, - license = {MIT}, - title = {{muspinsim}}, - url = {https://github.com/muon-spectroscopy-computational-project/muspinsim}, - version = {v2.0.2}, - month = {1}, - year = {2023} - doi = {10.5281/zenodo.7568830} - } - </token> + <import>muon_macros.xml</import> </macros> <creator> <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/> @@ -27,7 +12,7 @@ <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> </creator> <requirements> - <requirement type="package" version="@TOOL_VERSION@">muspinsim</requirement> + <requirement type="package" version="@MUSPINSIM_VERSION@">muspinsim</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ## remove spaces in names @@ -154,8 +139,6 @@ Command-line usage: muspinsim muspinsim.in ]]></help> <citations> - <citation type="bibtex"> - @TOOL_CITATION@ - </citation> + <citation type="doi">@MUSPINSIM_CITATION@</citation> </citations> </tool> |