Mercurial > repos > muon-spectroscopy-computational-project > muspinsim_plot
changeset 4:e15e8800c39e draft default tip
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit 70a4d37ecdf5d586703cfc509922311e95d3205c
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Tue, 18 Jul 2023 13:26:26 +0000 |
| parents | d7a0a31760b1 |
| children | |
| files | muon_macros.xml muspinsim_plot.xml |
| diffstat | 2 files changed, 37 insertions(+), 34 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muon_macros.xml Tue Jul 18 13:26:26 2023 +0000 @@ -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
--- a/muspinsim_plot.xml Fri Feb 03 15:39:12 2023 +0000 +++ b/muspinsim_plot.xml Tue Jul 18 13:26:26 2023 +0000 @@ -4,29 +4,16 @@ <!-- version of underlying tool (PEP 440) --> <token name="@TOOL_VERSION@">3.5.1</token> <!-- version of this tool wrapper (integer) --> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">2</token> <!-- citation should be updated with every underlying tool version --> <!-- typical fields to update are version, month, year, and doi --> - <token name="@TOOL_CITATION@"> - @article{Hunter:2007, - author = {Hunter, J. D.}, - title = {Matplotlib: A 2D graphics environment}, - journal = {Computing in Science & Engineering}, - volume = {9}, - number = {3}, - pages = {90--95}, - abstract = {Matplotlib is a 2D graphics package used for Python for - application development, interactive scripting, and publication-quality - image generation across user interfaces and operating systems.}, - publisher = {IEEE COMPUTER SOC}, - doi = {10.1109/MCSE.2007.55}, - year = {2007} - } - </token> + <token name="@TOOL_CITATION@">10.1109/MCSE.2007.55</token> + <import>muon_macros.xml</import> </macros> <creator> <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/> <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> + <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/> <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> </creator> <requirements> @@ -82,10 +69,10 @@ </repeat> </inputs> <outputs> - <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf"> + <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf" label="PDF plot on ${on_string}"> <filter>(out_file_type == 'pdf')</filter> </data> - <data format="png" name="out_file_png" from_work_dir="outfile.png"> + <data format="png" name="out_file_png" from_work_dir="outfile.png" label="PNG plot on ${on_string}"> <filter>(out_file_type == 'png')</filter> </data> </outputs> @@ -147,20 +134,7 @@ You can overlay multiple plots on top of each other by providing more than one data file. ]]></help> <citations> - <citation type="bibtex"> - @TOOL_CITATION@ - </citation> - <citation type="bibtex"> - @software{muspinsim, - author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}}, - license = {MIT}, - title = {{muspinsim}}, - url = {https://github.com/muon-spectroscopy-computational-project/muspinsim}, - version = {v1.1.0}, - month = {5}, - year = {2022}, - doi = {10.5281/zenodo.6563074} - } - </citation> + <citation type="doi">@TOOL_CITATION@</citation> + <citation type="doi">@MUSPINSIM_CONCEPT@</citation> </citations> </tool>