Mercurial > repos > muon-spectroscopy-computational-project > pm_muairss_read
diff pm_muairss_read.xml @ 4:40071ff77285 draft default tip
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Tue, 18 Jul 2023 13:26:40 +0000 |
| parents | 276a25ab05f2 |
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--- a/pm_muairss_read.xml Fri Feb 03 15:39:29 2023 +0000 +++ b/pm_muairss_read.xml Tue Jul 18 13:26:40 2023 +0000 @@ -1,67 +1,165 @@ -<tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> +<tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> <description>run clustering for optimised structures</description> <macros> - <!-- version of underlying tool (PEP 440) --> - <token name="@TOOL_VERSION@">0.2.3</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{Sturniolo_pymuon-suite_2022, - author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}}, - license = {GPL-3.0}, - month = {8}, - title = {{pymuon-suite}}, - url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, - version = {v0.2.3}, - doi = {10.5281/zenodo.7025644}, - year = {2022} - } - </token> + <import>muon_macros.xml</import> + <xml name="supercell"> + <param type="text" argument="supercell" value="1" label="Supercell" help="Supercell size and shape to use when saving cluster structures. This can either be a single int, a list of three integers or a 3x3 matrix of integers. For a single number a diagonal matrix will be generated with the integer repeated on the diagonals. For a list of three numbers a diagonal matrix will be generated where the diagonal elements are set to the list. A matrix will be used directly as is. Default is a 3x3 identity matrix."> + <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> + </param> + </xml> </macros> <creator> <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/> <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> + <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/> <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> </creator> <requirements> - <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement> + <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement> + <requirement type="package" version="3.0">zip</requirement> </requirements> <required_files> <include type="literal" path="get_out_folder.py"/> + <include type="literal" path="config.py"/> </required_files> <command detect_errors="exit_code"><![CDATA[ unzip '$optimisation_results' && if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi - && out_folder="`python '${__tool_directory__}/get_out_folder.py'`" && - pm-muairss -t r input_structure.* params.yaml + && out_folder="`python '${__tool_directory__}/get_out_folder.py'`" + && python '${__tool_directory__}/config.py' + && pm-muairss -t r input_structure.* params.yaml + #if $clustering_save.clustering_save_format != "none": + && ln -s *_clusters/* minimal_clusters + #end if ]]></command> + <configfiles> + <configfile filename="incoming_params">clustering_method: $clustering.clustering_method +#if $clustering.clustering_method == "hier": +clustering_hier_t: $clustering.clustering_hier_t +#else if $clustering.clustering_method == "kmeans": +clustering_kmeans_k: $clustering.clustering_kmeans_k +#end if +#if $clustering_save.clustering_save_format != "none": +clustering_save_type: structures +clustering_save_format: $clustering_save.clustering_save_format +supercell: $clustering_save.supercell.replace('__ob__', '[').replace('__cb__', ']') +#if $clustering_save.clustering_save_format == "cell": +mu_symbol: $clustering_save.mu_symbol +#end if +#end if</configfile> + </configfiles> <inputs> <param type="data" name="optimisation_results" label="optimised muonated structures (.zip)" format="zip" help="A zip folder containing a set of optimised muonated structures, the original structure, and a YAML parameter file. See below for the expected folder structure."/> + <conditional name="clustering"> + <param type="select" argument="clustering_method" display="radio" label="Clustering method" value="hier"> + <option value="hier">hierarchical</option> + <option value="kmeans">k-means</option> + </param> + <when value="hier"> + <param type="float" argument="clustering_hier_t" value="0.3" min="0.0" optional="true" label="t parameter for hierarchical clustering"/> + </when> + <when value="kmeans"> + <param type="integer" argument="clustering_kmeans_k" value="4" min="0" optional="true" label="Number of clusters for k-means clustering"/> + </when> + </conditional> + <conditional name="clustering_save"> + <param argument="clustering_save_format" type="select" label="Clustering Save Format" help="If set, for each cluster a structural file with the specified format will be generated, corresponding to the structure in the cluster with minimal energy."> + <option value="none" selected="true">Do not generate</option> + <option value="cell">CELL</option> + <option value="cif">CIF</option> + <option value="xyz">XYZ</option> + </param> + <when value="none"/> + <when value="cell"> + <expand macro="supercell"/> + <param argument="mu_symbol" type="text" value="H:mu" optional="true" label="Muon symbol" help="The symbol to use for the muon when writing out the CASTEP custom species. Should be a valid chemical symbol followed by `:`, then custom text."/> + </when> + <when value="cif"> + <expand macro="supercell"/> + </when> + <when value="xyz"> + <expand macro="supercell"/> + </when> + </conditional> </inputs> <outputs> <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/> <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/> + <collection name="saved_structures" type="list" label="Minimal energy structures" format="txt"> + <filter>clustering_save["clustering_save_format"] != "none"</filter> + <discover_datasets pattern="__name_and_ext__" directory="minimal_clusters"/> + </collection> </outputs> <tests> <test expect_num_outputs="2"> <param name="optimisation_results" value="uep-out.zip" ftype="zip"/> + <conditional name="clustering"> + <param name="clustering_hier_t" value="0.2"/> + </conditional> <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/> <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/> </test> + <test expect_num_outputs="3"> + <param name="optimisation_results" value="uep-out.zip" ftype="zip"/> + <conditional name="clustering"> + <param name="clustering_hier_t" value="0.2"/> + </conditional> + <conditional name="clustering_save"> + <param name="clustering_save_format" value="cell"/> + </conditional> + <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/> + <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/> + <output_collection name="saved_structures" type="list" count="2"/> + </test> + <!-- Test optional save params --> + <test expect_num_outputs="3"> + <param name="optimisation_results" value="uep-out.zip" ftype="zip"/> + <conditional name="clustering"> + <param name="clustering_hier_t" value="0.2"/> + </conditional> + <conditional name="clustering_save"> + <param name="clustering_save_format" value="cell"/> + <param name="supercell" value="2"/> + <param name="mu_symbol" value="H:nu"/> + </conditional> + <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/> + <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/> + <output_collection name="saved_structures" type="list" count="2"> + <element name="Si_uep_min_cluster_1" file="Si_uep_min_cluster_1.cell"/> + <element name="Si_uep_min_cluster_2" file="Si_uep_min_cluster_2.cell"/> + </output_collection> + </test> <test expect_num_outputs="2"> <param name="optimisation_results" value="dftb-out.zip" ftype="zip"/> + <conditional name="clustering"> + <param name="clustering_hier_t" value="0.2"/> + </conditional> <output name="cluster_report" file="clustout-dftb.txt" ftype="txt" lines_diff="2"/> <output name="cluster_data" file="clustout-dftb.dat" ftype="txt"/> </test> + <!-- Test overwrite of values in the existing params.yaml --> + <test expect_num_outputs="2"> + <param name="optimisation_results" value="uep-out.zip" ftype="zip"/> + <conditional name="clustering"> + <param name="clustering_method" value="kmeans"/> + <param name="clustering_kmeans_k" value="2"/> + </conditional> + <!-- kmeans gives predictable clusters, but orders them randomly --> + <!-- To prevent this from affecting tests, sort the lines --> + <!-- in the report and use regex matching for the dat file --> + <output name="cluster_report" file="clustout-uep-kmeans.txt" ftype="txt" lines_diff="2" sort="true"/> + <output name="cluster_data" file="clustout-uep-kmeans.dat" ftype="txt" compare="re_match"/> + </test> </tests> <help><![CDATA[ Given a set of optimised muonated structures, clusters the structures based on similarity. + This is intended to be used with the output from '`PyMuonSuite AIRSS UEP Optimise`_'. If you used the 'Run UEP optimisation' tool for optimisation, the output from that tool can be used as the input to this one. - If you are bringing files from elsewhere, make sure they fit the expected zip folder structure: + If you are bringing files from elsewhere (such as running PyMuonSuite from the command line, or with a different optimisation calculator), make sure they fit the expected zip folder structure: .. code-block:: @@ -77,24 +175,23 @@ ├─ input.cell ├─ params.yaml - This folder represents a run with the output folder name ``muon-airss-out``, the structure name ``struct``, and the UEP calculator. - If you use different parameters, these names should match your own settings. (``dftb+`` and ``castep`` are used as folder names for the respective calculators) - + This folder represents a run with the output folder name ``muon-airss-out``, the structure name ``struct``, and the ``uep`` calculator. + If you use different parameters, these names should match your own settings (``dftb+`` and ``castep`` are used as folder names for the respective calculators). The zip folder itself has been named ``optimised-structures.zip`` in this example, but it doesn't matter what you call it. The files ``input.cell`` and ``params.yaml`` must have those exact names. ``input.cell`` should be your original structure file, - and ``params.yaml`` is the YAML parameter file used to configure the clustering (as well as any prior muonation and optimisation). - You should have created this YAML file using the 'Create YAML for pm-muairss' tool or written it yourself, then passed it into the - 'Generate muon structures' tool or pm-muairss. + and ``params.yaml`` is the YAML parameter file used to configure the muonation and optimisation. + This file is created automatically when using '`PyMuonSuite AIRSS UEP Optimise`_'. + Any parameters relating to the clustering process present in the original file will be overwritten with the values selected here. Command-line usage: pm-muairss [-h] -t r structures parameter_file + .. _PyMuonSuite AIRSS UEP Optimise: /tool_runner?tool_id=pm_uep_opt + PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license. ]]></help> <citations> - <citation type="bibtex"> - @TOOL_CITATION@ - </citation> + <citation type="doi">@PYMUONSUITE_CITATION@</citation> <citation type="doi">10.1063/1.5024450</citation> <citation type="doi">10.1063/1.5085197</citation> <citation type="doi">10.1063/5.0012381</citation>