| Next changeset 1:6f271bc31aa8 (2022-09-15) |
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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 |
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added:
pm_yaml_config.xml test-data/config-default.yaml test-data/config.yaml |
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| diff -r 000000000000 -r ed74ddbf1e80 pm_yaml_config.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pm_yaml_config.xml Thu Aug 25 16:20:33 2022 +0000 |
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| b'@@ -0,0 +1,212 @@\n+<tool id="pm_yaml_config" name="PyMuonSuite AIRSS Configure" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">\n+ <description>define AIRSS parameters</description>\n+ <macros>\n+ <!-- version of underlying tool (PEP 440) -->\n+ <!-- this wrapper doesn\'t have pymuonsuite as a dependency, but it will change according\n+ to the pymuonsuite interface, so follow the same versioning pattern -->\n+ <token name="@TOOL_VERSION@">0.2.1</token>\n+ <!-- version of this tool wrapper (integer) -->\n+ <token name="@WRAPPER_VERSION@">0</token>\n+ <!-- citation should be updated with every underlying tool version -->\n+ <!-- typical fields to update are version, month, year, and doi -->\n+ <token name="@TOOL_CITATION@">\n+ @software{pymuon-suite,\n+ author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}},\n+ license = {GPL-3.0},\n+ title = {{pymuon-suite}},\n+ url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},\n+ version = {v0.2.1},\n+ month = {2},\n+ year = {2022},\n+ doi = {}\n+ }\n+ </token>\n+ </macros>\n+ <creator>\n+ <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>\n+ <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>\n+ <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>\n+ </creator>\n+ <requirements>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ touch outputx.yaml &&\n+ ([[ ! -z "$general_params.poisson_r" ]] && printf "poisson_r: $general_params.poisson_r\\n">>outputx.yaml || ( >&2 echo "poisson_r empty" && exit 2)) &&\n+ ([[ ! -z "$general_params.struct_name" ]] && printf "name: $general_params.struct_name\\n">>outputx.yaml || ( >&2 echo "structure name is empty" && exit 2)) &&\n+ ([[ ! -z "$general_params.charged" ]] && printf "charged: $general_params.charged\\n">>outputx.yaml || ( >&2 echo "charged muon empty" && exit 2)) &&\n+ ([[ ! -z "$general_params.geom_steps" ]] && printf "geom_steps: $general_params.geom_steps\\n">>outputx.yaml || ( >&2 echo "geom_steps empty" && exit 2)) &&\n+ ([[ ! -z "$general_params.vdw_scale" ]] && printf "vdw_scale: $general_params.vdw_scale\\n">>outputx.yaml || ( >&2 echo "vdw_scale empty" && exit 2)) &&\n+ ([[ ! -z "$calculator_params.calculator_cond.calculator" ]] && printf "calculator: $calculator_params.calculator_cond.calculator\\n">>outputx.yaml || ( >&2 echo "calculator unselected" && exit 2)) &&\n+ ([[ ! -z "$general_params.geom_force_tol" ]] && printf "geom_force_tol: $general_params.geom_force_tol\\n">>outputx.yaml || ( >&2 echo "geom_force_tol empty" && exit 2)) &&\n+ ([[ ! -z "$general_params.out_folder" ]] && printf "out_folder: $general_params.out_folder\\n">>outputx.yaml || printf "out_folder: muon-airss-out\\n">>outputx.yaml) &&\n+ ([[ ! -z "$general_params.random_seed" ]] && printf "random_seed: $general_params.random_seed\\n">>outputx.yaml || ( echo "random_seed empty")) &&\n+ ([[ ! -z "$clustering_params.supercell" ]] && (printf "supercell: $clustering_params.supercell\\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>outputx.yaml || ( >&2 echo "supercell empty" && exit 2)) &&\n+ ([[ ! -z "$clustering_params.k_points_grid" ]] && (printf "k_points_grid: $clustering_params.k_points_grid\\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || ( >&2 echo "k_points_grid empty" && exit 2)) &&\n+ ([[ ! -z "$clustering_params.max_scc_steps" ]] && printf'..b' </when>\n+ </conditional>\n+ <param type="integer" argument="supercell" name="supercell" value="1" label="Supercell" multiple="true" help="Supercell size and shape to use. 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."/>\n+ <param type="text" argument="k_points_grid" name="k_points_grid" value="[1,1,1]" label="K-points grid" multiple="true" help="List of three integer k-points. Default is [1,1,1]."/>\n+ <param type="integer" argument="max_scc_steps" name="max_scc_steps" value="200" optional="true" label="Max SCC steps" help="If applicable, max number of SCC steps to perform before giving up. Default is 200 for DFTB+ and 30 for CASTEP."/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data label="Configuration for $general_params.struct_name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <section name="general_params">\n+ <param name="poisson_r" value="0.8"/>\n+ <param name="struct_name" value="Si"/>\n+ <param name="charged" value="true"/>\n+ <param name="geom_steps" value="300"/>\n+ <param name="vwd_scale" value="0.25"/>\n+ <param name="out_folder" value="Si-out"/>\n+ <param name="geom_force_tol" value="0.05"/>\n+ </section>\n+ <section name="calculator_params">\n+ <conditional name="calculator_cond">\n+ <param name="calculator" value="uep"/>\n+ <param name="uep_gw_factor" value="0.4"/>\n+ <param name="uep_chden" value="test.den_fmt"/>\n+ </conditional>\n+ </section>\n+ <section name="clustering_params">\n+ <conditional name="clustering">\n+ <param name="clustering_method" value="hier"/>\n+ <param name="clustering_hier_t" value="0.2"/>\n+ </conditional>\n+ <param name="supercell" value="1"/>\n+ <param name="k_points_grid" value="[1,1,1]"/>\n+ <param name="max_scc_steps" value="200"/>\n+ </section>\n+ <output name="out_yaml" file="config.yaml" ftype="yaml" delta="100"/>\n+ </test>\n+ <test>\n+ <section name="general_params">\n+ </section>\n+ <section name="calculator_params">\n+ </section>\n+ <section name="clustering_params">\n+ </section>\n+ <output name="out_yaml" file="config-default.yaml" ftype="yaml" delta="100"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ Creates a YAML configuration file from input parameters.\n+\n+ **DFTB+ parameter sets:**\n+\n+ +------------+-------------------------------------+-----------------------------------+\n+ | set | elements | context |\n+ +============+=====================================+===================================+\n+ | 3ob-3-1 | Br-C-Ca-Cl-F-H-I-K-Mg-N-Na-O-P-S-Zn | DFTB3 files for bio and organic |\n+ | | | molecules |\n+ +------------+-------------------------------------+-----------------------------------+\n+ | pbc-0-3 | Si - F - O - N - C - H / Fe | SCC files for solids and surfaces |\n+ +------------+-------------------------------------+-----------------------------------+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+ @TOOL_CITATION@\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r ed74ddbf1e80 test-data/config-default.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config-default.yaml Thu Aug 25 16:20:33 2022 +0000 |
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| @@ -0,0 +1,14 @@ +poisson_r: 0.8 +name: struct +charged: true +geom_steps: 30 +vdw_scale: 0.5 +calculator: uep +geom_force_tol: 0.05 +out_folder: muon-airss-out +supercell: 1 +k_points_grid: [1,1,1] +max_scc_steps: 200 +uep_gw_factor: 5.0 +clustering_method: hier +clustering_hier_t: 0.3 |
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| diff -r 000000000000 -r ed74ddbf1e80 test-data/config.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config.yaml Thu Aug 25 16:20:33 2022 +0000 |
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| @@ -0,0 +1,15 @@ +poisson_r: 0.8 +name: Si +charged: true +geom_steps: 300 +vdw_scale: 0.5 +calculator: uep +geom_force_tol: 0.05 +out_folder: Si-out +supercell: 1 +k_points_grid: [1,1,1] +max_scc_steps: 200 +uep_gw_factor: 0.4 +uep_chden: test.den_fmt +clustering_method: hier +clustering_hier_t: 0.2 |