Mercurial > repos > muon-spectroscopy-computational-project > pm_yaml_config
diff pm_yaml_config.xml @ 3:03f4f2aaa91c draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c
author | muon-spectroscopy-computational-project |
---|---|
date | Tue, 18 Jul 2023 13:27:20 +0000 |
parents | 2d9b2ffec9d5 |
children | 84fe9136c8c8 |
line wrap: on
line diff
--- a/pm_yaml_config.xml Fri Feb 03 15:40:12 2023 +0000 +++ b/pm_yaml_config.xml Tue Jul 18 13:27:20 2023 +0000 @@ -4,75 +4,103 @@ <!-- version of underlying tool (PEP 440) --> <!-- this wrapper doesn't have pymuonsuite as a dependency, but it will change according to the pymuonsuite interface, so follow the same versioning pattern --> - <token name="@TOOL_VERSION@">0.2.3</token> + <token name="@TOOL_VERSION@">0.3.0</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> + <token name="@TOOL_CITATION@">10.5281/zenodo.8026711</token> <import>muon_macros.xml</import> </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> </requirements> <command detect_errors="exit_code"><![CDATA[ - touch outputx.yaml && - ([[ ! -z '$general_params.poisson_r' ]] && printf 'poisson_r: $general_params.poisson_r\n'>>outputx.yaml || ( >&2 echo "poisson_r empty" && exit 2)) && - ([[ ! -z '$general_params.name' ]] && printf 'name: $general_params.name\n'>>outputx.yaml || ( >&2 echo "structure name is empty" && exit 2)) && - ([[ ! -z '$general_params.charged' ]] && printf 'charged: $general_params.charged\n'>>outputx.yaml || ( >&2 echo "charged muon empty" && exit 2)) && - ([[ ! -z '$general_params.geom_steps' ]] && printf 'geom_steps: $general_params.geom_steps\n'>>outputx.yaml || ( >&2 echo "geom_steps empty" && exit 2)) && - ([[ ! -z '$general_params.vdw_scale' ]] && printf 'vdw_scale: $general_params.vdw_scale\n'>>outputx.yaml || ( >&2 echo "vdw_scale empty" && exit 2)) && - ([[ ! -z '$calculator_params.calculator_cond.calculator' ]] && printf 'calculator: $calculator_params.calculator_cond.calculator\n'>>outputx.yaml || ( >&2 echo "calculator unselected" && exit 2)) && - ([[ ! -z '$general_params.geom_force_tol' ]] && printf 'geom_force_tol: $general_params.geom_force_tol\n'>>outputx.yaml || ( >&2 echo "geom_force_tol empty" && exit 2)) && - ([[ ! -z '$general_params.out_folder' ]] && printf 'out_folder: $general_params.out_folder\n'>>outputx.yaml || printf "out_folder: muon-airss-out\n">>outputx.yaml) && - ([[ ! -z '$general_params.random_seed' ]] && printf 'random_seed: $general_params.random_seed\n'>>outputx.yaml || ( echo "random_seed empty")) && - ([[ ! -z '$clustering_params.supercell' ]] && (printf 'supercell: $clustering_params.supercell\n' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>outputx.yaml || ( >&2 echo "supercell empty" && exit 2)) && - ([[ ! -z '$clustering_params.k_points_grid' ]] && (printf 'k_points_grid: $clustering_params.k_points_grid\n' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || ( >&2 echo "k_points_grid empty" && exit 2)) && - ([[ ! -z '$clustering_params.max_scc_steps' ]] && printf 'max_scc_steps: $clustering_params.max_scc_steps\n'>>outputx.yaml || ( >&2 echo "max_scc_steps empty")) && - #if str($calculator_params.calculator_cond.calculator)=="uep": - ([[ ! -z '$calculator_params.calculator_cond.uep_gw_factor' ]] && printf 'uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n'>>outputx.yaml || ( >&2 echo "uep gaussian width unset" && exit 2)) && - ([[ ! -z '$calculator_params.calculator_cond.uep_chden' ]] && printf 'uep_chden: $calculator_params.calculator_cond.uep_chden.value\n'>>outputx.yaml || echo "den_fmt path unset") && - #else if str($calculator_params.calculator_cond.calculator)=="CASTEP": - ([[ ! -z '$calculator_params.calculator_cond.castep_command' ]] && printf 'castep_command: $calculator_params.calculator_cond.castep_command\n'>>outputx.yaml || echo "CASTEP command unset") && - ([[ ! -z '$calculator_params.calculator_cond.castep_param' ]] && printf 'castep_param: $calculator_params.calculator_cond.castep_param\n'>>outputx.yaml || echo "CASTEP param unset") && - ([[ ! -z '$calculator_params.calculator_cond.mu_symbol' ]] && printf 'mu_symbol: $calculator_params.calculator_cond.mu_symbol\n'>>outputx.yaml || echo "mu symbol unset") && - #else if str($calculator_params.calculator_cond.calculator)=="dftb+": - ([[ ! -z '$calculator_params.calculator_cond.dftb_set' ]] && printf 'dftb_set: $calculator_params.calculator_cond.dftb_set\n'>>outputx.yaml || ( >&2 echo "dftb parameter set unselected" && exit 2)) && - ([[ ! -z '$calculator_params.calculator_cond.dftb_optionals' ]] && (printf 'dftb_optionals: $calculator_params.calculator_cond.dftb_optionals\n' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || echo "dftb optional json files unset") && - ([[ ! -z '$calculator_params.calculator_cond.dftb_pbc' ]] && printf 'dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n'>>outputx.yaml || echo "dftb periodic boundary condition unselected") && - #else if str($calculator_params.calculator_cond.calculator)=="all": - ([[ ! -z '$calculator_params.calculator_cond.uep_gw_factor' ]] && printf 'uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n'>>outputx.yaml || echo "uep gaussian width unset") && - ([[ ! -z '$calculator_params.calculator_cond.uep_chden' ]] && printf 'uep_chden: $calculator_params.calculator_cond.uep_chden\n'>>outputx.yaml || echo "den_fmt path unset") && - ([[ ! -z '$calculator_params.calculator_cond.castep_command' ]] && printf 'castep_command: $calculator_params.calculator_cond.castep_command\n'>>outputx.yaml || echo "CASTEP command unset") && - ([[ ! -z '$calculator_params.calculator_cond.castep_param' ]] && printf 'castep_param: $calculator_params.calculator_cond.castep_param\n'>>outputx.yaml || echo "CASTEP param unset") && - ([[ ! -z '$calculator_params.calculator_cond.mu_symbol' ]] && printf 'mu_symbol: $calculator_params.calculator_cond.mu_symbol\n'>>outputx.yaml || echo "mu symbol unset") && - ([[ ! -z '$calculator_params.calculator_cond.dftb_set' ]] && printf 'dftb_set: $calculator_params.calculator_cond.dftb_set\n'>>outputx.yaml || echo "dftb parameter set unselected") && - ([[ ! -z '$calculator_params.calculator_cond.dftb_optionals' ]] && (printf 'dftb_optionals: $calculator_params.calculator_cond.dftb_optionals\n' | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" ) >>outputx.yaml || echo "dftb optional json files unset") && - ([[ ! -z '$calculator_params.calculator_cond.dftb_pbc' ]] && printf 'dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n'>>outputx.yaml || echo "dftb periodic boundary condition unselected") && - #end if - ([[ ! -z '$clustering_params.clustering.clustering_method' ]] && printf 'clustering_method: $clustering_params.clustering.clustering_method\n'>>outputx.yaml || ( echo "clustering method unselected" && exit 2)) && - #if str($clustering_params.clustering.clustering_method)=="hier": - ([[ ! -z '$clustering_params.clustering.clustering_hier_t' ]] && printf 'clustering_hier_t: $clustering_params.clustering.clustering_hier_t\n'>>outputx.yaml || echo "clustering_hier_t unset") && - #else if str($clustering_params.clustering.clustering_method)=="kmeans": - ([[ ! -z '$clustering_params.clustering.clustering_kmeans_k' ]] && printf 'clustering_kmeans_k: $clustering_params.clustering.clustering_kmeans_k\n'>>outputx.yaml || echo "clustering_kmeans_k unset") && - #end if - ln -s outputx.yaml output.yaml + cat $params_yaml > $out_yaml ]]></command> + <configfiles> + <configfile name="params_yaml">poisson_r: $general_params.poisson_r +name: $general_params.name +charged: $general_params.charged +geom_steps: $general_params.geom_steps +vdw_scale: $general_params.vdw_scale +calculator: $calculator_params.calculator_cond.calculator +geom_force_tol: $general_params.geom_force_tol +#if $general_params.out_folder: +out_folder: $general_params.out_folder +#else +out_folder: muon-airss-out +#end if +#if $general_params.random_seed: +random_seed: $general_params.random_seed +#end if +supercell: $clustering_params.supercell.replace('__ob__', '[').replace('__cb__', ']') +k_points_grid: $clustering_params.k_points_grid.replace('__ob__', '[').replace('__cb__', ']') +#if $clustering_params.max_scc_steps: +max_scc_steps: $clustering_params.max_scc_steps +#end if +#if str($calculator_params.calculator_cond.calculator)=="uep": +uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor +#if $calculator_params.calculator_cond.uep_chden.value: +uep_chden: $calculator_params.calculator_cond.uep_chden.value +#end if +#else if str($calculator_params.calculator_cond.calculator)=="CASTEP": +#if $calculator_params.calculator_cond.castep_command: +castep_command: $calculator_params.calculator_cond.castep_command +#end if +#if $calculator_params.calculator_cond.castep_param: +castep_param: $calculator_params.calculator_cond.castep_param +#end if +#if $calculator_params.calculator_cond.mu_symbol: +mu_symbol: $calculator_params.calculator_cond.mu_symbol +#end if +#else if str($calculator_params.calculator_cond.calculator)=="dftb+": +#if $calculator_params.calculator_cond.dftb_set: +dftb_set: $calculator_params.calculator_cond.dftb_set +#end if +#if $calculator_params.calculator_cond.dftb_optionals: +dftb_optionals: $calculator_params.calculator_cond.dftb_optionals.replace('__ob__', '[').replace('__cb__', ']') +#end if +#if $calculator_params.calculator_cond.dftb_pbc: +dftb_pbc: $calculator_params.calculator_cond.dftb_pbc +#end if +#else if str($calculator_params.calculator_cond.calculator)=="all": +#if $calculator_params.calculator_cond.uep_gw_factor: +uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor +#end if +#if $calculator_params.calculator_cond.uep_chden: +uep_chden: $calculator_params.calculator_cond.uep_chden +#end if +#if $calculator_params.calculator_cond.castep_command: +castep_command: $calculator_params.calculator_cond.castep_command +#end if +#if $calculator_params.calculator_cond.castep_param: +castep_param: $calculator_params.calculator_cond.castep_param +#end if +#if $calculator_params.calculator_cond.mu_symbol: +mu_symbol: $calculator_params.calculator_cond.mu_symbol +#end if +#if $calculator_params.calculator_cond.dftb_set: +dftb_set: $calculator_params.calculator_cond.dftb_set +#end if +#if $calculator_params.calculator_cond.dftb_optionals: +dftb_optionals: $calculator_params.calculator_cond.dftb_optionals.replace('__ob__', '[').replace('__cb__', ']') +#end if +#if $calculator_params.calculator_cond.dftb_pbc: +dftb_pbc: $calculator_params.calculator_cond.dftb_pbc +#end if +#end if +clustering_method: $clustering_params.clustering.clustering_method +#if str($clustering_params.clustering.clustering_method)=="hier": +clustering_hier_t: $clustering_params.clustering.clustering_hier_t +#else if str($clustering_params.clustering.clustering_method)=="kmeans": +clustering_kmeans_k: $clustering_params.clustering.clustering_kmeans_k +#end if</configfile> + </configfiles> <inputs> <section name="general_params" expanded="true" title="General Parameters"> <param type="float" argument="poisson_r" value="0.8" min="0.0" label="Poisson radius" help=" Poisson sphere radius to use for random generation. No two starting muon positions will be closer than this distance. Smaller values make for bigger structure sets."/> @@ -82,7 +110,7 @@ <param type="float" argument="vdw_scale" value="0.5" min="0.0" label="Van der Waals scale" help="Van der Waals scaling factor to use when generating muon sites to avoid existing atoms. Smaller values will allow muons to get closer to the other ions."/> <param type="text" argument="out_folder" optional="true" value="muon-airss-out" label="Output folder name" help="Name to call the output folder used to store the files that the script generates."/> <param type="float" argument="geom_force_tol" value="0.05" min="0.0" label="Geometry optimization tolerance" help="Tolerance on geometry optimisation in units of eV/Å."/> - <param type="integer" argument="random_seed" label="Random Seed" optional="true" help="Random seed for pymuonsuite."/> + <param type="integer" argument="random_seed" label="Random Seed" optional="true" help="Seed used to randomise the positions of the muons in the generated structures."/> </section> <section name="calculator_params" expanded="true" title="Calculator parameters"> <conditional name="calculator_cond"> @@ -137,7 +165,7 @@ </section> </inputs> <outputs> - <data label="Configuration for $general_params.name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/> + <data label="Configuration for $general_params.name" name="out_yaml" format="yaml"/> </outputs> <tests> <test expect_num_outputs="1"> @@ -166,7 +194,7 @@ <param name="k_points_grid" value="[1,1,1]"/> <param name="max_scc_steps" value="200"/> </section> - <output name="out_yaml" file="config.yaml" ftype="yaml" delta="100"/> + <output name="out_yaml" file="config.yaml" ftype="yaml"/> </test> <test expect_num_outputs="1"> <section name="general_params"> @@ -175,7 +203,7 @@ </section> <section name="clustering_params"> </section> - <output name="out_yaml" file="config-default.yaml" ftype="yaml" delta="100"/> + <output name="out_yaml" file="config-default.yaml" ftype="yaml"/> </test> <test expect_num_outputs="1"> <section name="general_params"> @@ -187,7 +215,7 @@ </section> <section name="clustering_params"> </section> - <output name="out_yaml" file="config-dftb.yaml" ftype="yaml" delta="100"/> + <output name="out_yaml" file="config-dftb.yaml" ftype="yaml"/> </test> <test expect_num_outputs="1"> <section name="general_params"> @@ -199,7 +227,7 @@ </section> <section name="clustering_params"> </section> - <output name="out_yaml" file="config-all.yaml" ftype="yaml" delta="100"/> + <output name="out_yaml" file="config-all.yaml" ftype="yaml"/> </test> <test expect_failure="true"> <section name="general_params"> @@ -237,8 +265,6 @@ +------------+-------------------------------------+-----------------------------------+ ]]></help> <citations> - <citation type="bibtex"> - @TOOL_CITATION@ - </citation> + <citation type="doi">@TOOL_CITATION@</citation> </citations> </tool>