pm_yaml_config: pm_yaml_config.xml annotate

annotate pm_yaml_config.xml @ 2:2d9b2ffec9d5 draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507

author	muon-spectroscopy-computational-project
date	Fri, 03 Feb 2023 15:40:12 +0000
parents	6f271bc31aa8
children	03f4f2aaa91c

rev	line source
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	1 <tool id="pm_yaml_config" name="PyMuonSuite AIRSS Configure" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	2 <description>define AIRSS parameters</description>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	3 <macros>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	4 <!-- version of underlying tool (PEP 440) -->
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	5 <!-- this wrapper doesn't have pymuonsuite as a dependency, but it will change according
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	6 to the pymuonsuite interface, so follow the same versioning pattern -->
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	7 <token name="@TOOL_VERSION@">0.2.3</token>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	8 <!-- version of this tool wrapper (integer) -->
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	9 <token name="@WRAPPER_VERSION@">0</token>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	10 <!-- citation should be updated with every underlying tool version -->
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	11 <!-- typical fields to update are version, month, year, and doi -->
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	12 <token name="@TOOL_CITATION@">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	13 @software{Sturniolo_pymuon-suite_2022,
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	14 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	15 license = {GPL-3.0},
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	16 month = {8},
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	17 title = {{pymuon-suite}},
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	18 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	19 version = {v0.2.3},
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	20 doi = {10.5281/zenodo.7025644},
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	21 year = {2022}
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	22 }
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	23 </token>
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	24 <import>muon_macros.xml</import>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	25 </macros>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	26 <creator>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	27 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	28 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	29 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	30 </creator>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	31 <requirements>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	32 </requirements>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	33 <command detect_errors="exit_code"><![CDATA[
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	34 touch outputx.yaml &&
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	35 ([[ ! -z '$general_params.poisson_r' ]] && printf 'poisson_r: $general_params.poisson_r\n'>>outputx.yaml \|\| ( >&2 echo "poisson_r empty" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	36 ([[ ! -z '$general_params.name' ]] && printf 'name: $general_params.name\n'>>outputx.yaml \|\| ( >&2 echo "structure name is empty" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	37 ([[ ! -z '$general_params.charged' ]] && printf 'charged: $general_params.charged\n'>>outputx.yaml \|\| ( >&2 echo "charged muon empty" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	38 ([[ ! -z '$general_params.geom_steps' ]] && printf 'geom_steps: $general_params.geom_steps\n'>>outputx.yaml \|\| ( >&2 echo "geom_steps empty" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	39 ([[ ! -z '$general_params.vdw_scale' ]] && printf 'vdw_scale: $general_params.vdw_scale\n'>>outputx.yaml \|\| ( >&2 echo "vdw_scale empty" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	40 ([[ ! -z '$calculator_params.calculator_cond.calculator' ]] && printf 'calculator: $calculator_params.calculator_cond.calculator\n'>>outputx.yaml \|\| ( >&2 echo "calculator unselected" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	41 ([[ ! -z '$general_params.geom_force_tol' ]] && printf 'geom_force_tol: $general_params.geom_force_tol\n'>>outputx.yaml \|\| ( >&2 echo "geom_force_tol empty" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	42 ([[ ! -z '$general_params.out_folder' ]] && printf 'out_folder: $general_params.out_folder\n'>>outputx.yaml \|\| printf "out_folder: muon-airss-out\n">>outputx.yaml) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	43 ([[ ! -z '$general_params.random_seed' ]] && printf 'random_seed: $general_params.random_seed\n'>>outputx.yaml \|\| ( echo "random_seed empty")) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	44 ([[ ! -z '$clustering_params.supercell' ]] && (printf 'supercell: $clustering_params.supercell\n' \| sed "s/__ob__/[/g" \| sed "s/__cb__/]/g" )>>outputx.yaml \|\| ( >&2 echo "supercell empty" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	45 ([[ ! -z '$clustering_params.k_points_grid' ]] && (printf 'k_points_grid: $clustering_params.k_points_grid\n' \| sed "s/__ob__/[/g" \| sed "s/__cb__/]/g" ) >>outputx.yaml \|\| ( >&2 echo "k_points_grid empty" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	46 ([[ ! -z '$clustering_params.max_scc_steps' ]] && printf 'max_scc_steps: $clustering_params.max_scc_steps\n'>>outputx.yaml \|\| ( >&2 echo "max_scc_steps empty")) &&
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	47 #if str($calculator_params.calculator_cond.calculator)=="uep":
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	48 ([[ ! -z '$calculator_params.calculator_cond.uep_gw_factor' ]] && printf 'uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n'>>outputx.yaml \|\| ( >&2 echo "uep gaussian width unset" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	49 ([[ ! -z '$calculator_params.calculator_cond.uep_chden' ]] && printf 'uep_chden: $calculator_params.calculator_cond.uep_chden.value\n'>>outputx.yaml \|\| echo "den_fmt path unset") &&
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	50 #else if str($calculator_params.calculator_cond.calculator)=="CASTEP":
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	51 ([[ ! -z '$calculator_params.calculator_cond.castep_command' ]] && printf 'castep_command: $calculator_params.calculator_cond.castep_command\n'>>outputx.yaml \|\| echo "CASTEP command unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	52 ([[ ! -z '$calculator_params.calculator_cond.castep_param' ]] && printf 'castep_param: $calculator_params.calculator_cond.castep_param\n'>>outputx.yaml \|\| echo "CASTEP param unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	53 ([[ ! -z '$calculator_params.calculator_cond.mu_symbol' ]] && printf 'mu_symbol: $calculator_params.calculator_cond.mu_symbol\n'>>outputx.yaml \|\| echo "mu symbol unset") &&
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	54 #else if str($calculator_params.calculator_cond.calculator)=="dftb+":
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	55 ([[ ! -z '$calculator_params.calculator_cond.dftb_set' ]] && printf 'dftb_set: $calculator_params.calculator_cond.dftb_set\n'>>outputx.yaml \|\| ( >&2 echo "dftb parameter set unselected" && exit 2)) &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	56 ([[ ! -z '$calculator_params.calculator_cond.dftb_optionals' ]] && (printf 'dftb_optionals: $calculator_params.calculator_cond.dftb_optionals\n' \| sed "s/__ob__/[/g" \| sed "s/__cb__/]/g" ) >>outputx.yaml \|\| echo "dftb optional json files unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	57 ([[ ! -z '$calculator_params.calculator_cond.dftb_pbc' ]] && printf 'dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n'>>outputx.yaml \|\| echo "dftb periodic boundary condition unselected") &&
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	58 #else if str($calculator_params.calculator_cond.calculator)=="all":
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	59 ([[ ! -z '$calculator_params.calculator_cond.uep_gw_factor' ]] && printf 'uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor\n'>>outputx.yaml \|\| echo "uep gaussian width unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	60 ([[ ! -z '$calculator_params.calculator_cond.uep_chden' ]] && printf 'uep_chden: $calculator_params.calculator_cond.uep_chden\n'>>outputx.yaml \|\| echo "den_fmt path unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	61 ([[ ! -z '$calculator_params.calculator_cond.castep_command' ]] && printf 'castep_command: $calculator_params.calculator_cond.castep_command\n'>>outputx.yaml \|\| echo "CASTEP command unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	62 ([[ ! -z '$calculator_params.calculator_cond.castep_param' ]] && printf 'castep_param: $calculator_params.calculator_cond.castep_param\n'>>outputx.yaml \|\| echo "CASTEP param unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	63 ([[ ! -z '$calculator_params.calculator_cond.mu_symbol' ]] && printf 'mu_symbol: $calculator_params.calculator_cond.mu_symbol\n'>>outputx.yaml \|\| echo "mu symbol unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	64 ([[ ! -z '$calculator_params.calculator_cond.dftb_set' ]] && printf 'dftb_set: $calculator_params.calculator_cond.dftb_set\n'>>outputx.yaml \|\| echo "dftb parameter set unselected") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	65 ([[ ! -z '$calculator_params.calculator_cond.dftb_optionals' ]] && (printf 'dftb_optionals: $calculator_params.calculator_cond.dftb_optionals\n' \| sed "s/__ob__/[/g" \| sed "s/__cb__/]/g" ) >>outputx.yaml \|\| echo "dftb optional json files unset") &&
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	66 ([[ ! -z '$calculator_params.calculator_cond.dftb_pbc' ]] && printf 'dftb_pbc: $calculator_params.calculator_cond.dftb_pbc\n'>>outputx.yaml \|\| echo "dftb periodic boundary condition unselected") &&
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	67 #end if
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	68 ([[ ! -z '$clustering_params.clustering.clustering_method' ]] && printf 'clustering_method: $clustering_params.clustering.clustering_method\n'>>outputx.yaml \|\| ( echo "clustering method unselected" && exit 2)) &&
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	69 #if str($clustering_params.clustering.clustering_method)=="hier":
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	70 ([[ ! -z '$clustering_params.clustering.clustering_hier_t' ]] && printf 'clustering_hier_t: $clustering_params.clustering.clustering_hier_t\n'>>outputx.yaml \|\| echo "clustering_hier_t unset") &&
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	71 #else if str($clustering_params.clustering.clustering_method)=="kmeans":
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	72 ([[ ! -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") &&
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	73 #end if
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	74 ln -s outputx.yaml output.yaml
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	75 ]]></command>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	76 <inputs>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	77 <section name="general_params" expanded="true" title="General Parameters">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	78 <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."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	79 <param type="text" argument="name" value="struct" label="Name" help="Name of the structure. This name will be postfixed with a unique number, e.g. struct_001 for each generated structure."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	80 <param argument="charged" type="boolean" checked="true" label="Charged muon" help="If true, the muon will be charged. Otherwise, will be muonium (with an accompanying electron). Must be true for UEP calculations."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	81 <param type="integer" argument="geom_steps" value="30" min="0" label="Geometry optimization steps" help="Maximum number of geometry optimisation steps."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	82 <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."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	83 <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."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	84 <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."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	85 <param type="integer" argument="random_seed" label="Random Seed" optional="true" help="Random seed for pymuonsuite."/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	86 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	87 <section name="calculator_params" expanded="true" title="Calculator parameters">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	88 <conditional name="calculator_cond">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	89 <param type="select" display="radio" label="Optimization calculator" argument="calculator" value="uep" help="Calculator to generate structure files for. Must be a single word or a comma seperated list of values. Currently supported calculators are CASTEP, DFTB+ and UEP. Can also select 'all' to generate files for all calculators.">
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	90 <option value="uep">UEP</option>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	91 <option value="castep">CASTEP</option>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	92 <option value="dftb+">DFTB+</option>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	93 <option value="all">all</option>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	94 </param>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	95 <when value="uep">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	96 <param type="float" argument="uep_gw_factor" optional="true" value="5.0" min="0.0" label="Gaussian width factor" help="Gaussian width factor for UEP calculation. Higher values will make the potential of atomic nuclei closer to the point-like approximation but may introduce artifacts."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	97 <param type="text" argument="uep_chden" optional="true" label="Path to .den_fmt and .castep files" help="Name of the .den_fmt file containing the electronic density for an Unperturbed Electrostatic Potential optimisation. The corresponding .castep file must be with the same seedname. Only required for use outside Muon Galaxy"/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	98 </when>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	99 <when value="castep">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	100 <param type="text" argument="castep_command" optional="true" value="castep.serial" label="CASTEP command" help="Command to use to run CASTEP."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	101 <param type="text" argument="castep_param" optional="true" label="PARAM path" help="File path to the CASTEP parameter file."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	102 <param type="text" argument="mu_symbol" optional="true" label="Muon symbol" value="H:mu" help="The symbol to use for the muon when writing out the CASTEP custom species."/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	103 </when>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	104 <when value="dftb+">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	105 <expand macro="dftb+"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	106 <expand macro="dftb_optionals"/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	107 </when>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	108 <when value="all">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	109 <param type="float" argument="uep_gw_factor" optional="true" value="5.0" min="0.0" label="Gaussian width factor" help="Gaussian width factor for UEP calculation. Higher values will make the potential of atomic nuclei closer to the point-like approximation but may introduce artifacts."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	110 <param type="text" argument="uep_chden" optional="true" label="Path to .den_fmt and CASTEP files" help="Name of the .den_fmt file containing the electronic density for an Unperturbed Electrostatic Potential optimisation. The corresponding .castep file must be with the same seedname. Only required for use outside Muon Galaxy"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	111 <param type="text" argument="castep_command" optional="true" value="castep.serial" label="CASTEP command" help="Command to use to run CASTEP."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	112 <param type="text" argument="castep_param" optional="true" label="PARAM path" help="File path to the CASTEP parameter file."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	113 <param type="text" argument="mu_symbol" optional="true" label="Muon symbol" value="H:mu" help="The symbol to use for the muon when writing out the CASTEP custom species."/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	114 <expand macro="dftb+"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	115 <expand macro="dftb_optionals"/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	116 </when>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	117 </conditional>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	118 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	119 <section name="clustering_params" expanded="true" title="Clustering Parameters">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	120 <conditional name="clustering">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	121 <param type="select" argument="clustering_method" display="radio" label="Clustering method" value="hier">
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	122 <option value="hier">hierarchical</option>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	123 <option value="kmeans">k-means</option>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	124 </param>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	125 <when value="hier">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	126 <param type="float" argument="clustering_hier_t" value="0.3" min="0.0" optional="true" label="t parameter for hierarchical clustering"/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	127 </when>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	128 <when value="kmeans">
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	129 <param type="integer" argument="clustering_kmeans_k" value="4" min="0" optional="true" label="Number of clusters for k-means clustering"/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	130 </when>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	131 </conditional>
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	132 <param type="text" argument="supercell" value="1" label="Supercell" 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.">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	133 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	134 </param>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	135 <expand macro="k_points_grid"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	136 <param type="integer" argument="max_scc_steps" value="200" min="0" 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."/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	137 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	138 </inputs>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	139 <outputs>
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	140 <data label="Configuration for $general_params.name" name="out_yaml" format="yaml" from_work_dir="output.yaml"/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	141 </outputs>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	142 <tests>
1 6f271bc31aa8 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb muon-spectroscopy-computational-project parents: 0 diff changeset	143 <test expect_num_outputs="1">
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	144 <section name="general_params">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	145 <param name="poisson_r" value="0.8"/>
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	146 <param name="name" value="Si"/>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	147 <param name="charged" value="true"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	148 <param name="geom_steps" value="300"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	149 <param name="vwd_scale" value="0.25"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	150 <param name="out_folder" value="Si-out"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	151 <param name="geom_force_tol" value="0.05"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	152 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	153 <section name="calculator_params">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	154 <conditional name="calculator_cond">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	155 <param name="calculator" value="uep"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	156 <param name="uep_gw_factor" value="0.4"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	157 <param name="uep_chden" value="test.den_fmt"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	158 </conditional>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	159 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	160 <section name="clustering_params">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	161 <conditional name="clustering">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	162 <param name="clustering_method" value="hier"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	163 <param name="clustering_hier_t" value="0.2"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	164 </conditional>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	165 <param name="supercell" value="1"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	166 <param name="k_points_grid" value="[1,1,1]"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	167 <param name="max_scc_steps" value="200"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	168 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	169 <output name="out_yaml" file="config.yaml" ftype="yaml" delta="100"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	170 </test>
1 6f271bc31aa8 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb muon-spectroscopy-computational-project parents: 0 diff changeset	171 <test expect_num_outputs="1">
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	172 <section name="general_params">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	173 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	174 <section name="calculator_params">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	175 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	176 <section name="clustering_params">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	177 </section>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	178 <output name="out_yaml" file="config-default.yaml" ftype="yaml" delta="100"/>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	179 </test>
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	180 <test expect_num_outputs="1">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	181 <section name="general_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	182 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	183 <section name="calculator_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	184 <conditional name="calculator_cond">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	185 <param name="calculator" value="dftb+"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	186 </conditional>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	187 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	188 <section name="clustering_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	189 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	190 <output name="out_yaml" file="config-dftb.yaml" ftype="yaml" delta="100"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	191 </test>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	192 <test expect_num_outputs="1">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	193 <section name="general_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	194 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	195 <section name="calculator_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	196 <conditional name="calculator_cond">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	197 <param name="calculator" value="all"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	198 </conditional>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	199 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	200 <section name="clustering_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	201 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	202 <output name="out_yaml" file="config-all.yaml" ftype="yaml" delta="100"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	203 </test>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	204 <test expect_failure="true">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	205 <section name="general_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	206 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	207 <section name="calculator_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	208 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	209 <section name="clustering_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	210 <param name="supercell" value="bad format"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	211 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	212 </test>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	213 <test expect_failure="true">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	214 <section name="general_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	215 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	216 <section name="calculator_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	217 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	218 <section name="clustering_params">
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	219 <param name="k_points_grid" value="bad format"/>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	220 </section>
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	221 </test>
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	222 </tests>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	223 <help><![CDATA[
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	224 Creates a YAML configuration file from input parameters.
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	225
2 2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	226 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
2d9b2ffec9d5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 1 diff changeset	227
0 ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	228 DFTB+ parameter sets:
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	229
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	230 +------------+-------------------------------------+-----------------------------------+
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	231 \| set \| elements \| context \|
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	232 +============+=====================================+===================================+
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	233 \| 3ob-3-1 \| Br-C-Ca-Cl-F-H-I-K-Mg-N-Na-O-P-S-Zn \| DFTB3 files for bio and organic \|
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	234 \| \| \| molecules \|
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	235 +------------+-------------------------------------+-----------------------------------+
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	236 \| pbc-0-3 \| Si - F - O - N - C - H / Fe \| SCC files for solids and surfaces \|
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	237 +------------+-------------------------------------+-----------------------------------+
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	238 ]]></help>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	239 <citations>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	240 <citation type="bibtex">
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	241 @TOOL_CITATION@
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	242 </citation>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	243 </citations>
ed74ddbf1e80 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	244 </tool>

Mercurial > repos > muon-spectroscopy-computational-project > pm_yaml_config

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