pm_yaml_config: pm_yaml_config.xml annotate

annotate pm_yaml_config.xml @ 4:84fe9136c8c8 draft default tip

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 389608650050596b28bc0c055de9f98c513a6f65

author	muon-spectroscopy-computational-project
date	Fri, 26 Jul 2024 12:58:09 +0000
parents	03f4f2aaa91c
children

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 -->
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	7 <token name="@TOOL_VERSION@">0.3.0</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) -->
4 84fe9136c8c8 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 3 diff changeset	9 <token name="@WRAPPER_VERSION@">1</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	10 <!-- citation should be updated with every underlying tool version -->
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	11 <token name="@TOOL_CITATION@">10.5281/zenodo.8026711</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	12 <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	13 </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	14 <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	15 <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	16 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	17 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
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	18 <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	19 </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	20 <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	21 </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	22 <command detect_errors="exit_code"><![CDATA[
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	23 cat $params_yaml > $out_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	24 ]]></command>
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	25 <configfiles>
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	26 <configfile name="params_yaml">poisson_r: $general_params.poisson_r
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	27 name: $general_params.name
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	28 charged: $general_params.charged
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	29 geom_steps: $general_params.geom_steps
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	30 vdw_scale: $general_params.vdw_scale
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	31 calculator: $calculator_params.calculator_cond.calculator
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	32 geom_force_tol: $general_params.geom_force_tol
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	33 #if $general_params.out_folder:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	34 out_folder: $general_params.out_folder
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	35 #else
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	36 out_folder: muon-airss-out
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	37 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	38 #if $general_params.random_seed:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	39 random_seed: $general_params.random_seed
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	40 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	41 supercell: $clustering_params.supercell.replace('__ob__', '[').replace('__cb__', ']')
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	42 k_points_grid: $clustering_params.k_points_grid.replace('__ob__', '[').replace('__cb__', ']')
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	43 #if $clustering_params.max_scc_steps:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	44 max_scc_steps: $clustering_params.max_scc_steps
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	45 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	46 #if str($calculator_params.calculator_cond.calculator)=="uep":
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	47 uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	48 #if $calculator_params.calculator_cond.uep_chden.value:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	49 uep_chden: $calculator_params.calculator_cond.uep_chden.value
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	50 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	51 #else if str($calculator_params.calculator_cond.calculator)=="CASTEP":
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	52 #if $calculator_params.calculator_cond.castep_command:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	53 castep_command: $calculator_params.calculator_cond.castep_command
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	54 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	55 #if $calculator_params.calculator_cond.castep_param:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	56 castep_param: $calculator_params.calculator_cond.castep_param
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	57 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	58 #if $calculator_params.calculator_cond.mu_symbol:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	59 mu_symbol: $calculator_params.calculator_cond.mu_symbol
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	60 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	61 #else if str($calculator_params.calculator_cond.calculator)=="dftb+":
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	62 #if $calculator_params.calculator_cond.dftb_set:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	63 dftb_set: $calculator_params.calculator_cond.dftb_set
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	64 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	65 #if $calculator_params.calculator_cond.dftb_optionals:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	66 dftb_optionals: $calculator_params.calculator_cond.dftb_optionals.replace('__ob__', '[').replace('__cb__', ']')
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	67 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	68 #if $calculator_params.calculator_cond.dftb_pbc:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	69 dftb_pbc: $calculator_params.calculator_cond.dftb_pbc
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	70 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	71 #else if str($calculator_params.calculator_cond.calculator)=="all":
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	72 #if $calculator_params.calculator_cond.uep_gw_factor:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	73 uep_gw_factor: $calculator_params.calculator_cond.uep_gw_factor
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	74 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	75 #if $calculator_params.calculator_cond.uep_chden:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	76 uep_chden: $calculator_params.calculator_cond.uep_chden
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	77 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	78 #if $calculator_params.calculator_cond.castep_command:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	79 castep_command: $calculator_params.calculator_cond.castep_command
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	80 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	81 #if $calculator_params.calculator_cond.castep_param:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	82 castep_param: $calculator_params.calculator_cond.castep_param
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	83 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	84 #if $calculator_params.calculator_cond.mu_symbol:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	85 mu_symbol: $calculator_params.calculator_cond.mu_symbol
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	86 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	87 #if $calculator_params.calculator_cond.dftb_set:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	88 dftb_set: $calculator_params.calculator_cond.dftb_set
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	89 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	90 #if $calculator_params.calculator_cond.dftb_optionals:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	91 dftb_optionals: $calculator_params.calculator_cond.dftb_optionals.replace('__ob__', '[').replace('__cb__', ']')
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	92 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	93 #if $calculator_params.calculator_cond.dftb_pbc:
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	94 dftb_pbc: $calculator_params.calculator_cond.dftb_pbc
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	95 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	96 #end if
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	97 clustering_method: $clustering_params.clustering.clustering_method
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	98 #if str($clustering_params.clustering.clustering_method)=="hier":
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	99 clustering_hier_t: $clustering_params.clustering.clustering_hier_t
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	100 #else if str($clustering_params.clustering.clustering_method)=="kmeans":
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	101 clustering_kmeans_k: $clustering_params.clustering.clustering_kmeans_k
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	102 #end if</configfile>
03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	103 </configfiles>
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	104 <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	105 <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	106 <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	107 <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	108 <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	109 <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	110 <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	111 <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	112 <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."/>
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	113 <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."/>
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	114 </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	115 <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	116 <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	117 <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	118 <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	119 <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	120 <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	121 <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	122 </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	123 <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	124 <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	125 <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	126 </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	127 <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	128 <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	129 <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	130 <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	131 </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	132 <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	133 <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	134 <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	135 </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	136 <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	137 <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	138 <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	139 <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	140 <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	141 <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	142 <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	143 <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	144 </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	145 </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	146 </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	147 <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	148 <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	149 <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	150 <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	151 <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	152 </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	153 <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	154 <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	155 </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	156 <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	157 <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	158 </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	159 </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	160 <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	161 <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	162 </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	163 <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	164 <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	165 </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	166 </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	167 <outputs>
4 84fe9136c8c8 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 3 diff changeset	168 <data name="out_yaml" format="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	169 </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	170 <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	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 <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	174 <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	175 <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	176 <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	177 <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	178 <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	179 <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	180 </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	181 <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	182 <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	183 <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	184 <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	185 <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	186 </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	187 </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	188 <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	189 <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	190 <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	191 <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	192 </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	193 <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	194 <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	195 <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	196 </section>
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	197 <output name="out_yaml" file="config.yaml" ftype="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	198 </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	199 <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	200 <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	201 </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	202 <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	203 </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	204 <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	205 </section>
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	206 <output name="out_yaml" file="config-default.yaml" ftype="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	207 </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	208 <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	209 <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	210 </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	211 <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	212 <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	213 <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	214 </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	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="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	217 </section>
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	218 <output name="out_yaml" file="config-dftb.yaml" ftype="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	219 </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	220 <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	221 <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	222 </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	223 <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	224 <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	225 <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	226 </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	227 </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	228 <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	229 </section>
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	230 <output name="out_yaml" file="config-all.yaml" ftype="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	231 </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	232 <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	233 <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	234 </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	235 <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	236 </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	237 <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	238 <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	239 </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	240 </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	241 <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	242 <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	243 </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	244 <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	245 </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	246 <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	247 <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	248 </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	249 </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	250 </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	251 <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	252 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	253
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	254 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	255
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	256 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	257
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	258 +------------+-------------------------------------+-----------------------------------+
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	259 \| 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	260 +============+=====================================+===================================+
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	261 \| 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	262 \| \| \| 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	263 +------------+-------------------------------------+-----------------------------------+
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	264 \| 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	265 +------------+-------------------------------------+-----------------------------------+
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	266 ]]></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	267 <citations>
3 03f4f2aaa91c planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_yaml_config commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 2 diff changeset	268 <citation type="doi">@TOOL_CITATION@</citation>
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	269 </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	270 </tool>

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

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