pm_nq: pm_nq.xml annotate

annotate pm_nq.xml @ 2:37a2a5686710 draft default tip

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

author	muon-spectroscopy-computational-project
date	Fri, 26 Jul 2024 12:57:47 +0000
parents	f08b8c705e74
children

rev	line source
1 f08b8c705e74 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 0 diff changeset	1 <tool id="pm_nq" name="PyMuonSuite Quantum Averaging" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05">
0 16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	2 <description>generate and average displaced structures</description>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	3 <macros>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	4 <!-- version of this tool wrapper (integer) -->
2 37a2a5686710 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 1 diff changeset	5 <token name="@WRAPPER_VERSION@">1</token>
0 16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	6 <import>muon_macros.xml</import>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	7 </macros>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	8 <creator>
1 f08b8c705e74 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 0 diff changeset	9 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
0 16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	10 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	11 </creator>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	12 <requirements>
1 f08b8c705e74 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 0 diff changeset	13 <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>
0 16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	14 <requirement type="package" version="1.0.0">euphonic</requirement>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	15 <requirement type="package" version="3.0">zip</requirement>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	16 </requirements>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	17 <command detect_errors="exit_code"><![CDATA[
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	18 structure_name=\$(sed 's/ //g' <<< '$structure.name') &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	19 #if $task.task == 'write':
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	20 out_folder=\$(sed 's/.$structure.extension/_displaced/g' <<< '$structure.name') &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	21 ln -s '$structure' \$structure_name &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	22 #if $task.phonon.phonon.phonon_source_type == "castep":
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	23 phonon_source_file_name=\$(sed 's/ //g' <<< '$task.phonon.phonon.phonon_source_castep.name') &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	24 ln -s '$task.phonon.phonon.phonon_source_castep' \$phonon_source_file_name &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	25 castep_file_name=\$(sed 's/ //g' <<< '$task.phonon.phonon.castep_file.name') &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	26 ln -s '$task.phonon.phonon.castep_file' \$castep_file_name &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	27 #else if $task.phonon.phonon.phonon_source_type == "dftb+":
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	28 phonon_source_file_name=\$(sed 's/ //g' <<< '$task.phonon.phonon.phonon_source_dftb.name') &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	29 ln -s '$task.phonon.phonon.phonon_source_dftb' \$phonon_source_file_name &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	30 gen_file_name=\$(sed 's/ //g' <<< '$task.phonon.phonon.gen_file.name') &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	31 ln -s '$task.phonon.phonon.gen_file' \$gen_file_name &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	32 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	33 #if $task.calculator.script_file:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	34 script_file_name=\$(sed 's/ //g' <<< '$task.calculator.script_file.name') &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	35 ln -s '$task.calculator.script_file' \$script_file_name &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	36 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	37 #if $task.calculator.calculator.calculator == 'castep' and $task.calculator.calculator.castep_param:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	38 castep_param_name=\$(sed 's/ //g' <<< '$task.calculator.calculator.castep_param.name') &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	39 ln -s '$task.calculator.calculator.castep_param' \$castep_param_name &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	40 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	41 ln -s '$params_yaml' params.yaml &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	42 pm-nq -t w \$structure_name params.yaml &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	43 find * > tree.txt &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	44 zip -r out_zip.zip *
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	45 #else if $task.task == 'read':
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	46 unzip '$task.zipped_input' &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	47 pm-nq -t r \$structure_name params.yaml &&
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	48 cat averages.dat
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	49 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	50 ]]></command>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	51 <configfiles>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	52 <configfile name="params_yaml">#if $task.task == 'write':
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	53 method: $task.sampling.method.method
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	54 mu_symbol: $task.mu_symbol
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	55 mu_index: $task.mu_index
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	56 grid_n: $task.sampling.grid_n
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	57 sigma_n: $task.sampling.sigma_n
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	58 #set $k_points_grid_formatted = $task.calculator.k_points_grid.replace('__ob__', '[').replace('__cb__', ']')
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	59 k_points_grid: $k_points_grid_formatted
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	60 avgprop: $task.sampling.avgprop
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	61 calculator: $task.calculator.calculator.calculator
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	62 write_allconf: $task.write_allconf
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	63 displace_T: $task.sampling.displace_T
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	64 #if $task.sampling.average_T:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	65 average_T: $task.sampling.average_T
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	66 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	67 #if $task.sampling.method.method == 'montecarlo' and $task.sampling.method.random_seed:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	68 random_seed: $task.sampling.random_seed
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	69 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	70 #if $task.calculator.calculator.calculator == 'dftb+':
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	71 dftb_set: $task.calculator.calculator.dftb_set
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	72 dftb_pbc: $task.calculator.calculator.dftb_pbc
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	73 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	74 phonon_source_type: $task.phonon.phonon.phonon_source_type
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	75 #if $task.phonon.phonon.phonon_source_type == 'castep':
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	76 #set $phonon_source_file_name = $task.phonon.phonon.phonon_source_castep.name.replace(' ', '')
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	77 #else if $task.phonon.phonon.phonon_source_type == 'dftb+':
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	78 #set $phonon_source_file_name = $task.phonon.phonon.phonon_source_dftb.name.replace(' ', '')
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	79 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	80 phonon_source_file: $phonon_source_file_name
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	81 #if $task.calculator.script_file:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	82 #set $script_file_name = $task.calculator.script_file.name.replace(' ', '')
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	83 script_file: $script_file_name
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	84 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	85 #if $task.calculator.calculator.calculator == 'castep' and $task.calculator.calculator.castep_param:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	86 #set $castep_param_name = $task.calculator.calculator.castep_param.name.replace(' ', '')
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	87 castep_param: $castep_param_name
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	88 #end if
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	89 #end if</configfile>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	90 </configfiles>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	91 <inputs>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	92 <param argument="structure" type="data" format="cell, cif, xyz, extxyz" label="Structure File" help="The muonated structure to make displacements to. The original file will be preserved. Accepted file types: CELL, CIF, XYZ (standard or extended)."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	93 <conditional name="task">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	94 <param argument="task" type="select" display="radio" label="Task" help="Task to perform with pm-nq. Either generate (write) displaced structures, or average (read) those structures.">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	95 <option value="write">Generate</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	96 <option value="read">Average</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	97 </param>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	98 <when value="write">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	99 <param argument="mu_symbol" type="text" value="H:mu" label="Muon Symbol" help="Custom label that will be used to identify muon in the structure file."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	100 <param argument="mu_index" type="integer" value="-1" label="Muon Index" help="If the Muon Symbol is not present in the cell, then the atom in the cell with this index will be treated as the muon instead. Not used if the Muon Symbol is present. Defaults to the last atom in the structure."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	101 <section name="phonon" expanded="true" title="Phonon Source">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	102 <conditional name="phonon">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	103 <param argument="phonon_source_type" type="select" display="radio" label="Phonon Type" help="The format of the phonon file.">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	104 <option value="castep">CASTEP</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	105 <option value="dftb+">DFTB+</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	106 </param>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	107 <when value="castep">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	108 <param name="phonon_source_castep" type="data" format="txt" label="Phonon File" help="Source file for phonon modes of the muonated structure."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	109 <param name="castep_file" type="data" format="castep" label="CASTEP Log (.castep)" help="The CASTEP log produced when generating the Phonon File."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	110 </when>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	111 <when value="dftb+">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	112 <param name="phonon_source_dftb" type="data" format="binary" label="Phonon File" help="Source file for phonon modes of the muonated structure."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	113 <param name="gen_file" type="data" format="txt" label="Gen File" help="GEN formatted geometry file for DFTB+."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	114 </when>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	115 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	116 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	117 <section name="calculator" expanded="true" title="Calculator Settings">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	118 <conditional name="calculator">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	119 <param argument="calculator" type="select" display="radio" label="Calculator Type" help="Which software to use to calculate the property.">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	120 <option value="castep">CASTEP</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	121 <option value="dftb+">DFTB+</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	122 </param>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	123 <when value="castep">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	124 <param argument="castep_param" type="data" format="txt" optional="true" label="Castep Parameters File" help="For convenience, this file is copied to all output directories (optional)."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	125 </when>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	126 <when value="dftb+">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	127 <expand macro="dftb+"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	128 </when>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	129 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	130 <expand macro="k_points_grid"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	131 <param argument="script_file" type="data" format="txt" optional="true" label="Script File" help="For convenience when running CASTEP or DFTB+, this script file is copied to all output directories. Occurences of {seedname} will be replaced according to the directory name for each job. (optional) "/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	132 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	133 <section name="sampling" expanded="true" title="Sampling Settings">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	134 <param argument="avgprop" type="select" display="radio" label="Averaged Property" help="Property to be calculated.">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	135 <option value="hyperfine">Hyperfine</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	136 <option value="charge">Charge</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	137 </param>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	138 <param argument="displace_T" type="float" value="0" min="0" label="Displacement Temperature" help="Temperature used to generate displacements."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	139 <param argument="average_T" type="float" optional="true" min="0" label="Averaging Temperature" help="Temperature used when averaging property (optional). If unset, will use the same value as Displacement Temperature."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	140
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	141 <conditional name="method">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	142 <param argument="method" type="select" display="radio" label="Method" help="Method used to calculate thermal average. Either displaces independently along the three most significant phonon modes (sampling a 3D grid of values) or uses Monte Carlo to randomly sample a fixed number of points from multiple modes at the same time.">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	143 <option value="independent">Independent</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	144 <option value="montecarlo">Monte Carlo</option>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	145 </param>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	146 <when value="independent"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	147 <when value="montecarlo">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	148 <param argument="random_seed" type="integer" optional="true" label="Random Seed" help="Seed to use for sampling Monte Carlo distribution."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	149 </when>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	150 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	151
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	152 <param argument="grid_n" type="integer" value="20" min="1" label="Grid Points" help="Number of points to sample along each phonon mode or thermal line."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	153 <param argument="sigma_n" type="float" value="3" min="0" label="Sigma Number" help="Number of sigmas to sample in the harmonic approximation."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	154 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	155 <param argument="write_allconf" type="boolean" label="Write All Configurations" help="Whether to write a 'collective' file containing all the displaced positions."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	156 </when>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	157 <when value="read">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	158 <param name="zipped_input" type="data" format="zip" label="Zipped Input" help="A zipped directory structure containing the output of the generate mode, and the results of running CASTEP or DFTB+ to generate the desired property."/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	159 </when>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	160 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	161 <param type="hidden" name="testing" label="Test mode" value="false"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	162 </inputs>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	163 <outputs>
2 37a2a5686710 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 1 diff changeset	164 <data label="Displaced Structures on ${on_string}" name="displaced_structures" format="zip" from_work_dir="out_zip.zip">
0 16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	165 <filter>(task['task'] == 'write')</filter>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	166 </data>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	167 <data label="File tree (testing only)" name="file_tree" format="txt" from_work_dir="tree.txt" hidden="true">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	168 <filter>(task['task'] == 'write' and testing == 'true')</filter>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	169 </data>
2 37a2a5686710 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 1 diff changeset	170 <data label="Averaged Property on ${on_string}" name="averaged_property" format="txt" from_work_dir="averages.dat">
0 16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	171 <filter>(task['task'] == 'read')</filter>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	172 </data>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	173 </outputs>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	174 <tests>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	175 <!-- Test CASTEP without default values -->
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	176 <test expect_num_outputs="2">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	177 <param name="testing" value="true"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	178 <param name="structure" value="Si.cell" ftype="cell"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	179 <conditional name="task">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	180 <param name="task" value="write"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	181 <section name="phonon">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	182 <conditional name="phonon">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	183 <param name="phonon_source_castep" value="Si.phonon" ftype="txt"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	184 <param name="castep_file" value="Si.castep"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	185 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	186 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	187 <section name="calculator">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	188 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	189 <section name="sampling">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	190 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	191 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	192 <output name="file_tree" file="tree.txt" ftype="txt" sort="true"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	193 </test>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	194 <!-- Test CASTEP with optional extra files -->
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	195 <test expect_num_outputs="2">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	196 <param name="testing" value="true"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	197 <param name="structure" value="Si.cell" ftype="cell"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	198 <conditional name="task">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	199 <param name="task" value="write"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	200 <section name="phonon">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	201 <conditional name="phonon">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	202 <param name="phonon_source_castep" value="Si.phonon" ftype="txt"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	203 <param name="castep_file" value="Si.castep"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	204 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	205 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	206 <section name="calculator">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	207 <param name="script_file" value="submit.sh" ftype="txt"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	208 <conditional name="calculator">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	209 <param name="castep_param" value="Si.param"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	210 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	211 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	212 <section name="sampling">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	213 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	214 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	215 <output name="file_tree" file="tree_extra_files.txt" ftype="txt" sort="true"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	216 </test>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	217 <!-- Test DFTB+ -->
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	218 <test expect_num_outputs="2">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	219 <param name="testing" value="true"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	220 <param name="structure" value="ethyleneMu_opt.xyz" ftype="xyz"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	221 <conditional name="task">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	222 <param name="task" value="write"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	223 <section name="phonon">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	224 <conditional name="phonon">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	225 <param name="phonon_source_type" value="dftb+"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	226 <param name="phonon_source_dftb" value="ethyleneMu_opt.phonons.pkl" ftype="auto"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	227 <param name="gen_file" value="geo_end.gen" ftype="txt"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	228 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	229 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	230 <section name="calculator">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	231 <conditional name="calculator">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	232 <param name="calculator" value="dftb+"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	233 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	234 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	235 <section name="sampling">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	236 <conditional name="method">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	237 <param name="method" value="montecarlo"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	238 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	239 </section>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	240 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	241 <output name="file_tree" file="tree_dftb.txt" ftype="txt" sort="true"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	242 </test>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	243 <!-- Test Read Task -->
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	244 <test expect_num_outputs="1">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	245 <param name="structure" value="Si.cell" ftype="cell"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	246 <conditional name="task">
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	247 <param name="task" value="read"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	248 <param name="zipped_input" value="zipped_input.zip" ftype="zip"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	249 </conditional>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	250 <output name="averaged_property" file="averages.dat" ftype="txt"/>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	251 </test>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	252 </tests>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	253 <help><![CDATA[
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	254 Given an input muonated structure (containing a muon), displaces the muon along its normal modes and performs vibrational averaging. There are three steps to using this tool:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	255 1. Generate displaced structures with `-t w` (write) flag
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	256 2. Calculate the property for all displaced structures using CASTEP or DFTB+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	257 3. Average the proprty across all displaced structures with `-t r` (read) flag
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	258
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	259 Note that currently only steps 1 and 3 are possible in Galaxy. In order to perform step 2, download the zipped output of step 1, run CASTEP/DFTB+ elsewhere, re-zip the directories including the output properties, and finally run step 3 using this zip file as the input.
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	260
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	261 Command-line usage: pm-nq [-h] [-t {r,w}] structure parameter_file
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	262
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	263 All data is licensed under the Creative Commons Attribution-ShareAlike 4.0
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	264 International License. The full text of the license can be found at:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	265
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	266 https://creativecommons.org/licenses/by-sa/4.0/legalcode
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	267
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	268 For specific data sets remember to cite the following papers, by element :
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	269
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	270 \| 3-ob-1
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	271
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	272 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	273 \| [JCTC2013] \| \ J. Chem. Theory Comput., 2013, 9, 338-354. \| (O, N, C, H) \| https://doi.org/10.1021/ct300849w \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	274 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	275 \| [JCTC2014] \| \ J. Chem. Theory Comput., 2014, 10, 1518-1537.\| (P,S-\*) \| https://doi.org/10.1021/ct401002w \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	276 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	277 \| [JCTC2015-1] \| \ J. Phys. Chem. B, 2015, 119, 1062-1082. \| (Mg,Zn-\*) \| https://doi.org/10.1021/jp506557r \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	278 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	279 \| [JCTC2015-2] \| \ J. Chem. Theory Comput., 2015, 11, 332-342. \| (Na,F,K,Ca,Cl,Br,I-\*) \| https://doi.org/10.1021/ct5009137 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	280 +--------------+------------------------------------------------+-----------------------------------+------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	281
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	282 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	283 \| pbc-0-3
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	284
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	285 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	286 \| [SiC] \| \ E. Rauls, R. Gutierrez, J. Elsner, and Th. Frauenheim, Sol. State Comm. 111, 459 (1999) \| (Si-C) \| https://doi.org/10.1016/S0038-1098(99)00137-4 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	287 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	288 \| [SiO] \| \ C. Koehler, Z. Hajnal, P. Deak, Th. Frauenheim, S. Suhai, Phys. Rev. B 64, 085333 (2001) \| (Si-O) \| https://doi.org/10.1103/PhysRevB.64.085333 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	289 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	290 \| [Silicon] \| \ A. Sieck, Th. Frauenheim, and K. A. Jackson, phys. stat. sol. (b) 240, 537 (2003). \| (Si) \| https://doi.org/10.1002/pssb.200301886 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	291 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	292 \| [Fluorine] \| \ C. Koehler and Th. Frauenheim, Surf. Sci. 600, 453 (2006). \| \ (F) \| https://doi.org/10.1016/j.susc.2005.10.044 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	293 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	294 \| [Iron] \| \ C. Koehler, G. Seifert and Th. Frauenheim, Chem. Phys. 309, 23 (2005). \| (Fe) \| https://doi.org/10.1016/j.chemphys.2004.03.034 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	295 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	296 \| [SiSi] \| \ A. Sieck, PhD. Thesis, University of Paderborn, 2000. \| (Si-Si) \| https://www.osti.gov/etdeweb/biblio/20249635 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	297 +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	298
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	299 \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	300 \| The full sets and all other data can be found at the following URLs:
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	301
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	302 +----------+------------------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	303 \| 3-ob-1 \| https://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/ \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	304 +----------+------------------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	305 \| pbc-0-3 \| https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/ \|
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	306 +----------+------------------------------------------------------------+
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	307
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	308 \|
1 f08b8c705e74 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 0 diff changeset	309
0 16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	310 .. _Generate muonated structures: /tool_runner?tool_id=pm_muairss_write
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	311 ]]></help>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	312 <citations>
1 f08b8c705e74 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 0 diff changeset	313 <citation type="doi">@PYMUONSUITE_CITATION@</citation>
0 16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	314 </citations>
16ef6bc73b17 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: diff changeset	315 </tool>

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

annotate pm_nq.xml @ 2:37a2a5686710 draft default tip