pm_muairss_read: pm_muairss

annotate pm_muairss_read.xml @ 5:17da9f67ed33 draft default tip

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

author	muon-spectroscopy-computational-project
date	Fri, 26 Jul 2024 12:57:38 +0000
parents	40071ff77285
children

rev	line source
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	1 <tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	2 <description>run clustering for optimised structures</description>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	3 <macros>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	4 <!-- version of this tool wrapper (integer) -->
5 17da9f67ed33 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 4 diff changeset	5 <token name="@WRAPPER_VERSION@">1</token>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	6 <import>muon_macros.xml</import>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	7 <xml name="supercell">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	8 <param type="text" argument="supercell" value="1" label="Supercell" help="Supercell size and shape to use when saving cluster structures. This can either be a single int, a list of three integers or a 3x3 matrix of integers. For a single number a diagonal matrix will be generated with the integer repeated on the diagonals. For a list of three numbers a diagonal matrix will be generated where the diagonal elements are set to the list. A matrix will be used directly as is. Default is a 3x3 identity matrix.">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	9 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	10 </param>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	11 </xml>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	12 </macros>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	13 <creator>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	14 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	15 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	16 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	17 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	18 </creator>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	19 <requirements>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	20 <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	21 <requirement type="package" version="3.0">zip</requirement>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	22 </requirements>
1 c5fba3c9f660 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 1f0d5da860dd5cd0ffceac7a292773ed53617324 muon-spectroscopy-computational-project parents: 0 diff changeset	23 <required_files>
c5fba3c9f660 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 1f0d5da860dd5cd0ffceac7a292773ed53617324 muon-spectroscopy-computational-project parents: 0 diff changeset	24 <include type="literal" path="get_out_folder.py"/>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	25 <include type="literal" path="config.py"/>
1 c5fba3c9f660 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 1f0d5da860dd5cd0ffceac7a292773ed53617324 muon-spectroscopy-computational-project parents: 0 diff changeset	26 </required_files>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	27 <command detect_errors="exit_code"><![CDATA[
3 276a25ab05f2 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 2 diff changeset	28 unzip '$optimisation_results' &&
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	29 if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	30 && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	31 && out_folder="`python '${__tool_directory__}/get_out_folder.py'`"
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	32 && python '${__tool_directory__}/config.py'
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	33 && pm-muairss -t r input_structure.* params.yaml
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	34 #if $clustering_save.clustering_save_format != "none":
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	35 && ln -s _clusters/ minimal_clusters
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	36 #end if
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	37 ]]></command>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	38 <configfiles>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	39 <configfile filename="incoming_params">clustering_method: $clustering.clustering_method
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	40 #if $clustering.clustering_method == "hier":
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	41 clustering_hier_t: $clustering.clustering_hier_t
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	42 #else if $clustering.clustering_method == "kmeans":
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	43 clustering_kmeans_k: $clustering.clustering_kmeans_k
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	44 #end if
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	45 #if $clustering_save.clustering_save_format != "none":
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	46 clustering_save_type: structures
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	47 clustering_save_format: $clustering_save.clustering_save_format
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	48 supercell: $clustering_save.supercell.replace('__ob__', '[').replace('__cb__', ']')
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	49 #if $clustering_save.clustering_save_format == "cell":
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	50 mu_symbol: $clustering_save.mu_symbol
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	51 #end if
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	52 #end if</configfile>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	53 </configfiles>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	54 <inputs>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	55 <param type="data" name="optimisation_results" label="optimised muonated structures (.zip)" format="zip" help="A zip folder containing a set of optimised muonated structures, the original structure, and a YAML parameter file. See below for the expected folder structure."/>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	56 <conditional name="clustering">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	57 <param type="select" argument="clustering_method" display="radio" label="Clustering method" value="hier">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	58 <option value="hier">hierarchical</option>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	59 <option value="kmeans">k-means</option>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	60 </param>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	61 <when value="hier">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	62 <param type="float" argument="clustering_hier_t" value="0.3" min="0.0" optional="true" label="t parameter for hierarchical clustering"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	63 </when>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	64 <when value="kmeans">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	65 <param type="integer" argument="clustering_kmeans_k" value="4" min="0" optional="true" label="Number of clusters for k-means clustering"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	66 </when>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	67 </conditional>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	68 <conditional name="clustering_save">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	69 <param argument="clustering_save_format" type="select" label="Clustering Save Format" help="If set, for each cluster a structural file with the specified format will be generated, corresponding to the structure in the cluster with minimal energy.">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	70 <option value="none" selected="true">Do not generate</option>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	71 <option value="cell">CELL</option>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	72 <option value="cif">CIF</option>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	73 <option value="xyz">XYZ</option>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	74 </param>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	75 <when value="none"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	76 <when value="cell">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	77 <expand macro="supercell"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	78 <param argument="mu_symbol" type="text" value="H:mu" optional="true" label="Muon symbol" help="The symbol to use for the muon when writing out the CASTEP custom species. Should be a valid chemical symbol followed by `:`, then custom text."/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	79 </when>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	80 <when value="cif">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	81 <expand macro="supercell"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	82 </when>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	83 <when value="xyz">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	84 <expand macro="supercell"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	85 </when>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	86 </conditional>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	87 </inputs>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	88 <outputs>
5 17da9f67ed33 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 4 diff changeset	89 <data label="Cluster report on ${on_string}" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/>
17da9f67ed33 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 4 diff changeset	90 <data label="Cluster data on ${on_string}" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/>
17da9f67ed33 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 389608650050596b28bc0c055de9f98c513a6f65 muon-spectroscopy-computational-project parents: 4 diff changeset	91 <collection name="saved_structures" type="list" label="Minimal energy structures on ${on_string}" format="txt">
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	92 <filter>clustering_save["clustering_save_format"] != "none"</filter>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	93 <discover_datasets pattern="__name_and_ext__" directory="minimal_clusters"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	94 </collection>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	95 </outputs>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	96 <tests>
2 eb6382889b92 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb muon-spectroscopy-computational-project parents: 1 diff changeset	97 <test expect_num_outputs="2">
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	98 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	99 <conditional name="clustering">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	100 <param name="clustering_hier_t" value="0.2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	101 </conditional>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	102 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	103 <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	104 </test>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	105 <test expect_num_outputs="3">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	106 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	107 <conditional name="clustering">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	108 <param name="clustering_hier_t" value="0.2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	109 </conditional>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	110 <conditional name="clustering_save">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	111 <param name="clustering_save_format" value="cell"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	112 </conditional>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	113 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	114 <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	115 <output_collection name="saved_structures" type="list" count="2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	116 </test>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	117 <!-- Test optional save params -->
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	118 <test expect_num_outputs="3">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	119 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	120 <conditional name="clustering">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	121 <param name="clustering_hier_t" value="0.2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	122 </conditional>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	123 <conditional name="clustering_save">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	124 <param name="clustering_save_format" value="cell"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	125 <param name="supercell" value="2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	126 <param name="mu_symbol" value="H:nu"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	127 </conditional>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	128 <output name="cluster_report" file="clustout-uep.txt" ftype="txt" lines_diff="2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	129 <output name="cluster_data" file="clustout-uep.dat" ftype="txt"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	130 <output_collection name="saved_structures" type="list" count="2">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	131 <element name="Si_uep_min_cluster_1" file="Si_uep_min_cluster_1.cell"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	132 <element name="Si_uep_min_cluster_2" file="Si_uep_min_cluster_2.cell"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	133 </output_collection>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	134 </test>
2 eb6382889b92 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb muon-spectroscopy-computational-project parents: 1 diff changeset	135 <test expect_num_outputs="2">
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	136 <param name="optimisation_results" value="dftb-out.zip" ftype="zip"/>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	137 <conditional name="clustering">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	138 <param name="clustering_hier_t" value="0.2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	139 </conditional>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	140 <output name="cluster_report" file="clustout-dftb.txt" ftype="txt" lines_diff="2"/>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	141 <output name="cluster_data" file="clustout-dftb.dat" ftype="txt"/>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	142 </test>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	143 <!-- Test overwrite of values in the existing params.yaml -->
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	144 <test expect_num_outputs="2">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	145 <param name="optimisation_results" value="uep-out.zip" ftype="zip"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	146 <conditional name="clustering">
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	147 <param name="clustering_method" value="kmeans"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	148 <param name="clustering_kmeans_k" value="2"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	149 </conditional>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	150 <!-- kmeans gives predictable clusters, but orders them randomly -->
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	151 <!-- To prevent this from affecting tests, sort the lines -->
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	152 <!-- in the report and use regex matching for the dat file -->
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	153 <output name="cluster_report" file="clustout-uep-kmeans.txt" ftype="txt" lines_diff="2" sort="true"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	154 <output name="cluster_data" file="clustout-uep-kmeans.dat" ftype="txt" compare="re_match"/>
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	155 </test>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	156 </tests>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	157 <help><![CDATA[
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	158 Given a set of optimised muonated structures, clusters the structures based on similarity.
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	159
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	160 This is intended to be used with the output from '`PyMuonSuite AIRSS UEP Optimise`_'.
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	161 If you used the 'Run UEP optimisation' tool for optimisation, the output from that tool can be used as the input to this one.
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	162 If you are bringing files from elsewhere (such as running PyMuonSuite from the command line, or with a different optimisation calculator), make sure they fit the expected zip folder structure:
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	163
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	164 .. code-block::
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	165
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	166 optimised-structures.zip/
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	167 ├─ muon-airss-out/
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	168 │ ├─ uep/
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	169 │ │ ├─ struct_1/
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	170 │ │ │ ├─ <files for optimised struct_1 go here>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	171 │ │ ├─ struct_2/
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	172 │ │ │ ├─ <files for optimised struct_2 go here>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	173 │ │ ├─ struct_N/
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	174 │ │ │ ├─ <files for optimised struct_N go here>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	175 ├─ input.cell
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	176 ├─ params.yaml
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	177
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	178 This folder represents a run with the output folder name ``muon-airss-out``, the structure name ``struct``, and the ``uep`` calculator.
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	179 If you use different parameters, these names should match your own settings (``dftb+`` and ``castep`` are used as folder names for the respective calculators).
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	180 The zip folder itself has been named ``optimised-structures.zip`` in this example, but it doesn't matter what you call it.
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	181
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	182 The files ``input.cell`` and ``params.yaml`` must have those exact names. ``input.cell`` should be your original structure file,
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	183 and ``params.yaml`` is the YAML parameter file used to configure the muonation and optimisation.
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	184 This file is created automatically when using '`PyMuonSuite AIRSS UEP Optimise`_'.
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	185 Any parameters relating to the clustering process present in the original file will be overwritten with the values selected here.
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	186
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	187 Command-line usage: pm-muairss [-h] -t r structures parameter_file
3 276a25ab05f2 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 2 diff changeset	188
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	189 .. _PyMuonSuite AIRSS UEP Optimise: /tool_runner?tool_id=pm_uep_opt
40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	190
3 276a25ab05f2 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 2 diff changeset	191 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	192 ]]></help>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	193 <citations>
4 40071ff77285 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 70a4d37ecdf5d586703cfc509922311e95d3205c muon-spectroscopy-computational-project parents: 3 diff changeset	194 <citation type="doi">@PYMUONSUITE_CITATION@</citation>
3 276a25ab05f2 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 2 diff changeset	195 <citation type="doi">10.1063/1.5024450</citation>
276a25ab05f2 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 2 diff changeset	196 <citation type="doi">10.1063/1.5085197</citation>
276a25ab05f2 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 muon-spectroscopy-computational-project parents: 2 diff changeset	197 <citation type="doi">10.1063/5.0012381</citation>
0 49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	198 <citation type="bibtex">
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	199 @article {castep,
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	200 author = {Clark, S. J. and Segall, M. D. and Pickard, C. J. and Hasnip, P. J. and Probert, M. I. J. and Refson, K. and Payne, M. C.},
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	201 title = {First principles methods using CASTEP},
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	202 journal = {Zeitschrift fuer Kristallographie},
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	203 volume = {220},
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	204 pages = {567},
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	205 year = {2005}
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	206 }
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	207 </citation>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	208 </citations>
49b6d76139da planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 muon-spectroscopy-computational-project parents: diff changeset	209 </tool>

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

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