Mercurial > repos > muon-spectroscopy-computational-project > pm_muairss_read
comparison 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 |
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date | Fri, 26 Jul 2024 12:57:38 +0000 |
parents | 40071ff77285 |
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4:40071ff77285 | 5:17da9f67ed33 |
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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"> | 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"> |
2 <description>run clustering for optimised structures</description> | 2 <description>run clustering for optimised structures</description> |
3 <macros> | 3 <macros> |
4 <!-- version of this tool wrapper (integer) --> | 4 <!-- version of this tool wrapper (integer) --> |
5 <token name="@WRAPPER_VERSION@">0</token> | 5 <token name="@WRAPPER_VERSION@">1</token> |
6 <import>muon_macros.xml</import> | 6 <import>muon_macros.xml</import> |
7 <xml name="supercell"> | 7 <xml name="supercell"> |
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."> | 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."> |
9 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> | 9 <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> |
10 </param> | 10 </param> |
84 <expand macro="supercell"/> | 84 <expand macro="supercell"/> |
85 </when> | 85 </when> |
86 </conditional> | 86 </conditional> |
87 </inputs> | 87 </inputs> |
88 <outputs> | 88 <outputs> |
89 <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/> | 89 <data label="Cluster report on ${on_string}" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/> |
90 <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/> | 90 <data label="Cluster data on ${on_string}" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/> |
91 <collection name="saved_structures" type="list" label="Minimal energy structures" format="txt"> | 91 <collection name="saved_structures" type="list" label="Minimal energy structures on ${on_string}" format="txt"> |
92 <filter>clustering_save["clustering_save_format"] != "none"</filter> | 92 <filter>clustering_save["clustering_save_format"] != "none"</filter> |
93 <discover_datasets pattern="__name_and_ext__" directory="minimal_clusters"/> | 93 <discover_datasets pattern="__name_and_ext__" directory="minimal_clusters"/> |
94 </collection> | 94 </collection> |
95 </outputs> | 95 </outputs> |
96 <tests> | 96 <tests> |