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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
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4:40071ff77285 5:17da9f67ed33
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>