larch_athena: larch_athena.xml annotate

annotate larch_athena.xml @ 4:a0d3b0fe0fa3 draft

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8

author	muon-spectroscopy-computational-project
date	Thu, 11 Apr 2024 09:01:59 +0000
parents	82e9dd980916
children	27015eaf9a78

rev	line source
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	1 <tool id="larch_athena" name="Larch Athena" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	2 <description>generate Athena projects from XAFS data</description>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	3 <macros>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	4 <!-- version of underlying tool (PEP 440) -->
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	5 <token name="@TOOL_VERSION@">0.9.75</token>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	6 <!-- version of this tool wrapper (integer) -->
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	7 <token name="@WRAPPER_VERSION@">0</token>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	8 <!-- citation should be updated with every underlying tool version -->
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	9 <!-- typical fields to update are version, month, year, and doi -->
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	11 <xml name="format">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	12 <param name="format" type="select" display="radio" label="Input format" help="Whether data is in tabular or NeXus (h5) format, or has already saved as an Athena project">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	13 <option value="plaintext" selected="true">NeXus/tabular</option>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	14 <option value="athena">Athena project</option>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	15 </param>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	16 </xml>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	17 <xml name="extract_group">
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	18 <conditional name="extract_group">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	19 <param name="extract_group" type="select" label="Group extraction" help="Method of handling group extraction. Extracting all or multiple named groups will result in multiple outputs, unless merging groups is also true.">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	20 <option value="single" selected="true">Extract single</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	21 <option value="multiple">Extract multiple</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	22 <option value="all">Extract all</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	23 </param>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	24 <when value="single">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	25 <param name="group_name" type="text" optional="true" label="Group label" help="Which group to extract and process from the Athena project (will use first group in file if unset)"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	26 </when>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	27 <when value="multiple">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	28 <repeat name="multiple" min="1" default="1" title="Groups">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	29 <param name="group_name" type="text" label="Group label" help="Which group to extract and process from the Athena project (will use first group in file if unset)"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	30 </repeat>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	31 </when>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	32 <when value="all"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	33 </conditional>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	34 </xml>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	35 <xml name="columns">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	36 <conditional name="energy_column">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	37 <param name="energy_column" type="select" label="Energy column" help="If set, this column will be used as 'energy'. Otherwise, will identify the first column ending with 'energy' or labelled 'col1' 'Ef'.">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	38 <option value="auto" selected="true">Automatic</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	39 <option value="qexafs_energy" selected="true">qexafs_energy</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	40 <option value="Ef" selected="true">Ef</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	41 <option value="other" selected="true">Other</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	42 </param>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	43 <when value="auto"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	44 <when value="qexafs_energy"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	45 <when value="Ef"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	46 <when value="other">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	47 <param name="energy_column_text" type="text" label="Energy column" help="The column to be used as 'energy'."/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	48 </when>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	49 </conditional>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	50 <conditional name="mu_column">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	51 <param name="mu_column" type="select" label="μ column" help="If set, this column will be used as 'mu'. Otherwise, will identify the first column labelled as either 'col2', 'xmu', 'lni0it', 'FFI0' or 'FF/I1'.">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	52 <option value="auto" selected="true">Automatic</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	53 <option value="lnI0It" selected="true">lnI0It</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	54 <option value="FFI0" selected="true">FFI0</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	55 <option value="FF/I1" selected="true">FF/I1</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	56 <option value="other" selected="true">Other</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	57 </param>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	58 <when value="auto"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	59 <when value="lnI0It"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	60 <when value="FFI0"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	61 <when value="FF/I1"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	62 <when value="other">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	63 <param name="mu_column_text" type="text" optional="true" label="μ column" help="The column to be used as 'mu'."/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	64 </when>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	65 </conditional>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	66 </xml>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	67 <xml name="is_zipped">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	68 <param name="is_zipped" type="select" display="radio" label="Inputs Zipped" help="Whether input files are zipped together into one directory, or not.">
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	69 <option value="" selected="true">No</option>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	70 <option value="true">Yes</option>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	71 </param>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	72 </xml>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	73 <import>macros.xml</import>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	74 </macros>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	75 <creator>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	76 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	77 </creator>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	78 <requirements>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	79 <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	80 <requirement type="package" version="3.5.2">matplotlib</requirement>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	81 <requirement type="package" version="3.0">zip</requirement>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	82 <requirement type="package" version="6.0">unzip</requirement>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	83 </requirements>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	84 <required_files>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	85 <include type="literal" path="larch_athena.py"/>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	86 <include type="literal" path="common.py"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	87 </required_files>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	88 <command detect_errors="exit_code"><![CDATA[
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	89 mkdir prj plot
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	90 #if $merge_inputs.format.format=="plaintext":
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	91 #if $merge_inputs.format.is_zipped.is_zipped=="true":
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	92 && echo Unzipping '$merge_inputs.format.is_zipped.dat_file.name'
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	93 && unzip '$merge_inputs.format.is_zipped.dat_file' -d dat_files
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	94 && python '${__tool_directory__}/larch_athena.py' dat_files '$inputs'
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	95 #else
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	96 && python '${__tool_directory__}/larch_athena.py' '$merge_inputs.format.is_zipped.dat_file' '$inputs'
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	97 #end if
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	98 #else
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	99 && python '${__tool_directory__}/larch_athena.py' '$merge_inputs.format.dat_file' '$inputs'
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	100 #end if
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	101 #if $zip_outputs:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	102 && zip out_zip.zip prj/* edge/* flat/* derivative/*
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	103 #end if
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	104 ]]></command>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	105 <configfiles>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	106 <inputs name="inputs"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	107 </configfiles>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	108 <inputs>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	109 <conditional name="merge_inputs" >
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	110 <param name="merge_inputs" type="select" display="radio" label="Merge multiple inputs" help="Whether to merge all input data into one Athena project, by default each dataset or file in a zip will result in a separate output.">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	111 <option value="" selected="true">No</option>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	112 <option value="true">Yes</option>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	113 </param>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	114 <when value="">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	115 <conditional name="format" >
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	116 <expand macro="format"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	117 <when value="plaintext">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	118 <conditional name="is_zipped" >
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	119 <expand macro="is_zipped"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	120 <when value="">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	121 <param name="dat_file" type="data" format="h5,tabular" label="XAFS data file" help="X-ray Absorption Fine Structure (XAFS) data, either in NeXus (h5) or tabular format."/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	122 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	123 <when value="true">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	124 <param name="dat_file" type="data" format="zip" label="Zipped XAFS data files" help="Zipped X-ray Absorption Fine Structure (XAFS) data, either in NeXus (h5) or tabular format."/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	125 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	126 </conditional>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	127 <expand macro="columns"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	128 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	129 <when value="athena">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	130 <param name="dat_file" type="data" format="prj" label="Athena project" help="X-ray Absorption Spectroscopy (XAS) data, in Athena project format"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	131 <expand macro="extract_group"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	132 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	133 </conditional>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	134 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	135 <when value="true">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	136 <conditional name="format" >
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	137 <expand macro="format"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	138 <when value="plaintext">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	139 <conditional name="is_zipped" >
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	140 <expand macro="is_zipped"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	141 <when value="">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	142 <param name="dat_file" type="data" format="h5,txt" multiple="true" label="XAFS data file" help="X-ray Absorption Fine Structure (XAFS) data, either in NeXus (h5) or tabular format, which will be merged. Accepts individual files or a zip."/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	143 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	144 <when value="true">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	145 <param name="dat_file" type="data" format="zip" label="Zipped XAFS data files" help="Zipped X-ray Absorption Fine Structure (XAFS) data, either in NeXus (h5) or tabular format. All files in the zip will be merged."/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	146 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	147 </conditional>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	148 <expand macro="columns"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	149 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	150 <when value="athena">
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	151 <param name="dat_file" type="data" format="prj" multiple="true" label="Athena project" help="X-ray Absorption Spectroscopy (XAS) data, which will be merged, in Athena project format. Note that when merging Athena groups, background parameters set in file will be lost, and automatic default used unless defined below."/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	152 <expand macro="extract_group"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	153 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	154 </conditional>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	155 </when>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	156 </conditional>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	157 <param name="annotation" type="text" label="Annotation" optional="true" help="If set, will annotate the output project(s) with this string. This will be used to generate legends when plotting data."/>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	158 <section name="processing" expanded="true" title="Processing Options" help="By default, the following processing steps will be performed either with default values, or those contained in the input Athena project (if used). If specified here, these values will be used instead for process in sequence.">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	159 <conditional name="calibrate">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	160 <param name="calibrate" type="select" display="radio" label="Calibrate energy" help="If set, will shift the spectrum so that its (automatically determined) edge occurs at the specified value, and any values outside the range will be discarded.">
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	161 <option value="" selected="true">False</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	162 <option value="true">True</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	163 </param>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	164 <when value=""/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	165 <when value="true">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	166 <param name="calibration_e0" type="float" label="Calibration energy (eV)" optional="true" help="If set, data will be calibrated so that the edge occurs at this energy (after merging, if relevant). Note that this is different from specifying E0 in the pre-edge normalization, as this will the x-axis of the data (so that the Nth x point will no longer align with the Nth y point)."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	167 <param name="energy_min" type="float" label="Minimum energy (eV)" optional="true" help="If set, data will be cropped below this value in electron volts (after re-calibrating)."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	168 <param name="energy_max" type="float" label="Maximum energy (eV)" optional="true" help="If set, data will be cropped above this value in electron volts (after re-calibrating)."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	169 </when>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	170 </conditional>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	171 <param name="rebin" type="boolean" label="Re-bin data" help="Whether to re-bin along the energy axis to automatically ensure appropriate levels of precision in the pre-edge, near-edge and extended region of the spectrum."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	172 <conditional name="pre_edge">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	173 <param name="pre_edge" type="select" display="radio" label="Pre-edge normalization" help="If set, will (re)perform forward pre-edge normalization using provided values.">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	174 <option value="" selected="true">Use default values</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	175 <option value="ref">Use reference channel</option>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	176 <option value="manual">Use manual values</option>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	177 </param>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	178 <when value=""/>
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	179 <when value="ref">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	180 <param name="ref_channel" type="text" label="Reference channel" help="The channel to be used as a refernce to determine the pre-edge settings which are then used for the main signal. This can help when the main signal is affected by signal noise."/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	181 </when>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	182 <when value="manual">
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	183 <param argument="e0" type="float" label="Edge energy (eV)" optional="true" help="If set, normalization will use this as the location of the edge rather than automatically determining it."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	184 <param argument="pre1" type="float" max="0" label="Pre-edge fit lower energy (eV)" optional="true" help="The lower end of the region used for the pre-edge fitting, relative to the edge energy (and therefore negative)."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	185 <param argument="pre2" type="float" max="0" label="Pre-edge fit upper energy (eV)" optional="true" help="The upper end of the region used for the pre-edge fitting, relative to the edge energy (and therefore negative)."/>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	186 <param argument="norm1" type="float" min="0" label="Post-edge fit lower energy (eV)" optional="true" help="The lower end of the region used for the post-edge fitting, relative to the edge energy (and therefore positive)."/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	187 <param argument="norm2" type="float" min="0" label="Post-edge fit upper energy (eV)" optional="true" help="The upper end of the region used for the post-edge fitting, relative to the edge energy (and therefore positive)."/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	188 <param argument="nnorm" type="integer" min="0" max="5" label="Post-edge fit polynomial degree" optional="true" help="The degree of the polynomial used to fit in the post-edge region."/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	189 <param argument="step" type="float" min="0" label="Edge step" optional="true" help="Magnitude of the step in μ between the pre and post-edge regions at the edge energy."/>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	190 <param argument="nvict" type="integer" label="Energy exponent" optional="true" help="Edge fitting will be performed against μE*n where n is defined here. This is 0 by default."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	191 </when>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	192 </conditional>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	193 <conditional name="xftf">
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	194 <param name="xftf" type="select" display="radio" label="XFTF" help="If set, will (re)perform forward Fourier Transform using provided values.">
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	195 <option value="" selected="true">False</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	196 <option value="true">True</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	197 </param>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	198 <when value=""/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	199 <when value="true">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	200 <param argument="kmin" type="float" optional="true" min="0.0" help="Minimum k value."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	201 <param argument="kmax" type="float" optional="true" min="0.0" help="Maximum k value."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	202 <param argument="kweight" type="float" optional="true" help="Exponent for weighting spectra by raising k to this power."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	203 <param argument="dk" type="float" optional="true" help="Tapering parameter for Fourier Transform window."/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	204 <param argument="window" type="select" optional="true" help="Fourier Transform window type.">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	205 <option value="hanning">Hanning (cosine-squared taper)</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	206 <option value="parzen">Parzen (linear taper)</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	207 <option value="welch">Welch (quadratic taper)</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	208 <option value="gaussian">Gaussian function window</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	209 <option value="sine">Sine function window</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	210 <option value="kaiser">Kaiser-Bessel function-derived window</option>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	211 </param>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	212 </when>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	213 </conditional>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	214 </section>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	215 <param name="plot_graph" type="select" multiple="true" display="checkboxes" label="Plot graphs">
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	216 <option value="edge">Pre/post edge fitting</option>
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	217 <option value="flat">Flattened xμ</option>
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	218 <option value="dmude">Derivative of xμ</option>
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	219 </param>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	220 <param name="zip_outputs" type="boolean" label="Zip outputs" help="Whether to zip all outputs into one dataset."/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	221 </inputs>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	222 <outputs>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	223 <!-- Single output if zipping outputs -->
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	224 <data name="out_zip" format="zip" from_work_dir="out_zip.zip" label="Zipped Athena project(s) ${annotation} ${on_string}">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	225 <filter>zip_outputs</filter>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	226 </data>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	227 <!-- Single outputs of different types if merging, or not using a zip -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	228 <data name="athena_project_file" format="prj" from_work_dir="prj/out.prj" label="Athena project ${annotation} ${on_string}">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	229 <filter>not zip_outputs</filter>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	230 <filter>not (merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")))</filter>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	231 </data>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	232 <data name="plot" format="png" from_work_dir="plot/out.png" label="Plot of ${annotation} ${on_string}">
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	233 <filter>plot_graph</filter>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	234 <filter>not zip_outputs</filter>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	235 <filter>not (merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")))</filter>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	236 </data>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	237 <!-- Directories of outputs if using single, non-merged zip as input or extracting multiple/all Athena groups -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	238 <collection name="athena_project_file_collection" format="prj" type="list" label="Athena projects ${annotation} ${on_string}">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	239 <discover_datasets pattern="__name_and_ext__" directory="prj"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	240 <filter>not zip_outputs</filter>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	241 <filter>merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	242 </collection>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	243 <collection name="plot_collection" format="png" type="list" label="Plots of ${annotation} ${on_string}">
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	244 <discover_datasets pattern="__name_and_ext__" directory="plot"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	245 <filter>plot_graph</filter>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	246 <filter>not zip_outputs</filter>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	247 <filter>merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	248 </collection>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	249 </outputs>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	250 <tests>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	251 <!-- 1 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	252 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	253 <param name="dat_file" value="test.xmu"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	254 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	255 <assert_contents>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	256 <has_size value="5400" delta="100"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	257 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	258 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	259 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	260 <!-- 2 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	261 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	262 <param name="dat_file" value="ffi0.tabular"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	263 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	264 <assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	265 <has_size value="34400" delta="100"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	266 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	267 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	268 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	269 <!-- 3 -->
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	270 <test expect_num_outputs="1">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	271 <param name="dat_file" value="ffi1.tabular"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	272 <output name="athena_project_file">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	273 <assert_contents>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	274 <has_size value="4400" delta="100"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	275 </assert_contents>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	276 </output>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	277 </test>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	278 <!-- 4 -->
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	279 <test expect_num_outputs="2">
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	280 <param name="dat_file" value="test.xmu"/>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	281 <param name="plot_graph" value="edge,flat,dmude"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	282 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	283 <assert_contents>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	284 <has_size value="5400" delta="100"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	285 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	286 </output>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	287 <output name="plot">
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	288 <assert_contents>
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	289 <has_size value="138100" delta="100"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	290 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	291 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	292 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	293 <!-- 5 -->
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	294 <test expect_num_outputs="2">
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	295 <param name="is_zipped" value="true"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	296 <param name="dat_file" value="test.zip"/>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	297 <param name="plot_graph" value="edge,flat,dmude"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	298 <output_collection name="athena_project_file_collection" type="list" count="2"/>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	299 <output_collection name="plot_collection" type="list" count="2"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	300 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	301 <!-- 6 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	302 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	303 <param name="is_zipped" value="true"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	304 <param name="dat_file" value="h5.zip"/>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	305 <param name="plot_graph" value="edge,flat,dmude"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	306 <param name="zip_outputs" value="true"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	307 <output name="out_zip">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	308 <assert_contents>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	309 <has_size value="75500" delta="500"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	310 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	311 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	312 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	313 <!-- 7 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	314 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	315 <param name="dat_file" value="test.xmu"/>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	316 <param name="calibrate" value="true"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	317 <param name="energy_min" value="7000"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	318 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	319 <assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	320 <has_size value="5300" delta="100"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	321 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	322 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	323 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	324 <!-- 8 -->
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	325 <test expect_num_outputs="2">
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	326 <param name="dat_file" value="test.xmu"/>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	327 <param name="calibrate" value="true"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	328 <param name="energy_min" value="7000"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	329 <param name="energy_max" value="7200"/>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	330 <param name="plot_graph" value="edge,flat,dmude"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	331 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	332 <assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	333 <has_size value="3300" delta="50"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	334 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	335 </output>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	336 <output name="plot">
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	337 <assert_contents>
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	338 <has_size value="137700" delta="100"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	339 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	340 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	341 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	342 <!-- 9 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	343 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	344 <param name="dat_file" value="test.xmu"/>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	345 <param name="calibrate" value="true"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	346 <param name="calibration_e0" value="7050"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	347 <param name="energy_min" value="7000"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	348 <param name="energy_max" value="7200"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	349 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	350 <assert_contents>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	351 <has_size value="3600" delta="100"/>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	352 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	353 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	354 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	355 <!-- 10 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	356 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	357 <param name="dat_file" value="test.xmu"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	358 <param name="rebin" value="true"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	359 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	360 <assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	361 <has_size value="8413" delta="10"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	362 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	363 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	364 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	365 <!-- 11 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	366 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	367 <param name="merge_inputs" value="true"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	368 <param name="dat_file" value="262875_PtSn_OCO_Abu_1.nxs,262876_PtSn_OCO_Abu_2.nxs"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	369 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	370 <assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	371 <has_size value="37550" delta="50"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	372 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	373 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	374 </test>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	375 <!-- 12 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	376 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	377 <param name="merge_inputs" value="true"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	378 <param name="is_zipped" value="true"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	379 <param name="dat_file" value="test.zip"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	380 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	381 <assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	382 <has_size value="18000" delta="50"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	383 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	384 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	385 </test>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	386 <!-- 13: Test merging and plotting multiple prj inputs -->
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	387 <test expect_num_outputs="2">
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	388 <param name="merge_inputs" value="true"/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	389 <param name="format" value="athena"/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	390 <param name="dat_file" value="test.prj,test.prj"/>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	391 <param name="plot_graph" value="edge,flat,dmude"/>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	392 <output name="athena_project_file">
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	393 <assert_contents>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	394 <has_size value="4500" delta="100"/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	395 </assert_contents>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	396 </output>
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	397 <output name="plot">
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	398 <assert_contents>
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	399 <has_size value="145700" delta="100"/>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	400 </assert_contents>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	401 </output>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	402 </test>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	403 <!-- 14 -->
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	404 <test expect_num_outputs="1">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	405 <param name="format" value="athena"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	406 <param name="dat_file" value="test.prj"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	407 <output name="athena_project_file">
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	408 <assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	409 <has_size value="5400" delta="200"/>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	410 </assert_contents>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	411 </output>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	412 </test>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	413 <!-- 15: Extract multiple groups from Athena .prj -->
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	414 <test expect_num_outputs="1">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	415 <param name="format" value="athena"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	416 <param name="extract_group" value="multiple"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	417 <param name="group_name" value="merge"/>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	418 <param name="group_name" value="d_Ref_PtSn_OC_MERGE_CALIBRATE"/>
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	419 <param name="dat_file" value="multiple.prj"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	420 <output_collection name="athena_project_file_collection" type="list" count="2"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	421 </test>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	422 <!-- 16: Extract all groups from Athena .prj -->
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	423 <test expect_num_outputs="1">
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	424 <param name="format" value="athena"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	425 <param name="extract_group" value="all"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	426 <param name="dat_file" value="multiple.prj"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	427 <output_collection name="athena_project_file_collection" type="list" count="9"/>
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	428 </test>
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	429 <!-- 17: Extract and merge all groups from Athena .prj -->
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	430 <test expect_num_outputs="1">
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	431 <param name="merge_inputs" value="true"/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	432 <param name="format" value="athena"/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	433 <param name="extract_group" value="all"/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	434 <param name="dat_file" value="multiple.prj"/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	435 <output name="athena_project_file">
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	436 <assert_contents>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	437 <has_size value="26000" delta="100"/>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	438 </assert_contents>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	439 </output>
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	440 </test>
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	441 <!-- 18: Use ref channel -->
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	442 <test expect_num_outputs="1">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	443 <param name="dat_file" value="ffi0.tabular"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	444 <param name="pre_edge" value="ref"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	445 <param name="ref_channel" value="lnitiref"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	446 <output name="athena_project_file">
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	447 <assert_contents>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	448 <has_size value="34400" delta="100"/>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	449 </assert_contents>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	450 </output>
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	451 </test>
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	452 </tests>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	453 <help><![CDATA[
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	454 Using Larch, create an Athena project file from the input X-ray Absorption Fine Structure (XAFS) data file.
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	455
4 a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	456 Accepts both tabular and NeXus/HDF5 formatted data or a zip file containing these formats.
a0d3b0fe0fa3 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8 muon-spectroscopy-computational-project parents: 3 diff changeset	457 If column names are not present in tabular data, then the first column is treated as `energy` and the second as `mu`.
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	458 Note that in order to ensure a consistent output, once unzipped all files will sorted first by their parent directories (alphabetically).
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	459 Within a given directory, if all filenames contain digits then the last block of digits will be used to sort the files numerically.
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	460 In the output, all files (regardless of initial filepath) are output in a flat hierarchy, with the number in which it was processed as the file name (zero-padded).
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	461 Care should therefore be taken to ensure input data is consistent with this treatment.
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	462
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	463 Optionally, plot the xμ data along with pre and post edge fitting lines for visual inspection.
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	464 ]]></help>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	465 <citations>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	466 <citation type="doi">@TOOL_CITATION@</citation>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	467 <citation type="doi">10.1107/S0909049505012719</citation>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	468 </citations>
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	469 </tool>

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

annotate larch_athena.xml @ 4:a0d3b0fe0fa3 draft