larch_artemis: larch_artemis.xml annotate

annotate larch_artemis.xml @ 0:2752b2dd7ad6 draft

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735

author	muon-spectroscopy-computational-project
date	Tue, 14 Nov 2023 15:34:23 +0000
parents
children	84c8e04bc1a1

rev	line source
0 2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	1 <tool id="larch_artemis" name="Larch Artemis" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	2 <description>generate Artemis projects from XAFS data</description>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	3 <macros>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	4 <!-- version of underlying tool (PEP 440) -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	5 <token name="@TOOL_VERSION@">0.9.71</token>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	6 <!-- version of this tool wrapper (integer) -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	7 <token name="@WRAPPER_VERSION@">0</token>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	8 <!-- citation should be updated with every underlying tool version -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	9 <!-- typical fields to update are version, month, year, and doi -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	11 <xml name="series_options">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	12 <param name="stop_on_error" type="boolean" label="Stop on error" help="Whether to stop gracefully or continue with subsequent projects if an error is encountered when fitting."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	13 <repeat name="report_criteria" title="Report Criteria">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	14 <param name="variable" type="text" label="Variable" help="Name of the variable of that appears in the statistics or variables sections of the report."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	15 <conditional name="action">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	16 <param name="action" type="select" display="radio" label="Action" help="What to do with the named variable.">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	17 <option value="log" selected="true">Log</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	18 <option value="warn">Warn</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	19 <option value="stop">Early stopping</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	20 </param>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	21 <when value="log"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	22 <when value="warn">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	23 <param name="threshold" type="float" value="0.0" min="0.0" label="Warning threshold" help="In addition to logging, a warning will be printed if the absolute value of this variable goes above this threshold."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	24 </when>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	25 <when value="stop">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	26 <param name="threshold" type="float" value="0.0" min="0.0" label="Early stopping threshold" help="In addition to logging, execution will stop if the absolute value of this variable goes above this threshold."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	27 </when>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	28 </conditional>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	29 </repeat>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	30 </xml>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	31 <import>macros.xml</import>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	32 </macros>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	33 <creator>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	34 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	35 </creator>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	36 <requirements>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	37 <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	38 <requirement type="package" version="3.5.2">matplotlib</requirement>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	39 <requirement type="package" version="3.0">zip</requirement>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	40 </requirements>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	41 <required_files>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	42 <include type="literal" path="larch_artemis.py"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	43 </required_files>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	44 <command detect_errors="exit_code"><![CDATA[
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	45 unzip '$feff_paths'
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	46 && mkdir report rmr chikr
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	47 #if $execution.execution=="zipped":
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	48 && unzip '$execution.prj_file'
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	49 && python '${__tool_directory__}/larch_artemis.py' prj '$gds_file' '$sp_file' '$inputs'
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	50 #else
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	51 && python '${__tool_directory__}/larch_artemis.py' '$execution.prj_file' '$gds_file' '$sp_file' '$inputs'
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	52 #end if
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	53 #if $zip_outputs:
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	54 && zip out_zip.zip report/* rmr/* chikr/* >/dev/null
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	55 #end if
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	56 ]]></command>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	57 <configfiles>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	58 <inputs name="inputs"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	59 </configfiles>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	60 <inputs>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	61 <conditional name="execution" >
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	62 <param name="execution" type="select" display="radio" label="Execution mode" help="Whether to execute: on individual Athena projects as parallel jobs, as one job with each project fit occurring in series, or as one job using a zipped input.">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	63 <option value="parallel" selected="true">Parallel</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	64 <option value="series">Series</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	65 <option value="zipped">Zipped</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	66 </param>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	67 <when value="parallel">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	68 <param name="prj_file" type="data" format="prj" label="Athena project file" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format. If a collection of files is provided, these will be submitted and executed in parallel."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	69 </when>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	70 <when value="series">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	71 <param name="prj_file" type="data" format="prj" multiple="true" label="Athena project files" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format. These will be submitted as a single job working in series, enabling early stopping criteria."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	72 <expand macro="series_options"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	73 </when>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	74 <when value="zipped">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	75 <param name="prj_file" type="data" format="zip" label="Zipped Athena outputs" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format, and zipped. These will be submitted as a single job working in series, enabling early stopping criteria."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	76 <expand macro="series_options"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	77 </when>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	78 </conditional>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	79 <param name="feff_paths" type="data" format="zip" label="FEFF paths file" help="Zipped directory of the FEFF paths."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	80 <param name="gds_file" type="data" format="gds" label="GDS parameters file" help="File defining the fitting parameters as a `guess` (to be varied in the fit), `def` (defined by an expression evaluated throughout fitting) or `set` (evaluated at the start of fitting, then left unchanged)."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	81 <param name="sp_file" type="data" format="sp" label="SP parameters file" help="File defining the scattering paths."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	82 <section name="fit_vars" title="Fitting Variables">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	83 <param argument="fitspace" type="select" help="Space in which the fitting is performed.">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	84 <option value="r" selected="true">Real</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	85 <option value="k">Unfiltered k-space</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	86 <option value="q">Filtered k-space</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	87 <option value="w">Wavelet transform</option>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	88 </param>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	89 <expand macro="xftf_params"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	90 </section>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	91 <param name="plot_graph" type="boolean" label="Plot graph" help="Whether to plot the data."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	92 <param name="zip_outputs" type="boolean" label="Zip outputs" help="Whether to zip all outputs into one dataset."/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	93 </inputs>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	94 <outputs>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	95 <data name="out_zip" format="zip" from_work_dir="out_zip.zip" label="Zipped Artemis outputs on ${on_string}">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	96 <filter>zip_outputs</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	97 </data>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	98 <data name="fit_report" format="feffit" from_work_dir="report/fit_report.txt" label="Fit report on ${on_string}">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	99 <filter>execution["execution"]=="parallel"</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	100 <filter>not zip_outputs</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	101 </data>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	102 <data name="rmr" format="png" from_work_dir="rmr/rmr.png" label="RMR plot on ${on_string}">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	103 <filter>execution["execution"]=="parallel"</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	104 <filter>plot_graph</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	105 <filter>not zip_outputs</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	106 </data>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	107 <data name="chikr" format="png" from_work_dir="chikr/chikr.png" label="ChiKR plot on ${on_string}">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	108 <filter>execution["execution"]=="parallel"</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	109 <filter>plot_graph</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	110 <filter>not zip_outputs</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	111 </data>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	112 <collection name="fit_report_collection" format="feffit" type="list" label="Fit reports on ${on_string}">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	113 <discover_datasets pattern="__name_and_ext__" directory="report"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	114 <filter>execution["execution"]!="parallel"</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	115 <filter>not zip_outputs</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	116 </collection>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	117 <collection name="rmr_collection" format="png" type="list" label="RMR plots on ${on_string}">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	118 <discover_datasets pattern="__name_and_ext__" directory="rmr"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	119 <filter>execution["execution"]!="parallel"</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	120 <filter>plot_graph</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	121 <filter>not zip_outputs</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	122 </collection>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	123 <collection name="chikr_collection" format="png" type="list" label="ChiKR plots on ${on_string}">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	124 <discover_datasets pattern="__name_and_ext__" directory="chikr"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	125 <filter>execution["execution"]!="parallel"</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	126 <filter>plot_graph</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	127 <filter>not zip_outputs</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	128 </collection>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	129 <data name="criteria_report" format="csv" from_work_dir="criteria_report.csv" label="Selected criteria from ${on_string}">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	130 <filter>execution["execution"]!="parallel"</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	131 <filter>len(execution["report_criteria"])>0</filter>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	132 </data>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	133 </outputs>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	134 <tests>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	135 <!-- Parallel, no plot -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	136 <test expect_num_outputs="1">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	137 <param name="execution" value="parallel"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	138 <param name="prj_file" value="test.prj"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	139 <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	140 <param name="gds_file" value="gds.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	141 <param name="sp_file" value="sp.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	142 <param name="fitspace" value="r"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	143 <param name="kmin" value="3"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	144 <param name="kmax" value="14"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	145 <param name="kweight" value="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	146 <param name="dk" value="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	147 <param name="window" value="hanning"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	148 <param name="rmin" value="1.4"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	149 <param name="rmax" value="3.0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	150 <output name="fit_report" file="fit_report.txt" compare="re_match"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	151 </test>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	152 <!-- Parallel, plot -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	153 <test expect_num_outputs="3">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	154 <param name="execution" value="parallel"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	155 <param name="prj_file" value="test.prj"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	156 <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	157 <param name="gds_file" value="gds.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	158 <param name="sp_file" value="sp.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	159 <param name="fitspace" value="r"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	160 <param name="kmin" value="3"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	161 <param name="kmax" value="14"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	162 <param name="kweight" value="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	163 <param name="dk" value="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	164 <param name="window" value="hanning"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	165 <param name="rmin" value="1.4"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	166 <param name="rmax" value="3.0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	167 <param name="plot_graph" value="true"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	168 <output name="fit_report" file="fit_report.txt" compare="re_match"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	169 <output name="rmr">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	170 <assert_contents>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	171 <has_size value="55000" delta="1000"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	172 </assert_contents>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	173 </output>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	174 <output name="chikr">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	175 <assert_contents>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	176 <has_size value="65000" delta="1000"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	177 </assert_contents>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	178 </output>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	179 </test>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	180 <!-- Series, no plot -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	181 <test expect_num_outputs="1">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	182 <param name="execution" value="series"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	183 <param name="prj_file" value="test.prj,test.prj"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	184 <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	185 <param name="gds_file" value="gds.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	186 <param name="sp_file" value="sp.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	187 <param name="fitspace" value="r"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	188 <param name="kmin" value="3"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	189 <param name="kmax" value="14"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	190 <param name="kweight" value="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	191 <param name="dk" value="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	192 <param name="window" value="hanning"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	193 <param name="rmin" value="1.4"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	194 <param name="rmax" value="3.0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	195 <output_collection name="fit_report_collection" type="list" count="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	196 </test>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	197 <!-- Series, plot -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	198 <test expect_num_outputs="3">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	199 <param name="execution" value="series"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	200 <param name="prj_file" value="test.prj"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	201 <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	202 <param name="gds_file" value="gds.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	203 <param name="sp_file" value="sp.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	204 <param name="fitspace" value="r"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	205 <param name="kmin" value="3"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	206 <param name="kmax" value="14"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	207 <param name="kweight" value="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	208 <param name="dk" value="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	209 <param name="window" value="hanning"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	210 <param name="rmin" value="1.4"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	211 <param name="rmax" value="3.0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	212 <param name="plot_graph" value="true"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	213 <output_collection name="fit_report_collection" type="list" count="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	214 <output_collection name="rmr_collection" type="list" count="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	215 <output_collection name="chikr_collection" type="list" count="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	216 </test>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	217 <!-- Series, plot, continue on error -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	218 <!-- NB: Using NaNs to force an error now causes an error at an earlier stage where it is not caught, so cannot use these tests -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	219 <!-- <test expect_num_outputs="3">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	220 <param name="execution" value="series"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	221 <param name="prj_file" value="NaN.binary,test.prj"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	222 <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	223 <param name="gds_file" value="gds.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	224 <param name="sp_file" value="sp.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	225 <param name="fitspace" value="r"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	226 <param name="kmin" value="3"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	227 <param name="kmax" value="14"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	228 <param name="kweight" value="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	229 <param name="dk" value="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	230 <param name="window" value="hanning"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	231 <param name="rmin" value="1.4"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	232 <param name="rmax" value="3.0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	233 <param name="plot_graph" value="true"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	234 <output_collection name="fit_report_collection" type="list" count="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	235 <output_collection name="rmr_collection" type="list" count="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	236 <output_collection name="chikr_collection" type="list" count="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	237 </test> -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	238 <!-- Series, plot, stop on error -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	239 <!-- NB: Using NaNs to force an error now causes an error at an earlier stage where it is not caught, so cannot use these tests -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	240 <!-- <test expect_num_outputs="3">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	241 <param name="execution" value="series"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	242 <param name="prj_file" value="NaN.binary,test.prj"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	243 <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	244 <param name="gds_file" value="gds.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	245 <param name="sp_file" value="sp.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	246 <param name="fitspace" value="r"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	247 <param name="kmin" value="3"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	248 <param name="kmax" value="14"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	249 <param name="kweight" value="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	250 <param name="dk" value="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	251 <param name="window" value="hanning"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	252 <param name="rmin" value="1.4"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	253 <param name="rmax" value="3.0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	254 <param name="plot_graph" value="true"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	255 <output_collection name="fit_report_collection" type="list" count="0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	256 <output_collection name="rmr_collection" type="list" count="0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	257 <output_collection name="chikr_collection" type="list" count="0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	258 </test> -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	259 <!-- Series, early stopping -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	260 <test expect_num_outputs="2">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	261 <param name="execution" value="series"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	262 <param name="prj_file" value="test.prj,test.prj"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	263 <param name="variable" value="rfactor"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	264 <param name="action" value="stop"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	265 <param name="variable" value="alpha"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	266 <param name="action" value="log"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	267 <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	268 <param name="gds_file" value="gds.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	269 <param name="sp_file" value="sp.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	270 <param name="fitspace" value="r"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	271 <param name="kmin" value="3"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	272 <param name="kmax" value="14"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	273 <param name="kweight" value="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	274 <param name="dk" value="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	275 <param name="window" value="hanning"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	276 <param name="rmin" value="1.4"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	277 <param name="rmax" value="3.0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	278 <output_collection name="fit_report_collection" type="list" count="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	279 <output name="criteria_report" file="criteria_report.csv" compare="re_match"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	280 </test>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	281 <!-- Zipped -->
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	282 <test expect_num_outputs="1">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	283 <param name="execution" value="zipped"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	284 <param name="prj_file" value="test.zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	285 <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	286 <param name="gds_file" value="gds.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	287 <param name="sp_file" value="sp.csv"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	288 <param name="fitspace" value="r"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	289 <param name="kmin" value="3"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	290 <param name="kmax" value="14"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	291 <param name="kweight" value="2"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	292 <param name="dk" value="1"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	293 <param name="window" value="hanning"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	294 <param name="rmin" value="1.4"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	295 <param name="rmax" value="3.0"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	296 <param name="plot_graph" value="true"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	297 <param name="zip_outputs" value="true"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	298 <output name="out_zip">
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	299 <assert_contents>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	300 <has_size value="230000" delta="500"/>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	301 </assert_contents>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	302 </output>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	303 </test>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	304 </tests>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	305 <help><![CDATA[
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	306 Using Larch, perform fitting on an Athena project file, originally from the input X-ray Absorption Fine Structure (XAFS) data file.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	307
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	308 Optionally, plot the xμ data along with RMR and ChiKR plots for visual inspection of the fit.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	309
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	310 By default, if multiple files or a collection is provided then these jobs will be executed independently, in parallel.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	311
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	312 Alternatively, series execution will submit a single job with each file being executed in order as part of the job.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	313 A single zip file containing multiple Athena projects can also be extracted and run in series.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	314 If a fit is unsuccessful and results in an error, the job can either be stopped there or the fit attempted for the remaining projects.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	315 Criteria of interest from each individual report can be collected and logged.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	316 Additionally, thresholds can be set, with either warnings being printed or the job stopping early if these are exceeded by the criteria of interest.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	317 Parameters in both the "Statistics" and "Variables" sections of the report are supported.
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	318 ]]></help>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	319 <citations>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	320 <citation type="doi">@TOOL_CITATION@</citation>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	321 <citation type="doi">10.1107/S0909049505012719</citation>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	322 </citations>
2752b2dd7ad6 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	323 </tool>

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

annotate larch_artemis.xml @ 0:2752b2dd7ad6 draft