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

comparison larch_lcf.xml @ 1:6c28339b73f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
author muon-spectroscopy-computational-project
date Wed, 06 Dec 2023 13:04:01 +0000
parents f59731986b61
children 85284c3e1354
comparison
equal deleted inserted replaced
0:f59731986b61 1:6c28339b73f7
2 <description>perform linear combination fit on XAS data</description> 2 <description>perform linear combination fit on XAS data</description>
3 <macros> 3 <macros>
4 <!-- version of underlying tool (PEP 440) --> 4 <!-- version of underlying tool (PEP 440) -->
5 <token name="@TOOL_VERSION@">0.9.71</token> 5 <token name="@TOOL_VERSION@">0.9.71</token>
6 <!-- version of this tool wrapper (integer) --> 6 <!-- version of this tool wrapper (integer) -->
7 <token name="@WRAPPER_VERSION@">0</token> 7 <token name="@WRAPPER_VERSION@">1</token>
8 <!-- citation should be updated with every underlying tool version --> 8 <!-- citation should be updated with every underlying tool version -->
9 <!-- typical fields to update are version, month, year, and doi --> 9 <!-- typical fields to update are version, month, year, and doi -->
10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token> 10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>
11 <import>macros.xml</import> 11 <import>macros.xml</import>
12 </macros> 12 </macros>
17 <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement>
18 <requirement type="package" version="3.5.2">matplotlib</requirement> 18 <requirement type="package" version="3.5.2">matplotlib</requirement>
19 </requirements> 19 </requirements>
20 <required_files> 20 <required_files>
21 <include type="literal" path="larch_lcf.py"/> 21 <include type="literal" path="larch_lcf.py"/>
22 <include type="literal" path="common.py"/>
22 </required_files> 23 </required_files>
23 <command detect_errors="exit_code"><![CDATA[ 24 <command detect_errors="exit_code"><![CDATA[
24 python '${__tool_directory__}/larch_lcf.py' '$prj_file' '$inputs' 25 python '${__tool_directory__}/larch_lcf.py' '$prj_file' '$inputs'
25 ]]></command> 26 ]]></command>
26 <configfiles> 27 <configfiles>
31 <param name="prj_file" type="data" format="prj" label="Athena project to fit" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format, to be fit."/> 32 <param name="prj_file" type="data" format="prj" label="Athena project to fit" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format, to be fit."/>
32 <repeat name="components" title="Fit components"> 33 <repeat name="components" title="Fit components">
33 <param name="label" type="text" optional="true" label="Component label" help="The label to use for this component. If unset, the label will be taken from the Athena project metadata."/> 34 <param name="label" type="text" optional="true" label="Component label" help="The label to use for this component. If unset, the label will be taken from the Athena project metadata."/>
34 <param name="component_file" type="data" format="prj" label="Athena project to fit" help="Reference X-ray Absorption Fine Structure (XAFS) data, in Athena project format, to be used as components in the fit."/> 35 <param name="component_file" type="data" format="prj" label="Athena project to fit" help="Reference X-ray Absorption Fine Structure (XAFS) data, in Athena project format, to be used as components in the fit."/>
35 </repeat> 36 </repeat>
36 <expand macro="energy_limits"/> 37 <!-- Energy range for LCF -->
38 <param name="energy_min" type="float" label="Minimum fit energy (eV)" optional="true" help="If set, only data above this value will be used for the LCF."/>
39 <param name="energy_max" type="float" label="Maximum fit energy (eV)" optional="true" help="If set, only data below this value will be used for the LCF."/>
40 <!-- Plot limits -->
41 <expand macro="plot_limits_energy"/>
37 </inputs> 42 </inputs>
38 <outputs> 43 <outputs>
39 <data name="plot" format="png" from_work_dir="plot.png" label="Larch LCF ${label} ${on_string}"/> 44 <data name="plot" format="png" from_work_dir="plot.png"/>
40 </outputs> 45 </outputs>
41 <tests> 46 <tests>
47 <!-- 1 -->
42 <test expect_num_outputs="1"> 48 <test expect_num_outputs="1">
43 <param name="prj_file" value="PtSn_OCO_Abu_1.prj"/> 49 <param name="prj_file" value="PtSn_OCO_Abu_1_29204.5.prj"/>
44 <param name="component_file" value="Sn_foil_extracted.prj"/> 50 <param name="component_file" value="Sn_foil_29200.prj"/>
45 <param name="component_file" value="SnO2_extracted.prj"/> 51 <param name="component_file" value="SnO2_29206.prj"/>
46 <param name="energy_format" value="relative"/> 52 <param name="energy_min" value="29190"/>
47 <param name="energy_max" value="10"/> 53 <param name="energy_max" value="29230"/>
54 <param name="x_limit_min" value="29190"/>
55 <param name="x_limit_max" value="29230"/>
48 <output name="plot"> 56 <output name="plot">
49 <assert_contents> 57 <assert_contents>
50 <has_size value="55100" delta="100"/> 58 <has_size value="59500" delta="100"/>
51 </assert_contents> 59 </assert_contents>
52 </output> 60 </output>
61 <assert_stdout>
62 <has_text text="Goodness of fit (rfactor): 0.532130%"/>
63 </assert_stdout>
53 </test> 64 </test>
54 </tests> 65 </tests>
55 <help><![CDATA[ 66 <help><![CDATA[
56 Performs a Linear Combination Fit (LCF) on an Athena project, using a number of other projects as components to the fit. 67 Performs a Linear Combination Fit (LCF) on an Athena project, using a number of other projects as components to the fit.
57 The extent to which each component contributes to the target is recorded in the output plot of the normalised absorption co-efficient. 68 The extent to which each component contributes to the target is recorded in the output plot of the normalised absorption co-efficient.