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comparison larch_lcf.xml @ 0:f59731986b61 draft

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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
author muon-spectroscopy-computational-project
date Tue, 14 Nov 2023 15:35:22 +0000
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children 6c28339b73f7
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-1:000000000000 0:f59731986b61
1 <tool id="larch_lcf" name="Larch LCF" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
2 <description>perform linear combination fit on XAS data</description>
3 <macros>
4 <!-- version of underlying tool (PEP 440) -->
5 <token name="@TOOL_VERSION@">0.9.71</token>
6 <!-- version of this tool wrapper (integer) -->
7 <token name="@WRAPPER_VERSION@">0</token>
8 <!-- citation should be updated with every underlying tool version -->
9 <!-- typical fields to update are version, month, year, and doi -->
10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>
11 <import>macros.xml</import>
12 </macros>
13 <creator>
14 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
15 </creator>
16 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement>
18 <requirement type="package" version="3.5.2">matplotlib</requirement>
19 </requirements>
20 <required_files>
21 <include type="literal" path="larch_lcf.py"/>
22 </required_files>
23 <command detect_errors="exit_code"><![CDATA[
24 python '${__tool_directory__}/larch_lcf.py' '$prj_file' '$inputs'
25 ]]></command>
26 <configfiles>
27 <inputs name="inputs" data_style="paths"/>
28 </configfiles>
29 <inputs>
30 <param name="label" type="text" optional="true" label="Main data label" help="The label to use for the main data (target of the fit). If unset, the label will be taken from the Athena project metadata."/>
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 <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="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 <expand macro="energy_limits"/>
37 </inputs>
38 <outputs>
39 <data name="plot" format="png" from_work_dir="plot.png" label="Larch LCF ${label} ${on_string}"/>
40 </outputs>
41 <tests>
42 <test expect_num_outputs="1">
43 <param name="prj_file" value="PtSn_OCO_Abu_1.prj"/>
44 <param name="component_file" value="Sn_foil_extracted.prj"/>
45 <param name="component_file" value="SnO2_extracted.prj"/>
46 <param name="energy_format" value="relative"/>
47 <param name="energy_max" value="10"/>
48 <output name="plot">
49 <assert_contents>
50 <has_size value="55100" delta="100"/>
51 </assert_contents>
52 </output>
53 </test>
54 </tests>
55 <help><![CDATA[
56 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.
58 ]]></help>
59 <citations>
60 <citation type="doi">@TOOL_CITATION@</citation>
61 <citation type="doi">10.1107/S0909049505012719</citation>
62 </citations>
63 </tool>