view larch_lcf.xml @ 3:6bb927e155fc draft

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

<tool id="larch_lcf" name="Larch LCF" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
    <description>perform linear combination fit on XAS data</description>
    <macros>
        <!-- version of underlying tool (PEP 440) -->
        <token name="@TOOL_VERSION@">0.9.75</token>
        <!-- version of this tool wrapper (integer) -->
        <token name="@WRAPPER_VERSION@">0</token>
        <!-- citation should be updated with every underlying tool version -->
        <!-- typical fields to update are version, month, year, and doi -->
        <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>
        <import>macros.xml</import>
    </macros>
    <creator>
        <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
    </creator>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement>
        <requirement type="package" version="3.5.2">matplotlib</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="larch_lcf.py"/>
        <include type="literal" path="common.py"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        python '${__tool_directory__}/larch_lcf.py' '$prj_file' '$inputs'
    ]]></command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <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."/>
        <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."/>
        <repeat name="components" title="Fit components">
            <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."/>
            <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."/>
        </repeat>
        <!-- Energy range for LCF -->
        <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."/>
        <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."/>
        <!-- Plot limits -->
        <expand macro="plot_limits_energy"/>
    </inputs>
    <outputs>
        <data name="plot" format="png" from_work_dir="plot.png"/>
    </outputs>
    <tests>
        <!-- 1 -->
        <test expect_num_outputs="1">
            <param name="prj_file" value="PtSn_OCO_Abu_1_29204.5.prj"/>
            <param name="component_file" value="Sn_foil_29200.prj"/>
            <param name="component_file" value="SnO2_29206.prj"/>
            <param name="energy_min" value="29190"/>
            <param name="energy_max" value="29230"/>
            <param name="x_limit_min" value="29190"/>
            <param name="x_limit_max" value="29230"/>
            <output name="plot">
                <assert_contents>
                    <has_size value="59500" delta="100"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="Goodness of fit (rfactor): 0.532130%"/>
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[
        Performs a Linear Combination Fit (LCF) on an Athena project, using a number of other projects as components to the fit.
        The extent to which each component contributes to the target is recorded in the output plot of the normalised absorption co-efficient.
    ]]></help>
    <citations>
        <citation type="doi">@TOOL_CITATION@</citation>
        <citation type="doi">10.1107/S0909049505012719</citation>
    </citations>
</tool>