annotate muspinsim.xml @ 2:136ed45d1ea9 draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507

<tool id="muspinsim" name="MuSpinSim Simulate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
    <description>perform spin dynamics calculations for muon science experiments</description>
    <macros>
        <!-- version of underlying tool (PEP 440) -->
        <token name="@TOOL_VERSION@">2.0.2</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@">
            @software{muspinsim,
                author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and Davies, Joel and Wilkinson, John and {Muon Spectroscopy Computational Project}},
                license = {MIT},
                title = {{muspinsim}},
                url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
                version = {v2.0.2},
                month = {1},
                year = {2023}
                doi = {10.5281/zenodo.7568830}
            }
        </token>
    </macros>
    <creator>
        <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
        <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
        <person givenName="Joel" familyName="Davies" url="https://github.com/joelvdavies" identifier="https://orcid.org/0000-0002-4153-6819"/>
        <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
    </creator>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">muspinsim</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## remove spaces in names
        mu_sim_name=\$(sed 's/ //g' <<< '$mu_sim.name') &&
        ## input file name without extension
        mu_in_name=\${mu_sim_name%.*} &&
        ## create links
        ln -s '$mu_sim' \$mu_sim_name &&
        ## grab 'name' field from input file, if it doesn't exist, set name as 'muspinsim'
        mu_out=\$(grep -A1 '^name' \$mu_sim_name | grep -v 'name' | sed -e 's/^[ \t]*//') &&
        fit_report_out=\${mu_in_name:-"fitting_data"}_fit_report.txt &&
        mu_out=\${mu_out:-"muspinsim"} &&
        log_out=\$(echo \$mu_sim_name | cut -d '.' -f1).log &&
        ## if fitting data required, check if fitting data exists
        ## create symlink and change filepath in input file to point to symlink
        if grep '^fitting_data' '$mu_sim'; then
            if [[ '$mu_exp_in.name' != 'None' ]]; then
                mu_exp_in_name=\$(sed 's/ //g' <<< '$mu_exp_in.name') &&
                ln -s '$mu_exp_in' \$mu_exp_in_name &&
                sed -iE "/^fitting_data/{n;s/([^)]*)/(\"\$mu_exp_in_name\")/g}" \$mu_sim_name;
            else
                echo "Fitting data required, but no experiment data given" && exit 64;
            fi;
        fi &&
        muspinsim \$mu_sim_name &&
        mkdir data &&
        mv \$mu_out*.dat data &&
        if test -f \$fit_report_out; then mv -f \$fit_report_out fit_report.txt; fi &&
        mv \$log_out log_out.log
    ]]></command>
    <inputs>
        <param type="data" name="mu_sim" format="txt" label="Configuration file containing simulation parameters"/>
        <param type="data" name="mu_exp_in" format="txt" optional="true" label="Experiment data to fit (.dat) (Optional)" help="Only required if the 'fitting_data' parameter is set in the configuration file above."/>
    </inputs>
    <outputs>
        <collection name="muspinsim_results" type="list" label="Muspinsim output collection">
            <discover_datasets pattern="__name__" directory="data" format="txt"/>
        </collection>
        <data label="muspinsim log for $mu_sim.name" name="log_out" format="txt" from_work_dir="log_out.log"/>
        <data label="fit report for $mu_sim.name" name="fit_report" format="txt" from_work_dir="fit_report.txt">
            <filter>mu_exp_in</filter>
        </data>
    </outputs>
    <tests>
        <!-- log files have a timestamp on each line, and .dat files vary by machine
                so use compare="re_match" or "contains" with some generalised test files -->
        <test expect_num_outputs="2">
            <param name="mu_sim" value="hfine.in" ftype="txt"/>
            <output_collection name="muspinsim_results" type="list">
                <element name="hfine.dat" file="hfine.dat" ftype="txt" compare="re_match"/>
            </output_collection>
            <output name="log_out" file="hfine.log" ftype="txt" compare="re_match"/>
        </test>
        <test expect_num_outputs="2">
            <param name="mu_sim" value="hfine_powder.in" ftype="txt"/>
            <output_collection name="muspinsim_results" type="list">
                <element name="muspinsim.dat" file="generic_out.dat" ftype="txt" compare="re_match_multiline">
                    <assert_contents>
                        <has_size value="5100" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="log_out" file="hfine_powder.log" ftype="txt" compare="re_match">
                <assert_contents>
                    <has_size value="803" delta="2"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="mu_sim" value="celio.in" ftype="txt"/>
            <output_collection name="muspinsim_results" type="list">
                <element name="celio.dat" file="generic_out.dat" ftype="txt" compare="re_match_multiline"/>
            </output_collection>
            <output name="log_out" file="celio.log" ftype="txt" compare="re_match"/>
        </test>
        <test expect_num_outputs="3">
            <param name="mu_sim" value="fitting.in" ftype="txt"/>
            <param name="mu_exp_in" value="fitting_input.dat" ftype="txt"/>
            <output_collection name="muspinsim_results" type="list">
                <element name="fitting_data.dat" file="fitting_data.dat" ftype="txt" lines_diff="4"/>
            </output_collection>
            <output name="log_out" file="fitting.log" ftype="txt" compare="contains">
                <assert_contents>
                    <has_size value="17145"/>
                </assert_contents>
            </output>
            <output name="fit_report" file="fitting_fit_report.txt" ftype="txt" lines_diff="2"/>
        </test>
        <test expect_num_outputs="2">
            <param name="mu_sim" value="multi_out.in" ftype="txt"/>
            <output_collection name="muspinsim_results" type="list">
                <element name="multi_out_0_0.dat" file="multi_out_0_0.dat" ftype="txt" compare="re_match_multiline">
                    <assert_contents>
                        <has_size value="1164" delta="100"/>
                    </assert_contents>
                </element>
                <element name="multi_out_0_1.dat" file="multi_out_0_1.dat" ftype="txt" compare="re_match_multiline">
                    <assert_contents>
                        <has_size value="1164" delta="100"/>
                    </assert_contents>
                </element>
                <element name="multi_out_1_0.dat" file="multi_out_1_0.dat" ftype="txt" compare="re_match_multiline">
                    <assert_contents>
                        <has_size value="1164" delta="100"/>
                    </assert_contents>
                </element>
                <element name="multi_out_1_1.dat" file="multi_out_1_1.dat" ftype="txt" compare="re_match_multiline">
                    <assert_contents>
                        <has_size value="1164" delta="100"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="log_out" file="multi_out.log" ftype="txt" compare="re_match"/>
        </test>
    </tests>
    <help><![CDATA[
        MuSpinSim is a program designed to carry out spin dynamics calculations.

        Tool requires an input (.in) file which describes system and experiment details.
        This is a text file containing keywords and values in indented blocks.

        Full documentation: https://muon-spectroscopy-computational-project.github.io/muspinsim/

        Command-line usage: muspinsim muspinsim.in
    ]]></help>
    <citations>
        <citation type="bibtex">
            @TOOL_CITATION@
        </citation>
    </citations>
</tool>