diff muspinsim.xml @ 0:64e6816a6727 draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muspinsim.xml	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,151 @@
+<tool id="muspinsim" name="MuSpinSim Simulate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">
+    <description>perform spin dynamics calculations for muon science experiments</description>
+    <macros>
+        <!-- version of underlying tool (PEP 440) -->
+        <token name="@TOOL_VERSION@">1.1.0</token>
+        <!-- version of this tool wrapper (integer) -->
+        <token name="@WRAPPER_VERSION@">1</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 {Muon Spectroscopy Computational Project}},
+                license = {MIT},
+                title = {{muspinsim}},
+                url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
+                version = {v1.1.0},
+                month = {5},
+                year = {2022},
+                doi = {10.5281/zenodo.6563074}
+            }
+        </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"/>
+        <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") &&
+        ## 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]*//') &&
+        fitreport_out=\${mu_out:-"fitting_data"}_fitreport.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 \$fitreport_out; then mv -f \$fitreport_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>
+            <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" lines_diff="4"/>
+            </output_collection>
+            <output name="log_out" file="hfine.log" ftype="txt" compare="re_match"/>
+        </test>
+        <test>
+            <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="802"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <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_fitreport.txt" ftype="txt" lines_diff="4"/>
+        </test>
+        <test>
+            <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>