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comparison muspinsim.xml @ 0:64e6816a6727 draft

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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
author muon-spectroscopy-computational-project
date Thu, 25 Aug 2022 16:16:19 +0000
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1 <tool id="muspinsim" name="MuSpinSim Simulate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">
2 <description>perform spin dynamics calculations for muon science experiments</description>
3 <macros>
4 <!-- version of underlying tool (PEP 440) -->
5 <token name="@TOOL_VERSION@">1.1.0</token>
6 <!-- version of this tool wrapper (integer) -->
7 <token name="@WRAPPER_VERSION@">1</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@">
11 @software{muspinsim,
12 author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
13 license = {MIT},
14 title = {{muspinsim}},
15 url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
16 version = {v1.1.0},
17 month = {5},
18 year = {2022},
19 doi = {10.5281/zenodo.6563074}
20 }
21 </token>
22 </macros>
23 <creator>
24 <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
25 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
26 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
27 </creator>
28 <requirements>
29 <requirement type="package" version="@TOOL_VERSION@">muspinsim</requirement>
30 </requirements>
31 <command detect_errors="exit_code"><![CDATA[
32 ## remove spaces in names
33 mu_sim_name=\$(sed 's/ //g' <<< "$mu_sim.name") &&
34 ## create links
35 ln -s $mu_sim \$mu_sim_name &&
36 ## grab 'name' field from input file, if it doesn't exist, set name as 'muspinsim'
37 mu_out=\$(grep -A1 '^name' \$mu_sim_name | grep -v 'name' | sed -e 's/^[ \t]*//') &&
38 fitreport_out=\${mu_out:-"fitting_data"}_fitreport.txt &&
39 mu_out=\${mu_out:-"muspinsim"} &&
40 log_out=\$(echo \$mu_sim_name | cut -d '.' -f1).log &&
41 ## if fitting data required, check if fitting data exists
42 ## create symlink and change filepath in input file to point to symlink
43 if grep '^fitting_data' $mu_sim; then
44 if [[ '$mu_exp_in.name' != 'None' ]]; then
45 mu_exp_in_name=\$(sed 's/ //g' <<< "$mu_exp_in.name") &&
46 ln -s $mu_exp_in \$mu_exp_in_name &&
47 sed -iE "/^fitting_data/{n;s/([^)]*)/(\"\$mu_exp_in_name\")/g}" \$mu_sim_name;
48 else
49 echo "fitting data required, but no experiment data given" && exit 64;
50 fi;
51 fi &&
52 muspinsim \$mu_sim_name &&
53 mkdir data &&
54 mv \$mu_out*.dat data &&
55 if test -f \$fitreport_out; then mv -f \$fitreport_out fit_report.txt; fi &&
56 mv \$log_out log_out.log
57 ]]></command>
58 <inputs>
59 <param type="data" name="mu_sim" format="txt" label="Configuration file containing simulation parameters"/>
60 <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."/>
61 </inputs>
62 <outputs>
63 <collection name="muspinsim_results" type="list" label="Muspinsim output collection">
64 <discover_datasets pattern="__name__" directory="data" format="txt"/>
65 </collection>
66 <data label="muspinsim log for $mu_sim.name" name="log_out" format="txt" from_work_dir="log_out.log"/>
67 <data label="fit report for $mu_sim.name" name="fit_report" format="txt" from_work_dir="fit_report.txt">
68 <filter>mu_exp_in</filter>
69 </data>
70 </outputs>
71 <tests>
72 <!-- log files have a timestamp on each line, and .dat files vary by machine
73 so use compare="re_match" or "contains" with some generalised test files -->
74 <test>
75 <param name="mu_sim" value="hfine.in" ftype="txt"/>
76 <output_collection name="muspinsim_results" type="list">
77 <element name="hfine.dat" file="hfine.dat" ftype="txt" lines_diff="4"/>
78 </output_collection>
79 <output name="log_out" file="hfine.log" ftype="txt" compare="re_match"/>
80 </test>
81 <test>
82 <param name="mu_sim" value="hfine_powder.in" ftype="txt"/>
83 <output_collection name="muspinsim_results" type="list">
84 <element name="muspinsim.dat" file="generic_out.dat" ftype="txt" compare="re_match_multiline">
85 <assert_contents>
86 <has_size value="5100" delta="100"/>
87 </assert_contents>
88 </element>
89 </output_collection>
90 <output name="log_out" file="hfine_powder.log" ftype="txt" compare="re_match">
91 <assert_contents>
92 <has_size value="802"/>
93 </assert_contents>
94 </output>
95 </test>
96 <test>
97 <param name="mu_sim" value="fitting.in" ftype="txt"/>
98 <param name="mu_exp_in" value="fitting_input.dat" ftype="txt"/>
99 <output_collection name="muspinsim_results" type="list">
100 <element name="fitting_data.dat" file="fitting_data.dat" ftype="txt" lines_diff="4"/>
101 </output_collection>
102 <output name="log_out" file="fitting.log" ftype="txt" compare="contains">
103 <assert_contents>
104 <has_size value="17145"/>
105 </assert_contents>
106 </output>
107 <output name="fit_report" file="fitting_fitreport.txt" ftype="txt" lines_diff="4"/>
108 </test>
109 <test>
110 <param name="mu_sim" value="multi_out.in" ftype="txt"/>
111 <output_collection name="muspinsim_results" type="list">
112 <element name="multi_out_0_0.dat" file="multi_out_0_0.dat" ftype="txt" compare="re_match_multiline">
113 <assert_contents>
114 <has_size value="1164" delta="100"/>
115 </assert_contents>
116 </element>
117 <element name="multi_out_0_1.dat" file="multi_out_0_1.dat" ftype="txt" compare="re_match_multiline">
118 <assert_contents>
119 <has_size value="1164" delta="100"/>
120 </assert_contents>
121 </element>
122 <element name="multi_out_1_0.dat" file="multi_out_1_0.dat" ftype="txt" compare="re_match_multiline">
123 <assert_contents>
124 <has_size value="1164" delta="100"/>
125 </assert_contents>
126 </element>
127 <element name="multi_out_1_1.dat" file="multi_out_1_1.dat" ftype="txt" compare="re_match_multiline">
128 <assert_contents>
129 <has_size value="1164" delta="100"/>
130 </assert_contents>
131 </element>
132 </output_collection>
133 <output name="log_out" file="multi_out.log" ftype="txt" compare="re_match"/>
134 </test>
135 </tests>
136 <help><![CDATA[
137 MuSpinSim is a program designed to carry out spin dynamics calculations.
138
139 Tool requires an input (.in) file which describes system and experiment details.
140 This is a text file containing keywords and values in indented blocks.
141
142 Full documentation: https://muon-spectroscopy-computational-project.github.io/muspinsim/
143
144 Command-line usage: muspinsim muspinsim.in
145 ]]></help>
146 <citations>
147 <citation type="bibtex">
148 @TOOL_CITATION@
149 </citation>
150 </citations>
151 </tool>