Mercurial > repos > muon-spectroscopy-computational-project > muspinsim_plot
comparison muspinsim_plot.xml @ 0:89ae4a5724a5 draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
author | muon-spectroscopy-computational-project |
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date | Thu, 25 Aug 2022 16:17:15 +0000 |
parents | |
children | 193ed5c2d443 |
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1 <tool id="muspinsim_plot" name="MuSpinSim Plot" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01"> | |
2 <macros> | |
3 <!-- version of underlying tool (PEP 440) --> | |
4 <token name="@TOOL_VERSION@">3.5.1</token> | |
5 <!-- version of this tool wrapper (integer) --> | |
6 <token name="@WRAPPER_VERSION@">0</token> | |
7 <!-- citation should be updated with every underlying tool version --> | |
8 <!-- typical fields to update are version, month, year, and doi --> | |
9 <token name="@TOOL_CITATION@"> | |
10 @article{Hunter:2007, | |
11 author = {Hunter, J. D.}, | |
12 title = {Matplotlib: A 2D graphics environment}, | |
13 journal = {Computing in Science & Engineering}, | |
14 volume = {9}, | |
15 number = {3}, | |
16 pages = {90--95}, | |
17 abstract = {Matplotlib is a 2D graphics package used for Python for | |
18 application development, interactive scripting, and publication-quality | |
19 image generation across user interfaces and operating systems.}, | |
20 publisher = {IEEE COMPUTER SOC}, | |
21 doi = {10.1109/MCSE.2007.55}, | |
22 year = {2007} | |
23 } | |
24 </token> | |
25 </macros> | |
26 <creator> | |
27 <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/> | |
28 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> | |
29 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> | |
30 </creator> | |
31 <requirements> | |
32 <requirement type="package" version="@TOOL_VERSION@">matplotlib</requirement> | |
33 </requirements> | |
34 <command detect_errors="exit_code"><![CDATA[ | |
35 python ${__tool_directory__}/generate_plot.py inputs.json | |
36 ]]></command> | |
37 <configfiles> | |
38 <inputs name="inputs" data_style="paths" filename="inputs.json"/> | |
39 </configfiles> | |
40 <inputs> | |
41 <param type="text" name="title" label="Plot Title" value=""/> | |
42 <param type="text" name="xlab" label="Label for x axis" value=""/> | |
43 <param type="text" name="ylab" label="Label for y axis" value=""/> | |
44 <param name="out_file_type" type="select" label="Output File Type"> | |
45 <option value="pdf">PDF</option> | |
46 <option value="png">PNG</option> | |
47 </param> | |
48 <repeat name="mu_out_series" title="Muspinsim File Series"> | |
49 <param type="data" name="mu_data" format="txt" label="Muspinsim Experiment Data (.dat)"/> | |
50 <param type="text" name="mu_label" optional="true" label="Muspinsim Experiment Label" value="" help="Label to use for this series in the plot legend."/> | |
51 <param type="select" name="colour" label="Line/Point Color"> | |
52 <option value="k">Black</option> | |
53 <option value="r">Red</option> | |
54 <option value="g">Green</option> | |
55 <option value="b">Blue</option> | |
56 </param> | |
57 <conditional name="series_type"> | |
58 <param type="select" name="type" label="Series Type"> | |
59 <option value="line">Line</option> | |
60 <option value="points">Points</option> | |
61 </param> | |
62 <when value="line"> | |
63 <param type="select" name="linestyle" label="Line type"> | |
64 <option value="solid">Solid</option> | |
65 <option value="dashed">Dashed</option> | |
66 <option value="dotted">Dotted</option> | |
67 </param> | |
68 <param type="float" name="linewidth" label="Line width" value="1.0"/> | |
69 </when> | |
70 <when value="points"> | |
71 <param type="select" name="pointstyle" label="Point Type"> | |
72 <option value="s">Square</option> | |
73 <option value="o">Circle</option> | |
74 </param> | |
75 <param type="float" name="pointscale" label="Point Scale" value="1.0"/> | |
76 </when> | |
77 </conditional> | |
78 </repeat> | |
79 </inputs> | |
80 <outputs> | |
81 <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf"> | |
82 <filter>(out_file_type == 'pdf')</filter> | |
83 </data> | |
84 <data format="png" name="out_file_png" from_work_dir="outfile.png"> | |
85 <filter>(out_file_type == 'png')</filter> | |
86 </data> | |
87 </outputs> | |
88 <tests> | |
89 <test> | |
90 <param name="title" value="Temperature Example"/> | |
91 <param name="xlab" value="Time"/> | |
92 <param name="ylab" value="Asymmetry"/> | |
93 <param name="out_file_type" value="png"/> | |
94 <param name="mu_data" value="high_T.dat" ftype="txt"/> | |
95 <param name="mu_label" value="High T limit"/> | |
96 <param name="type" value="points"/> | |
97 <param name="pointstyle" value="s"/> | |
98 <param name="colour" value="r"/> | |
99 <param name="pointscale" value="2.0"/> | |
100 <param name="mu_data" value="low_T.dat" ftype="txt"/> | |
101 <param name="mu_label" value="T=1 K"/> | |
102 <param name="type" value="line"/> | |
103 <param name="linestyle" value="solid"/> | |
104 <param name="colour" value="k"/> | |
105 <param name="linewidth" value="1.0"/> | |
106 <output name="out_file_png" ftype="png"> | |
107 <assert_contents> | |
108 <has_size value="52486" delta="20"/> | |
109 </assert_contents> | |
110 </output> | |
111 </test> | |
112 <test> | |
113 <param name="title" value="Fitting Example"/> | |
114 <param name="xlab" value="Time"/> | |
115 <param name="ylab" value="Asymmetry"/> | |
116 <param name="out_file_type" value="pdf"/> | |
117 <param name="mu_data" value="experiment.dat" ftype="txt"/> | |
118 <param name="mu_label" value="Data"/> | |
119 <param name="type" value="points"/> | |
120 <param name="pointstyle" value="o"/> | |
121 <param name="pointscale" value="3.0"/> | |
122 <param name="colour" value="b"/> | |
123 <param name="mu_data" value="fitting.dat" ftype="txt"/> | |
124 <param name="mu_label" value="Fitting"/> | |
125 <param name="type" value="line"/> | |
126 <param name="linestyle" value="solid"/> | |
127 <param name="colour" value="b"/> | |
128 <param name="linewidth" value="1.0"/> | |
129 <output name="out_file_pdf" ftype="pdf"> | |
130 <assert_contents> | |
131 <has_size value="14785" delta="20"/> | |
132 </assert_contents> | |
133 </output> | |
134 </test> | |
135 </tests> | |
136 <help><![CDATA[ | |
137 This tool allows you to plot values generated from muspinsim using Matplotlib. | |
138 | |
139 | |
140 You can plot them as points or as lines. | |
141 | |
142 | |
143 You can overlay multiple plots on top of each other by providing more than one data file. | |
144 ]]></help> | |
145 <citations> | |
146 <citation type="bibtex"> | |
147 @TOOL_CITATION@ | |
148 </citation> | |
149 <citation type="bibtex"> | |
150 @software{muspinsim, | |
151 author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}}, | |
152 license = {MIT}, | |
153 title = {{muspinsim}}, | |
154 url = {https://github.com/muon-spectroscopy-computational-project/muspinsim}, | |
155 version = {v1.1.0}, | |
156 month = {5}, | |
157 year = {2022}, | |
158 doi = {10.5281/zenodo.6563074} | |
159 } | |
160 </citation> | |
161 </citations> | |
162 </tool> |