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author muon-spectroscopy-computational-project
date Fri, 03 Feb 2023 15:39:12 +0000
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children e15e8800c39e
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3
d7a0a31760b1 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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1 <tool id="muspinsim_plot" name="MuSpinSim Plot" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
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2 <description>plot values generated from MuSpinSim</description>
0
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3 <macros>
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4 <!-- version of underlying tool (PEP 440) -->
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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5 <token name="@TOOL_VERSION@">3.5.1</token>
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6 <!-- version of this tool wrapper (integer) -->
3
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7 <token name="@WRAPPER_VERSION@">1</token>
0
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8 <!-- citation should be updated with every underlying tool version -->
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9 <!-- typical fields to update are version, month, year, and doi -->
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10 <token name="@TOOL_CITATION@">
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11 @article{Hunter:2007,
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12 author = {Hunter, J. D.},
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13 title = {Matplotlib: A 2D graphics environment},
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14 journal = {Computing in Science &amp; Engineering},
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15 volume = {9},
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16 number = {3},
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17 pages = {90--95},
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18 abstract = {Matplotlib is a 2D graphics package used for Python for
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19 application development, interactive scripting, and publication-quality
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20 image generation across user interfaces and operating systems.},
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21 publisher = {IEEE COMPUTER SOC},
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22 doi = {10.1109/MCSE.2007.55},
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23 year = {2007}
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24 }
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25 </token>
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26 </macros>
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27 <creator>
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28 <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
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29 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
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30 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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31 </creator>
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32 <requirements>
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33 <requirement type="package" version="@TOOL_VERSION@">matplotlib</requirement>
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34 </requirements>
1
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35 <required_files>
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36 <include type="literal" path="generate_plot.py"/>
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37 </required_files>
0
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38 <command detect_errors="exit_code"><![CDATA[
3
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39 python '${__tool_directory__}/generate_plot.py' inputs.json
0
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40 ]]></command>
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41 <configfiles>
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42 <inputs name="inputs" data_style="paths" filename="inputs.json"/>
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43 </configfiles>
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44 <inputs>
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45 <param type="text" name="title" label="Plot Title" value=""/>
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46 <param type="text" name="xlab" label="Label for x axis" value=""/>
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47 <param type="text" name="ylab" label="Label for y axis" value=""/>
3
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48 <param name="out_file_type" type="select" label="Output File Type" display="radio">
0
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49 <option value="pdf">PDF</option>
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50 <option value="png">PNG</option>
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51 </param>
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52 <repeat name="mu_out_series" title="Muspinsim File Series">
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53 <param type="data" name="mu_data" format="txt" label="Muspinsim Experiment Data (.dat)"/>
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54 <param type="text" name="mu_label" optional="true" label="Muspinsim Experiment Label" value="" help="Label to use for this series in the plot legend."/>
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55 <param type="select" name="colour" label="Line/Point Color">
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56 <option value="k">Black</option>
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57 <option value="r">Red</option>
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58 <option value="g">Green</option>
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59 <option value="b">Blue</option>
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60 </param>
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61 <conditional name="series_type">
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62 <param type="select" name="type" label="Series Type">
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63 <option value="line">Line</option>
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64 <option value="points">Points</option>
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65 </param>
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66 <when value="line">
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67 <param type="select" name="linestyle" label="Line type">
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68 <option value="solid">Solid</option>
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69 <option value="dashed">Dashed</option>
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70 <option value="dotted">Dotted</option>
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71 </param>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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72 <param type="float" name="linewidth" label="Line width" value="1.0"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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73 </when>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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74 <when value="points">
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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75 <param type="select" name="pointstyle" label="Point Type">
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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76 <option value="s">Square</option>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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77 <option value="o">Circle</option>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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78 </param>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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79 <param type="float" name="pointscale" label="Point Scale" value="1.0"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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80 </when>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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81 </conditional>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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82 </repeat>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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83 </inputs>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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84 <outputs>
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85 <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf">
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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86 <filter>(out_file_type == 'pdf')</filter>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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87 </data>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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88 <data format="png" name="out_file_png" from_work_dir="outfile.png">
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89 <filter>(out_file_type == 'png')</filter>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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90 </data>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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91 </outputs>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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92 <tests>
2
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93 <test expect_num_outputs="1">
0
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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94 <param name="title" value="Temperature Example"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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95 <param name="xlab" value="Time"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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96 <param name="ylab" value="Asymmetry"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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97 <param name="out_file_type" value="png"/>
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98 <param name="mu_data" value="high_T.dat" ftype="txt"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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99 <param name="mu_label" value="High T limit"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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100 <param name="type" value="points"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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101 <param name="pointstyle" value="s"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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102 <param name="colour" value="r"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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103 <param name="pointscale" value="2.0"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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104 <param name="mu_data" value="low_T.dat" ftype="txt"/>
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105 <param name="mu_label" value="T=1 K"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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106 <param name="type" value="line"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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107 <param name="linestyle" value="solid"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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108 <param name="colour" value="k"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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109 <param name="linewidth" value="1.0"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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110 <output name="out_file_png" ftype="png">
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111 <assert_contents>
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112 <has_size value="52486" delta="20"/>
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113 </assert_contents>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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114 </output>
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115 </test>
2
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116 <test expect_num_outputs="1">
0
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117 <param name="title" value="Fitting Example"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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118 <param name="xlab" value="Time"/>
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119 <param name="ylab" value="Asymmetry"/>
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120 <param name="out_file_type" value="pdf"/>
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121 <param name="mu_data" value="experiment.dat" ftype="txt"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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122 <param name="mu_label" value="Data"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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123 <param name="type" value="points"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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124 <param name="pointstyle" value="o"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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125 <param name="pointscale" value="3.0"/>
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126 <param name="colour" value="b"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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127 <param name="mu_data" value="fitting.dat" ftype="txt"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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128 <param name="mu_label" value="Fitting"/>
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129 <param name="type" value="line"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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130 <param name="linestyle" value="solid"/>
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131 <param name="colour" value="b"/>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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132 <param name="linewidth" value="1.0"/>
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133 <output name="out_file_pdf" ftype="pdf">
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134 <assert_contents>
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135 <has_size value="14785" delta="20"/>
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136 </assert_contents>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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137 </output>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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138 </test>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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139 </tests>
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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140 <help><![CDATA[
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141 This tool allows you to plot values generated from muspinsim using Matplotlib.
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142
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143
89ae4a5724a5 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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144 You can plot them as points or as lines.
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145
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146
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147 You can overlay multiple plots on top of each other by providing more than one data file.
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148 ]]></help>
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149 <citations>
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150 <citation type="bibtex">
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151 @TOOL_CITATION@
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152 </citation>
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153 <citation type="bibtex">
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154 @software{muspinsim,
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155 author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
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156 license = {MIT},
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157 title = {{muspinsim}},
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158 url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
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159 version = {v1.1.0},
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160 month = {5},
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161 year = {2022},
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162 doi = {10.5281/zenodo.6563074}
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163 }
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164 </citation>
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165 </citations>
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166 </tool>