Mercurial > repos > astroteam > plot_tools_astro_tool

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
author astroteam
date Fri, 25 Apr 2025 21:48:27 +0000
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2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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1 <tool id="plot_tools_astro_tool" name="Plot Tools" version="0.0.1+galaxy0" profile="24.0">
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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2 <requirements>
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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3 <requirement type="package" version="2.2.3">pandas</requirement>
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4 <requirement type="package" version="3.9.2">matplotlib</requirement>
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5 <requirement type="package" version="5.3">astropy</requirement>
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6 <requirement type="package" version="1.2.37">oda-api</requirement>
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7 <requirement type="package" version="1.2">gammapy</requirement>
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8 <requirement type="package" version="9.1.0">ipython</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">python '$__tool_directory__/${C_data_product_.DPselector_}.py'</command>
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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11 <environment_variables>
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12 <environment_variable name="BASEDIR">$__tool_directory__</environment_variable>
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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13 <environment_variable name="GALAXY_TOOL_DIR">$__tool_directory__</environment_variable>
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14 </environment_variables>
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15 <configfiles>
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16 <inputs name="inputs" filename="inputs.json" data_style="paths" />
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17 </configfiles>
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18 <inputs>
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19 <conditional name="C_data_product_">
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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20 <param name="DPselector_" type="select" label="Data Product">
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21 <option value="light_curve" selected="true">light_curve</option>
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22 <option value="spectrum" selected="false">spectrum</option>
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23 <option value="sky_plot" selected="false">sky_plot</option>
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24 </param>
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25 <when value="light_curve">
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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26 <param name="fn" type="data" label="fn" format="data" optional="false" />
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27 <param name="skiprows" type="integer" value="0" label="skiprows" optional="false" />
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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28 <param name="sep" type="select" label="sep" optional="false">
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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29 <option value="comma">comma</option>
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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30 <option value="semicolon">semicolon</option>
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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31 <option value="space">space</option>
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32 <option value="tab">tab</option>
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33 <option value="whitespace" selected="true">whitespace</option>
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34 </param>
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35 <param name="column" type="text" value="T" label="column" optional="false" />
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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36 <param name="weight_col" type="text" value="" label="weight_col" optional="false" />
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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37 <param name="binning" type="select" label="binning" optional="false">
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38 <option value="linear">linear</option>
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39 <option value="logarithmic" selected="true">logarithmic</option>
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40 </param>
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41 <param name="minval" type="float" value="0" label="minval" optional="false" />
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42 <param name="maxval" type="float" value="0" label="maxval" optional="false" />
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43 <param name="use_quantile_values" type="boolean" label="use_quantile_values" optional="false" />
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44 <param name="nbins" type="integer" value="15" label="nbins" optional="false" />
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45 <param name="xlabel" type="text" value="time, s" label="xlabel" optional="false" />
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46 <param name="ylabel" type="text" value="Ncounts" label="ylabel" optional="false" />
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47 <param name="plot_mode" type="select" label="plot_mode" optional="false">
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48 <option value="counts">counts</option>
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49 <option value="flux" selected="true">flux</option>
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50 </param>
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51 </when>
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52 <when value="spectrum">
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53 <param name="fn" type="data" label="fn" format="data" optional="false" />
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54 <param name="skiprows" type="integer" value="0" label="skiprows" optional="false" />
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55 <param name="sep" type="select" label="sep" optional="false">
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56 <option value="auto">auto</option>
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57 <option value="comma">comma</option>
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58 <option value="semicolon">semicolon</option>
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59 <option value="tab">tab</option>
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60 <option value="whitespace" selected="true">whitespace</option>
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61 </param>
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62 <param name="column" type="text" value="c1" label="column" optional="false" />
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63 <param name="weight_col" type="text" value="" label="weight_col" optional="false" />
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64 <param name="binning" type="select" label="binning" optional="false">
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65 <option value="linear">linear</option>
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66 <option value="logarithmic" selected="true">logarithmic</option>
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67 </param>
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68 <param name="minval" type="float" value="0" label="minval" optional="false" />
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69 <param name="maxval" type="float" value="0" label="maxval" optional="false" />
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70 <param name="nbins" type="integer" value="15" label="nbins" optional="false" />
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71 <param name="xlabel" type="text" value="Energy, [eV]" label="xlabel" optional="false" />
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72 <param name="ylabel" type="text" value="Flux E^2, [eV]" label="ylabel" optional="false" />
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73 <param name="spec_power" type="float" value="2.0" label="spec_power" optional="false" />
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74 </when>
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75 <when value="sky_plot">
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76 <param name="fn" type="data" label="fn" format="data" optional="false" />
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77 <param name="skiprows" type="integer" value="0" label="skiprows" optional="false" />
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78 <param name="sep" type="select" label="sep" optional="false">
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79 <option value="auto">auto</option>
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80 <option value="comma">comma</option>
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81 <option value="semicolon">semicolon</option>
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82 <option value="tab">tab</option>
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83 <option value="whitespace" selected="true">whitespace</option>
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84 </param>
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85 <param name="ra_col" type="text" value="c3" label="ra_col" optional="false" />
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86 <param name="dec_col" type="text" value="c4" label="dec_col" optional="false" />
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87 <param name="weight_col" type="text" value="" label="weight_col" optional="false" />
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88 <param name="binsz" type="float" value="0.02" label="binsz" optional="false" />
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89 <param name="window_size_RA" type="float" value="2.0" label="window_size_RA" optional="false" />
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90 <param name="window_size_DEC" type="float" value="2.0" label="window_size_DEC" optional="false" />
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91 </when>
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92 </conditional>
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93 </inputs>
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94 <outputs>
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95 <data label="${tool.name} -&gt; light_curve histogram_data" name="out_light_curve_histogram_data" format="auto" from_work_dir="histogram_data_galaxy.output">
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96 <filter>C_data_product_['DPselector_'] == 'light_curve'</filter>
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97 </data>
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98 <data label="${tool.name} -&gt; light_curve histogram_picture" name="out_light_curve_histogram_picture" format="auto" from_work_dir="histogram_picture_galaxy.output">
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99 <filter>C_data_product_['DPselector_'] == 'light_curve'</filter>
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100 </data>
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101 <data label="${tool.name} -&gt; spectrum histogram_data" name="out_spectrum_histogram_data" format="auto" from_work_dir="histogram_data_galaxy.output">
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102 <filter>C_data_product_['DPselector_'] == 'spectrum'</filter>
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103 </data>
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104 <data label="${tool.name} -&gt; spectrum histogram_picture" name="out_spectrum_histogram_picture" format="auto" from_work_dir="histogram_picture_galaxy.output">
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105 <filter>C_data_product_['DPselector_'] == 'spectrum'</filter>
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106 </data>
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107 <data label="${tool.name} -&gt; sky_plot plot" name="out_sky_plot_plot" format="auto" from_work_dir="plot_galaxy.output">
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108 <filter>C_data_product_['DPselector_'] == 'sky_plot'</filter>
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109 </data>
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110 <data label="${tool.name} -&gt; sky_plot fits_image" name="out_sky_plot_fits_image" format="auto" from_work_dir="fits_image_galaxy.output">
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111 <filter>C_data_product_['DPselector_'] == 'sky_plot'</filter>
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112 </data>
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113 </outputs>
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114 <tests>
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115 <test expect_num_outputs="2">
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116 <conditional name="C_data_product_">
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117 <param name="DPselector_" value="light_curve" />
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118 <param name="fn" location="https://gitlab.renkulab.io/astronomy/mmoda/plot-tools/-/raw/57cc7b8180fa6c1a286114a9e7b903923f786631/data.tsv" />
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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119 <param name="skiprows" value="0" />
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120 <param name="sep" value="whitespace" />
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121 <param name="column" value="T" />
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122 <param name="weight_col" value="" />
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123 <param name="binning" value="logarithmic" />
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124 <param name="minval" value="0" />
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125 <param name="maxval" value="0" />
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126 <param name="use_quantile_values" value="False" />
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127 <param name="nbins" value="15" />
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128 <param name="xlabel" value="time, s" />
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129 <param name="ylabel" value="Ncounts" />
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130 <param name="plot_mode" value="flux" />
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131 </conditional>
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132 <assert_stdout>
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133 <has_text text="*** Job finished successfully ***" />
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134 </assert_stdout>
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135 </test>
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136 <test expect_num_outputs="2">
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137 <conditional name="C_data_product_">
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138 <param name="DPselector_" value="spectrum" />
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139 <param name="fn" location="https://gitlab.renkulab.io/astronomy/mmoda/plot-tools/-/raw/57cc7b8180fa6c1a286114a9e7b903923f786631/data.tsv" />
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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140 <param name="skiprows" value="0" />
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141 <param name="sep" value="whitespace" />
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142 <param name="column" value="c1" />
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143 <param name="weight_col" value="" />
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144 <param name="binning" value="logarithmic" />
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145 <param name="minval" value="0" />
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146 <param name="maxval" value="0" />
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147 <param name="nbins" value="15" />
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148 <param name="xlabel" value="Energy, [eV]" />
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149 <param name="ylabel" value="Flux E^2, [eV]" />
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150 <param name="spec_power" value="2.0" />
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151 </conditional>
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152 <assert_stdout>
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153 <has_text text="*** Job finished successfully ***" />
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154 </assert_stdout>
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155 </test>
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156 <test expect_num_outputs="2">
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157 <conditional name="C_data_product_">
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158 <param name="DPselector_" value="sky_plot" />
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159 <param name="fn" location="https://gitlab.renkulab.io/astronomy/mmoda/plot-tools/-/raw/57cc7b8180fa6c1a286114a9e7b903923f786631/data.tsv" />
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160 <param name="skiprows" value="0" />
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161 <param name="sep" value="whitespace" />
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162 <param name="ra_col" value="c3" />
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163 <param name="dec_col" value="c4" />
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164 <param name="weight_col" value="" />
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165 <param name="binsz" value="0.02" />
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166 <param name="window_size_RA" value="2.0" />
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167 <param name="window_size_DEC" value="2.0" />
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168 </conditional>
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169 <assert_stdout>
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170 <has_text text="*** Job finished successfully ***" />
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171 </assert_stdout>
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172 </test>
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173 </tests>
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174 <help>Plot Tools
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175 ==========
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176
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177 Set of tools for astronomical data visualization
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178
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179 - sky_plot - visualize sky map using set of events as input
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180 - light_cure - calculate and visualize light curve from a set of evebts
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181 - spectrum - calculate energy spectrum using set of events as input
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182
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183 Parameters
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184 ----------
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185
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186 common parameters
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187 ~~~~~~~~~~~~~~~~~
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188
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189 fn - input data file
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190
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191 skiprows - number of rows to skip
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192
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193 sep - separator value
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194
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195 sky_plot parameters
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196 ~~~~~~~~~~~~~~~~~~~
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197
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198 ra_col - RA column (either column name of string cXX, where XX &gt;= 1 is
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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199 column number)
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200
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201 dec_col - DEC column (either column name of string cXX, where XX &gt;= 1 is
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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202 column number)
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203
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204 weight_col - weight column (either column name of string cXX, where XX
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205 &gt;= 1 is column number, or empty string if data doesn&#8217;t contain weights)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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206
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207 binsz - bin size in degrees
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208
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209 window_size_RA - size of window (RA) in degrees
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210
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211 window_size_DEC - size of window (DEC) in degrees
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212
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213 light_cure parameters
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214 ~~~~~~~~~~~~~~~~~~~~~
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215
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216 column - time column (either column name of string cXX, where XX &gt;= 1 is
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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217 column number)
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218
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219 weight_col - weight column (either column name of string cXX, where XX
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220 &gt;= 1 is column number, or empty string if data doesn&#8217;t contain weights)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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221
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222 binning - binning type (&#8216;logarithmic&#8217; or &#8220;linear&#8221;)
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223
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224 minval - minimal value (use 0 to infer from data)
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225
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226 maxval - maximal value (use 0 to infer from data)
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227
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228 use_quantile_values - interpret minval and maxval as quantiles
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229
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230 nbins=15 - number of bins
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231
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232 xlabel - plot x-label
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233
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234 ylabel - plot y-label
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235
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236 plot_mode - plotting mode (&#8220;counts&#8221; or &#8220;flux&#8221;)
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237
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238 spectrum parameters
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239 ~~~~~~~~~~~~~~~~~~~
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240
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241 column - energy column (either column name of string cXX, where XX &gt;= 1
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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242 is column number)
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243
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244 weight_col- weight column (either column name of string cXX, where XX &gt;=
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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245 1 is column number, or empty string if data doesn&#8217;t contain weights)
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246
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247 binning - binning type (&#8216;logarithmic&#8217; or &#8220;linear&#8221;)
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248
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249 minval - minimal value (use 0 to infer from data)
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250
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251 maxval - maximal value (use 0 to infer from data)
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252
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253 nbins - number of bins
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254
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255 xlabel - plot x-label
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256
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257 ylabel - plot y-label
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258
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259 spec_power - multiply spectrum by energy in this power on plot
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260 </help>
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261 <citations>
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262 <citation type="bibtex">@misc{label,
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263 title = {Tool repository},
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264 url = {https://renkulab.io/projects/astronomy/mmoda/plot-tools},
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265 author = {Oleg Kalashev},
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266 year = {2024},
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267 note = {}
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268 }</citation>
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269 </citations>
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270 </tool>