Mercurial > repos > astroteam > hess_astro_tool

annotate hess_astro_tool.xml @ 0:02e4bb4fa10c draft

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
author astroteam
date Mon, 19 Feb 2024 10:56:44 +0000
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children 593c4b45eda5
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02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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1 <tool id="hess_astro_tool" name="HESS" version="0.0.1+galaxy0" profile="23.0">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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2 <requirements>
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3 <requirement type="package" version="8.21.0">ipython</requirement>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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4 <requirement type="package" version="5.3.4">astropy</requirement>
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5 <requirement type="package" version="1.11.4">scipy</requirement>
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6 <requirement type="package" version="1.10.13">pydantic</requirement>
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7 <requirement type="package" version="4.66.2">tqdm</requirement>
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8 <requirement type="package" version="1.1">gammapy</requirement>
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9 <requirement type="package" version="3.8.3">matplotlib</requirement>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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10 <requirement type="package" version="1.2.12">oda-api</requirement>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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11 <!--Requirements string 'nb2workflow[cwl,service,rdf,mmoda]>=1.3.30
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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12 ' can't be converted automatically. Please add the galaxy/conda requirement manually or modify the requirements file!-->
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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13 <requirement type="package" version="7.16.0">nbconvert</requirement>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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14 <requirement type="package" version="1.20.3">wget</requirement>
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15 </requirements>
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16 <command detect_errors="exit_code">ipython '$__tool_directory__/${_data_product._selector}.py'</command>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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17 <configfiles>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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18 <inputs name="inputs" filename="inputs.json" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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19 </configfiles>
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20 <inputs>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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21 <conditional name="_data_product">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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22 <param name="_selector" type="select" label="Data Product">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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23 <option value="Image" selected="true">Image</option>
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24 <option value="Spectrum" selected="false">Spectrum</option>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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25 <option value="Spectrum_gammapy" selected="false">Spectrum_gammapy</option>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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26 <option value="Lightcurve" selected="false">Lightcurve</option>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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27 </param>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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28 <when value="Image">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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29 <param name="src_name" type="text" value="Crab" label="src_name" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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30 <param name="RA" type="float" value="83.6287" label="RA Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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31 <param name="DEC" type="float" value="22.0147" label="DEC Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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32 <param name="T1" type="text" value="2000-10-09T13:16:00.0" label="T1" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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33 <param name="T2" type="text" value="2022-10-10T13:16:00.0" label="T2" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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34 <param name="Radius" type="float" value="2.5" label="Radius Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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35 <param name="pixsize" type="float" value="0.1" label="Pixel size Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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36 <param name="Emin" type="float" value="100.0" label="Emin Units: GeV" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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37 <param name="Emax" type="float" value="10000.0" label="Emax Units: GeV" />
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38 </when>
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39 <when value="Spectrum">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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40 <param name="src_name" type="text" value="PKS 2155-304" label="src_name" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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41 <param name="RA" type="float" value="329.716938" label="RA Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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42 <param name="DEC" type="float" value="-30.225588" label="DEC Units: deg" />
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43 <param name="T1" type="text" value="2000-10-09T13:16:00.0" label="T1" />
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44 <param name="T2" type="text" value="2022-10-10T13:16:00.0" label="T2" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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45 <param name="Radius" type="float" value="2.5" label="Radius Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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46 <param name="R_s" type="float" value="0.2" label="R_s Units: deg" />
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47 <param name="Emin" type="float" value="100.0" label="Emin Units: GeV" />
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48 <param name="Emax" type="float" value="10000.0" label="Emax Units: GeV" />
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49 <param name="NEbins" type="integer" value="20" label="NEbins" />
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50 </when>
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51 <when value="Spectrum_gammapy">
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52 <param name="src_name" type="text" value="PKS 2155-304" label="src_name" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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53 <param name="RA" type="float" value="329.716938" label="RA Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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54 <param name="DEC" type="float" value="-30.225588" label="DEC Units: deg" />
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55 <param name="T1" type="text" value="2000-10-09T13:16:00.0" label="T1" />
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56 <param name="T2" type="text" value="2022-10-10T13:16:00.0" label="T2" />
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57 <param name="Radius" type="float" value="2.5" label="Radius Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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58 <param name="R_s" type="float" value="0.5" label="R_s Units: deg" />
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59 <param name="Emin" type="float" value="100.0" label="Emin Units: GeV" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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60 <param name="Emax" type="float" value="10000.0" label="Emax Units: GeV" />
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61 <param name="NEbins" type="integer" value="20" label="NEbins" />
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62 </when>
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63 <when value="Lightcurve">
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64 <param name="src_name" type="text" value="Crab" label="src_name" />
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65 <param name="RA" type="float" value="83.6287" label="RA Units: deg" />
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66 <param name="DEC" type="float" value="22.0147" label="DEC Units: deg" />
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67 <param name="T1" type="text" value="2003-10-09T13:16:00.0" label="T1" />
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68 <param name="T2" type="text" value="2005-10-10T13:16:00.0" label="T2" />
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69 <param name="Radius" type="float" value="2.5" label="Radius Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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70 <param name="R_s" type="float" value="0.2" label="R_s Units: deg" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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71 <param name="Emin" type="float" value="100.0" label="Emin Units: GeV" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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72 <param name="Emax" type="float" value="10000.0" label="Emax Units: GeV" />
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73 <param name="NTbins" type="integer" value="10" label="NTbins" />
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74 </when>
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75 </conditional>
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76 </inputs>
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77 <outputs>
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78 <data label="${tool.name} -&gt; Image picture" name="out_Image_picture" format="auto" from_work_dir="picture_galaxy.output">
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79 <filter>_data_product['_selector'] == 'Image'</filter>
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80 </data>
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81 <data label="${tool.name} -&gt; Image image" name="out_Image_image" format="auto" from_work_dir="image_galaxy.output">
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82 <filter>_data_product['_selector'] == 'Image'</filter>
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83 </data>
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84 <data label="${tool.name} -&gt; Spectrum picture_png" name="out_Spectrum_picture_png" format="auto" from_work_dir="picture_png_galaxy.output">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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85 <filter>_data_product['_selector'] == 'Spectrum'</filter>
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86 </data>
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87 <data label="${tool.name} -&gt; Spectrum spectrum_astropy_table" name="out_Spectrum_spectrum_astropy_table" format="auto" from_work_dir="spectrum_astropy_table_galaxy.output">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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88 <filter>_data_product['_selector'] == 'Spectrum'</filter>
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89 </data>
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90 <data label="${tool.name} -&gt; Spectrum_gammapy picture_png" name="out_Spectrum_gammapy_picture_png" format="auto" from_work_dir="picture_png_galaxy.output">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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91 <filter>_data_product['_selector'] == 'Spectrum_gammapy'</filter>
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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92 </data>
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93 <data label="${tool.name} -&gt; Spectrum_gammapy spectrum_astropy_table" name="out_Spectrum_gammapy_spectrum_astropy_table" format="auto" from_work_dir="spectrum_astropy_table_galaxy.output">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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94 <filter>_data_product['_selector'] == 'Spectrum_gammapy'</filter>
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95 </data>
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96 <data label="${tool.name} -&gt; Lightcurve picture" name="out_Lightcurve_picture" format="auto" from_work_dir="picture_galaxy.output">
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97 <filter>_data_product['_selector'] == 'Lightcurve'</filter>
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98 </data>
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99 <data label="${tool.name} -&gt; Lightcurve lightcurve_astropy_table" name="out_Lightcurve_lightcurve_astropy_table" format="auto" from_work_dir="lightcurve_astropy_table_galaxy.output">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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100 <filter>_data_product['_selector'] == 'Lightcurve'</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <test expect_num_outputs="2">
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105 <conditional name="_data_product">
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106 <param name="_selector" value="Image" />
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107 <param name="src_name" value="Crab" />
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108 <param name="RA" value="83.6287" />
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109 <param name="DEC" value="22.0147" />
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110 <param name="T1" value="2000-10-09T13:16:00.0" />
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111 <param name="T2" value="2022-10-10T13:16:00.0" />
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112 <param name="Radius" value="2.5" />
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113 <param name="pixsize" value="0.1" />
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114 <param name="Emin" value="100.0" />
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115 <param name="Emax" value="10000.0" />
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116 </conditional>
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117 <assert_stdout>
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118 <has_text text="*** Job finished successfully ***" />
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119 </assert_stdout>
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120 </test>
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121 <test expect_num_outputs="2">
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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122 <conditional name="_data_product">
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123 <param name="_selector" value="Spectrum" />
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124 <param name="src_name" value="PKS 2155-304" />
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125 <param name="RA" value="329.716938" />
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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126 <param name="DEC" value="-30.225588" />
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127 <param name="T1" value="2000-10-09T13:16:00.0" />
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128 <param name="T2" value="2022-10-10T13:16:00.0" />
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129 <param name="Radius" value="2.5" />
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130 <param name="R_s" value="0.2" />
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131 <param name="Emin" value="100.0" />
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132 <param name="Emax" value="10000.0" />
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133 <param name="NEbins" value="20" />
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134 </conditional>
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135 <assert_stdout>
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136 <has_text text="*** Job finished successfully ***" />
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137 </assert_stdout>
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138 </test>
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139 <test expect_num_outputs="2">
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140 <conditional name="_data_product">
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141 <param name="_selector" value="Spectrum_gammapy" />
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142 <param name="src_name" value="PKS 2155-304" />
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143 <param name="RA" value="329.716938" />
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144 <param name="DEC" value="-30.225588" />
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145 <param name="T1" value="2000-10-09T13:16:00.0" />
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146 <param name="T2" value="2022-10-10T13:16:00.0" />
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147 <param name="Radius" value="2.5" />
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148 <param name="R_s" value="0.5" />
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149 <param name="Emin" value="100.0" />
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150 <param name="Emax" value="10000.0" />
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151 <param name="NEbins" value="20" />
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152 </conditional>
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153 <assert_stdout>
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154 <has_text text="*** Job finished successfully ***" />
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155 </assert_stdout>
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156 </test>
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157 <test expect_num_outputs="2">
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158 <conditional name="_data_product">
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159 <param name="_selector" value="Lightcurve" />
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160 <param name="src_name" value="Crab" />
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161 <param name="RA" value="83.6287" />
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162 <param name="DEC" value="22.0147" />
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163 <param name="T1" value="2003-10-09T13:16:00.0" />
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164 <param name="T2" value="2005-10-10T13:16:00.0" />
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165 <param name="Radius" value="2.5" />
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166 <param name="R_s" value="0.2" />
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167 <param name="Emin" value="100.0" />
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168 <param name="Emax" value="10000.0" />
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169 <param name="NTbins" value="10" />
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170 </conditional>
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171 <assert_stdout>
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172 <has_text text="*** Job finished successfully ***" />
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173 </assert_stdout>
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174 </test>
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175 </tests>
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176 <help>This service provides analysis of publicly available sample &#8220;Data Level
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177 3&#8221; (DL3) data of HESS gamma-ray telescope, described by `Hess
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178 Collaboration (2018) &lt;https://arxiv.org/abs/1810.04516&gt;`__. Three types
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179 of data products are generated: sky images, source lightcurves and
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180 spectra.
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181
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182 The sky images are count maps produced by histogramming of the events in
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183 sky coordinates (Right Ascention and Declinaiton), in the energy range
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184 that can be set by adjusting the ``Emin`` and ``Emax`` parameters and in
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185 the time range that can be adjusted setting the ``T1`` (start time) and
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186 ``T2`` (stop time) parameters.
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187
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188 The lightcurves are produced by hystrogramming of the events in time, in
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189 the number ``NTbins`` of time intervals of equalt time width between
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190 ``T1`` (start time) and ``T2`` (stop time). The events are selected in a
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191 desired energy range between ``Emin`` and ``Emax`` from a circular
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192 region of the radius ``R_s`` (in degrees) around the source position
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193 ``RA``,\ ``DEC``. Conversion of the counts to the physical flux units is
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194 done by dividing by the exposure time and effective area that is
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195 extracted from the Instrument Response Functions (IRF).
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196
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197 For the spectra, two alternative tools are considered. The service
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198 ``Spectrum`` performs histogramming of the events in energy, in the
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199 number ``NEbins`` of energy bins homogeneously spaces in logarithm of
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200 energy, beterrn ``Emin`` and ``Emax``. Conversion of the counts to the
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201 physical flux units is done by dividing by the exposure time and
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202 effective area that is extracted from the IRF. This method does not take
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203 into account the energy bias and can result in a wrong spectral shape at
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204 the low-energy threshold where the bias is strongest.
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205
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206 An alternative spectral extraction is done using
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207 `Gammapy &lt;https://gammapy.org/&gt;`__, following the script `Spectrum
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208 Analysis &lt;https://docs.gammapy.org/0.18.2/tutorials/spectrum_analysis.html&gt;`__.
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209 It performs forward folding of the spectral model (a cut-off powerlaw by
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210 default) with the IRF and fits the folded model to the binned count data
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211 in the energy range between ``Emin`` and ``Emax`` in ``NEbins``
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212 logarithmically spaced energy bins.
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213 </help>
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214 <citations>
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215 <citation type="doi">10.5281/zenodo.1421098</citation>
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216 </citations>
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217 </tool>