Mercurial > repos > astroteam > crbeam_astro_tool

annotate crbeam_astro_tool.xml @ 0:f40d05521dca draft default tip

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
author astroteam
date Fri, 25 Apr 2025 19:33:20 +0000
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f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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1 <tool id="crbeam_astro_tool" name="CRbeam" version="0.0.2+galaxy0" profile="24.0">
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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2 <requirements>
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3 <requirement type="package" version="1.1.1">crbeam</requirement>
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4 <requirement type="package" version="19.0.1">pyarrow</requirement>
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5 <requirement type="package" version="6.0">unzip</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="3.9.4">matplotlib</requirement>
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8 <requirement type="package" version="0.13.2">seaborn</requirement>
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9 <requirement type="package" version="7.2.15">minio</requirement>
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10 <requirement type="package" version="1.19.0">specutils</requirement>
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11 <requirement type="package" version="1.11.4">scipy</requirement>
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12 <requirement type="package" version="1.3">gammapy</requirement>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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13 <requirement type="package" version="0.4.10">astroquery</requirement>
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14 <requirement type="package" version="5.3">astropy</requirement>
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15 <requirement type="package" version="9.1.0">ipython</requirement>
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16 </requirements>
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17 <command detect_errors="exit_code">ipython '$__tool_directory__/${C_data_product_.DPselector_}.py'</command>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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18 <environment_variables>
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19 <environment_variable name="BASEDIR">$__tool_directory__</environment_variable>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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20 <environment_variable name="GALAXY_TOOL_DIR">$__tool_directory__</environment_variable>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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21 </environment_variables>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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22 <configfiles>
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23 <inputs name="inputs" filename="inputs.json" data_style="paths" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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24 </configfiles>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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25 <inputs>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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26 <conditional name="C_data_product_">
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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27 <param name="DPselector_" type="select" label="Data Product">
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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28 <option value="Generate_events" selected="true">Generate_events</option>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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29 <option value="Generate_figures" selected="false">Generate_figures</option>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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30 </param>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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31 <when value="Generate_events">
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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32 <param name="src_name" type="text" value="1ES 1215+303" label="src_name" optional="false" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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33 <param name="z_start" type="float" value="0.13" label="z_start" optional="false" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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34 <param name="Npart" type="integer" value="10000" label="Npart" min="1" max="100000" optional="false" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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35 <param name="particle_type" type="select" label="particle_type" optional="false">
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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36 <option value="electron">electron</option>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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37 <option value="gamma" selected="true">gamma</option>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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38 <option value="proton">proton</option>
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39 </param>
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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40 <param name="Emax" type="float" value="50" label="Emax (unit: TeV)" optional="false" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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41 <param name="Emin" type="float" value="0.01" label="Emin (unit: TeV)" optional="false" />
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42 <param name="EminSource" type="float" value="0.01" label="EminSource (unit: TeV)" optional="false" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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43 <param name="Gamma" type="float" value="2.0" label="Gamma" optional="false" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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44 <param name="EGMF_fG" type="float" value="100" label="EGMF_fG" optional="false" />
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45 <param name="lmaxEGMF_Mpc" type="float" value="5" label="lmaxEGMF_Mpc" optional="false" />
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46 <param name="jet_half_size" type="float" value="180.0" label="jet_half_size (unit: deg)" optional="false" />
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47 <param name="jet_direction" type="float" value="0.0" label="jet_direction (unit: deg)" optional="false" />
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48 <param name="psf" type="float" value="180.0" label="psf (unit: deg)" optional="false" />
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49 <param name="window_size_RA" type="float" value="4.0" label="window_size_RA (unit: deg)" optional="false" />
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50 <param name="window_size_DEC" type="float" value="4.0" label="window_size_DEC (unit: deg)" optional="false" />
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51 <param name="EBL" type="select" label="EBL" optional="false">
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52 <option value="Franceschini 2017" selected="true">Franceschini 2017</option>
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53 <option value="Inoue 2012 Baseline">Inoue 2012 Baseline</option>
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54 <option value="Inoue 2012 lower limit">Inoue 2012 lower limit</option>
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55 <option value="Inoue 2012 upper limit">Inoue 2012 upper limit</option>
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56 <option value="Stecker 2016 lower limit">Stecker 2016 lower limit</option>
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57 <option value="Stecker 2016 upper limit">Stecker 2016 upper limit</option>
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58 </param>
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59 </when>
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60 <when value="Generate_figures">
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61 <param name="src_name" type="text" value="NGC 1365" label="src_name" optional="false" />
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62 <param name="z_start" type="float" value="0" label="z_start" optional="false" />
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63 <param name="Npart" type="integer" value="2000" label="Npart" min="1" max="100000" optional="false" />
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64 <param name="particle_type" type="select" label="particle_type" optional="false">
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65 <option value="electron">electron</option>
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66 <option value="gamma" selected="true">gamma</option>
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67 <option value="proton">proton</option>
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68 </param>
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69 <param name="Emax" type="float" value="30" label="Emax (unit: TeV)" optional="false" />
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70 <param name="Emin" type="float" value="0.01" label="Emin (unit: TeV)" optional="false" />
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71 <param name="EminSource" type="float" value="1.0" label="EminSource (unit: TeV)" optional="false" />
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72 <param name="Gamma" type="float" value="2.0" label="Gamma" optional="false" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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73 <param name="EGMF_fG" type="float" value="10" label="EGMF_fG" optional="false" />
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74 <param name="lmaxEGMF_Mpc" type="float" value="5" label="lmaxEGMF_Mpc" optional="false" />
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75 <param name="jet_half_size" type="float" value="5.0" label="jet_half_size (unit: deg)" optional="false" />
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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76 <param name="jet_direction" type="float" value="0.0" label="jet_direction (unit: deg)" optional="false" />
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77 <param name="psf" type="float" value="1.0" label="psf (unit: deg)" optional="false" />
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78 <param name="window_size_RA" type="float" value="2.0" label="window_size_RA (unit: deg)" optional="false" />
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79 <param name="window_size_DEC" type="float" value="1.0" label="window_size_DEC (unit: deg)" optional="false" />
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80 <param name="EBL" type="select" label="EBL" optional="false">
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81 <option value="Franceschini 2017" selected="true">Franceschini 2017</option>
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82 <option value="Inoue 2012 Baseline">Inoue 2012 Baseline</option>
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83 <option value="Inoue 2012 lower limit">Inoue 2012 lower limit</option>
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84 <option value="Inoue 2012 upper limit">Inoue 2012 upper limit</option>
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85 <option value="Stecker 2016 lower limit">Stecker 2016 lower limit</option>
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86 <option value="Stecker 2016 upper limit">Stecker 2016 upper limit</option>
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87 </param>
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88 </when>
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89 </conditional>
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90 </inputs>
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91 <outputs>
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92 <data label="${tool.name} -&gt; Generate_events Event_file" name="out_Generate_events_Event_file" format="auto" from_work_dir="Event_file_galaxy.output">
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93 <filter>C_data_product_['DPselector_'] == 'Generate_events'</filter>
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94 </data>
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95 <data label="${tool.name} -&gt; Generate_figures spectrum_png" name="out_Generate_figures_spectrum_png" format="auto" from_work_dir="spectrum_png_galaxy.output">
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96 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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97 </data>
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98 <data label="${tool.name} -&gt; Generate_figures light_curve_png" name="out_Generate_figures_light_curve_png" format="auto" from_work_dir="light_curve_png_galaxy.output">
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99 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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100 </data>
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101 <data label="${tool.name} -&gt; Generate_figures total_spectrum_table" name="out_Generate_figures_total_spectrum_table" format="auto" from_work_dir="total_spectrum_table_galaxy.output">
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102 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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103 </data>
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104 <data label="${tool.name} -&gt; Generate_figures psf_spectrum_table" name="out_Generate_figures_psf_spectrum_table" format="auto" from_work_dir="psf_spectrum_table_galaxy.output">
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105 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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106 </data>
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107 <data label="${tool.name} -&gt; Generate_figures lc_result" name="out_Generate_figures_lc_result" format="auto" from_work_dir="lc_result_galaxy.output">
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108 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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109 </data>
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110 <data label="${tool.name} -&gt; Generate_figures spectrum" name="out_Generate_figures_spectrum" format="auto" from_work_dir="spectrum_galaxy.output">
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111 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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112 </data>
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113 <data label="${tool.name} -&gt; Generate_figures spectrum_rotated" name="out_Generate_figures_spectrum_rotated" format="auto" from_work_dir="spectrum_rotated_galaxy.output">
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114 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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115 </data>
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116 <data label="${tool.name} -&gt; Generate_figures map3d" name="out_Generate_figures_map3d" format="auto" from_work_dir="map3d_galaxy.output">
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117 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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118 </data>
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119 <data label="${tool.name} -&gt; Generate_figures map4d" name="out_Generate_figures_map4d" format="auto" from_work_dir="map4d_galaxy.output">
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120 <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter>
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121 </data>
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122 </outputs>
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123 <tests>
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124 <test expect_num_outputs="1">
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125 <conditional name="C_data_product_">
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126 <param name="DPselector_" value="Generate_events" />
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127 <param name="src_name" value="1ES 1215+303" />
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128 <param name="z_start" value="0.13" />
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129 <param name="Npart" value="10000" />
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130 <param name="particle_type" value="gamma" />
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131 <param name="Emax" value="50" />
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132 <param name="Emin" value="0.01" />
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133 <param name="EminSource" value="0.01" />
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134 <param name="Gamma" value="2.0" />
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135 <param name="EGMF_fG" value="100" />
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136 <param name="lmaxEGMF_Mpc" value="5" />
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137 <param name="jet_half_size" value="180.0" />
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138 <param name="jet_direction" value="0.0" />
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139 <param name="psf" value="180.0" />
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140 <param name="window_size_RA" value="4.0" />
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141 <param name="window_size_DEC" value="4.0" />
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142 <param name="EBL" value="Franceschini 2017" />
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143 </conditional>
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144 <assert_stdout>
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145 <has_text text="*** Job finished successfully ***" />
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146 </assert_stdout>
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147 </test>
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148 <test expect_num_outputs="9">
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149 <conditional name="C_data_product_">
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150 <param name="DPselector_" value="Generate_figures" />
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151 <param name="src_name" value="NGC 1365" />
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152 <param name="z_start" value="0" />
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153 <param name="Npart" value="2000" />
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154 <param name="particle_type" value="gamma" />
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155 <param name="Emax" value="30" />
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156 <param name="Emin" value="0.01" />
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157 <param name="EminSource" value="1.0" />
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158 <param name="Gamma" value="2.0" />
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159 <param name="EGMF_fG" value="10" />
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160 <param name="lmaxEGMF_Mpc" value="5" />
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161 <param name="jet_half_size" value="5.0" />
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162 <param name="jet_direction" value="0.0" />
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163 <param name="psf" value="1.0" />
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164 <param name="window_size_RA" value="2.0" />
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165 <param name="window_size_DEC" value="1.0" />
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166 <param name="EBL" value="Franceschini 2017" />
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167 </conditional>
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168 <assert_stdout>
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169 <has_text text="*** Job finished successfully ***" />
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170 </assert_stdout>
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171 </test>
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172 </tests>
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173 <help>CRbeam
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174 ======
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175
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176 This service provides simulation [1] of electron-photon cascade
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177 propagation in the intergalactic space. The simulation accounts for the
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178 interactions of photons and electrons with extragalactic background
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179 light (EBL) and magnetic field. As a first step and main part of
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180 simulation the code traces trajectories of every particle and records
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181 it&#8217;s position and momentum at *z=0* assuming that initially particles
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182 were emitted at fixed redshift *z_start* with given power law spectrum
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183 in the direction of *z*-axis. The source jet geometry is then taken into
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184 account in the second step by rotating the source image obtained during
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185 the first stage within the jet openning angle. This allows to reuse the
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186 simulation results for different jet geometries. The tool has two
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187 available data products:
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188
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189 - list of events
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190 - list of figures
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191
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192 Both modes have common list of input parameters:
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193
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194 *src_name* e.g.&#160;&#8216;GRB221009A&#8217; - optional source name from Simbad database
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195 (ignored if *z_start* is given)
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196
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197 *z_start* e.g.&#160;0.1 - source redshift or 0 if src_name should be used
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198
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199 *Npart* e.g.&#160;100000 - number of particles to simulate
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200
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201 *particle_type* - initial particle type, one of &#8220;gamma&#8221;,&#8220;electron&#8221; or
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202 &#8220;proton&#8221;
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203
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204 *Emax* - maximal energy of particles emitted by the source in TeV
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205
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206 *Emin* - minimal energy in TeV of secondary particles to trace in the
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207 simulation
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208
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209 *EminSource* - minimal energy of particles emitted by the source in TeV.
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210 If *EminSourceTeV=EmaxTeV* fixed energy injection is assumed
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211
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212 *Gamma* - injection spectrum power low index: dN/dE = E^{-gamma}
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213
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214 *EGMF_fG* - amplitude of the intergalactic magnetic field in femtogauss.
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215 The Kolmogorov turbulence model is assumed for the magnetic field
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216
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217 *lmaxEGMF_Mpc* - maximal scale of the magnetic field turbulence in Mpc
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218
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219 *jet_half_size* - jet half size in degrees
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220
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221 *jet_direction* - angle in degrees between the jet axis and the
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222 direction to the observer
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223
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224 *psf* - observer instrument psf in degrees
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225
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226 *EBL* - extragalactic background light model to use. Below is the list
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227 of models supported:
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228
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229 - *Franceschini 2017*, see Ref. [2]
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230 - *Stecker 2016 lower limit* : lower limit model from Ref. [3]
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231 - *Stecker 2016 upper limit* : upper limit model from Ref. [3]
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232 - *Inoue 2012 Baseline* : baseline model from Ref. [4]
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233 - *Inoue 2012 lower limit* : lower limit model from Ref. [4]
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234 - *Inoue 2012 upper limit* : upper limit model from Ref. [4]
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235 - *zero* : CMB only
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236
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237 References
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238 ----------
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239
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240 [1] O. Kalashev, A. Korochkin, A. Neronov, D. Semikoz,
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241 *Astron.Astrophys.* 675 (2023) A132
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242
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243 [2] Alberto Franceschini, Giulia Rodighiero, *Astron.Astrophys.* 603
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244 (2017) A34
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245
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246 [3] Floyd W. Stecker, Sean T. Scully, Matthew A. Malkan, *Astrophys.J.*
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247 827 (2016)
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248
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249 [4] Yoshiyuki Inoue et al., *Astrophys.J.* 768 (2013) 197
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250 </help>
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251 <citations>
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252 <citation type="bibtex">@misc{label,
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253 title = {Tool CRbeam},
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254 url = {https://renkulab.io/projects/astronomy/mmoda/crbeam},
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255 author = {Oleg Kalashev and Andrii Neronov},
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256 year = {2024},
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257 note = {}
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258 }</citation>
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259 </citations>
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260 </tool>