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| author | astroteam |
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| date | Fri, 25 Apr 2025 19:33:20 +0000 |
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<tool id="crbeam_astro_tool" name="CRbeam" version="0.0.2+galaxy0" profile="24.0"> <requirements> <requirement type="package" version="1.1.1">crbeam</requirement> <requirement type="package" version="19.0.1">pyarrow</requirement> <requirement type="package" version="6.0">unzip</requirement> <requirement type="package" version="1.2.37">oda-api</requirement> <requirement type="package" version="3.9.4">matplotlib</requirement> <requirement type="package" version="0.13.2">seaborn</requirement> <requirement type="package" version="7.2.15">minio</requirement> <requirement type="package" version="1.19.0">specutils</requirement> <requirement type="package" version="1.11.4">scipy</requirement> <requirement type="package" version="1.3">gammapy</requirement> <requirement type="package" version="0.4.10">astroquery</requirement> <requirement type="package" version="5.3">astropy</requirement> <requirement type="package" version="9.1.0">ipython</requirement> </requirements> <command detect_errors="exit_code">ipython '$__tool_directory__/${C_data_product_.DPselector_}.py'</command> <environment_variables> <environment_variable name="BASEDIR">$__tool_directory__</environment_variable> <environment_variable name="GALAXY_TOOL_DIR">$__tool_directory__</environment_variable> </environment_variables> <configfiles> <inputs name="inputs" filename="inputs.json" data_style="paths" /> </configfiles> <inputs> <conditional name="C_data_product_"> <param name="DPselector_" type="select" label="Data Product"> <option value="Generate_events" selected="true">Generate_events</option> <option value="Generate_figures" selected="false">Generate_figures</option> </param> <when value="Generate_events"> <param name="src_name" type="text" value="1ES 1215+303" label="src_name" optional="false" /> <param name="z_start" type="float" value="0.13" label="z_start" optional="false" /> <param name="Npart" type="integer" value="10000" label="Npart" min="1" max="100000" optional="false" /> <param name="particle_type" type="select" label="particle_type" optional="false"> <option value="electron">electron</option> <option value="gamma" selected="true">gamma</option> <option value="proton">proton</option> </param> <param name="Emax" type="float" value="50" label="Emax (unit: TeV)" optional="false" /> <param name="Emin" type="float" value="0.01" label="Emin (unit: TeV)" optional="false" /> <param name="EminSource" type="float" value="0.01" label="EminSource (unit: TeV)" optional="false" /> <param name="Gamma" type="float" value="2.0" label="Gamma" optional="false" /> <param name="EGMF_fG" type="float" value="100" label="EGMF_fG" optional="false" /> <param name="lmaxEGMF_Mpc" type="float" value="5" label="lmaxEGMF_Mpc" optional="false" /> <param name="jet_half_size" type="float" value="180.0" label="jet_half_size (unit: deg)" optional="false" /> <param name="jet_direction" type="float" value="0.0" label="jet_direction (unit: deg)" optional="false" /> <param name="psf" type="float" value="180.0" label="psf (unit: deg)" optional="false" /> <param name="window_size_RA" type="float" value="4.0" label="window_size_RA (unit: deg)" optional="false" /> <param name="window_size_DEC" type="float" value="4.0" label="window_size_DEC (unit: deg)" optional="false" /> <param name="EBL" type="select" label="EBL" optional="false"> <option value="Franceschini 2017" selected="true">Franceschini 2017</option> <option value="Inoue 2012 Baseline">Inoue 2012 Baseline</option> <option value="Inoue 2012 lower limit">Inoue 2012 lower limit</option> <option value="Inoue 2012 upper limit">Inoue 2012 upper limit</option> <option value="Stecker 2016 lower limit">Stecker 2016 lower limit</option> <option value="Stecker 2016 upper limit">Stecker 2016 upper limit</option> </param> </when> <when value="Generate_figures"> <param name="src_name" type="text" value="NGC 1365" label="src_name" optional="false" /> <param name="z_start" type="float" value="0" label="z_start" optional="false" /> <param name="Npart" type="integer" value="2000" label="Npart" min="1" max="100000" optional="false" /> <param name="particle_type" type="select" label="particle_type" optional="false"> <option value="electron">electron</option> <option value="gamma" selected="true">gamma</option> <option value="proton">proton</option> </param> <param name="Emax" type="float" value="30" label="Emax (unit: TeV)" optional="false" /> <param name="Emin" type="float" value="0.01" label="Emin (unit: TeV)" optional="false" /> <param name="EminSource" type="float" value="1.0" label="EminSource (unit: TeV)" optional="false" /> <param name="Gamma" type="float" value="2.0" label="Gamma" optional="false" /> <param name="EGMF_fG" type="float" value="10" label="EGMF_fG" optional="false" /> <param name="lmaxEGMF_Mpc" type="float" value="5" label="lmaxEGMF_Mpc" optional="false" /> <param name="jet_half_size" type="float" value="5.0" label="jet_half_size (unit: deg)" optional="false" /> <param name="jet_direction" type="float" value="0.0" label="jet_direction (unit: deg)" optional="false" /> <param name="psf" type="float" value="1.0" label="psf (unit: deg)" optional="false" /> <param name="window_size_RA" type="float" value="2.0" label="window_size_RA (unit: deg)" optional="false" /> <param name="window_size_DEC" type="float" value="1.0" label="window_size_DEC (unit: deg)" optional="false" /> <param name="EBL" type="select" label="EBL" optional="false"> <option value="Franceschini 2017" selected="true">Franceschini 2017</option> <option value="Inoue 2012 Baseline">Inoue 2012 Baseline</option> <option value="Inoue 2012 lower limit">Inoue 2012 lower limit</option> <option value="Inoue 2012 upper limit">Inoue 2012 upper limit</option> <option value="Stecker 2016 lower limit">Stecker 2016 lower limit</option> <option value="Stecker 2016 upper limit">Stecker 2016 upper limit</option> </param> </when> </conditional> </inputs> <outputs> <data label="${tool.name} -> Generate_events Event_file" name="out_Generate_events_Event_file" format="auto" from_work_dir="Event_file_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_events'</filter> </data> <data label="${tool.name} -> Generate_figures spectrum_png" name="out_Generate_figures_spectrum_png" format="auto" from_work_dir="spectrum_png_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> <data label="${tool.name} -> Generate_figures light_curve_png" name="out_Generate_figures_light_curve_png" format="auto" from_work_dir="light_curve_png_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> <data label="${tool.name} -> Generate_figures total_spectrum_table" name="out_Generate_figures_total_spectrum_table" format="auto" from_work_dir="total_spectrum_table_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> <data label="${tool.name} -> Generate_figures psf_spectrum_table" name="out_Generate_figures_psf_spectrum_table" format="auto" from_work_dir="psf_spectrum_table_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> <data label="${tool.name} -> Generate_figures lc_result" name="out_Generate_figures_lc_result" format="auto" from_work_dir="lc_result_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> <data label="${tool.name} -> Generate_figures spectrum" name="out_Generate_figures_spectrum" format="auto" from_work_dir="spectrum_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> <data label="${tool.name} -> Generate_figures spectrum_rotated" name="out_Generate_figures_spectrum_rotated" format="auto" from_work_dir="spectrum_rotated_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> <data label="${tool.name} -> Generate_figures map3d" name="out_Generate_figures_map3d" format="auto" from_work_dir="map3d_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> <data label="${tool.name} -> Generate_figures map4d" name="out_Generate_figures_map4d" format="auto" from_work_dir="map4d_galaxy.output"> <filter>C_data_product_['DPselector_'] == 'Generate_figures'</filter> </data> </outputs> <tests> <test expect_num_outputs="1"> <conditional name="C_data_product_"> <param name="DPselector_" value="Generate_events" /> <param name="src_name" value="1ES 1215+303" /> <param name="z_start" value="0.13" /> <param name="Npart" value="10000" /> <param name="particle_type" value="gamma" /> <param name="Emax" value="50" /> <param name="Emin" value="0.01" /> <param name="EminSource" value="0.01" /> <param name="Gamma" value="2.0" /> <param name="EGMF_fG" value="100" /> <param name="lmaxEGMF_Mpc" value="5" /> <param name="jet_half_size" value="180.0" /> <param name="jet_direction" value="0.0" /> <param name="psf" value="180.0" /> <param name="window_size_RA" value="4.0" /> <param name="window_size_DEC" value="4.0" /> <param name="EBL" value="Franceschini 2017" /> </conditional> <assert_stdout> <has_text text="*** Job finished successfully ***" /> </assert_stdout> </test> <test expect_num_outputs="9"> <conditional name="C_data_product_"> <param name="DPselector_" value="Generate_figures" /> <param name="src_name" value="NGC 1365" /> <param name="z_start" value="0" /> <param name="Npart" value="2000" /> <param name="particle_type" value="gamma" /> <param name="Emax" value="30" /> <param name="Emin" value="0.01" /> <param name="EminSource" value="1.0" /> <param name="Gamma" value="2.0" /> <param name="EGMF_fG" value="10" /> <param name="lmaxEGMF_Mpc" value="5" /> <param name="jet_half_size" value="5.0" /> <param name="jet_direction" value="0.0" /> <param name="psf" value="1.0" /> <param name="window_size_RA" value="2.0" /> <param name="window_size_DEC" value="1.0" /> <param name="EBL" value="Franceschini 2017" /> </conditional> <assert_stdout> <has_text text="*** Job finished successfully ***" /> </assert_stdout> </test> </tests> <help>CRbeam ====== This service provides simulation [1] of electron-photon cascade propagation in the intergalactic space. The simulation accounts for the interactions of photons and electrons with extragalactic background light (EBL) and magnetic field. As a first step and main part of simulation the code traces trajectories of every particle and records it’s position and momentum at *z=0* assuming that initially particles were emitted at fixed redshift *z_start* with given power law spectrum in the direction of *z*-axis. The source jet geometry is then taken into account in the second step by rotating the source image obtained during the first stage within the jet openning angle. This allows to reuse the simulation results for different jet geometries. The tool has two available data products: - list of events - list of figures Both modes have common list of input parameters: *src_name* e.g. ‘GRB221009A’ - optional source name from Simbad database (ignored if *z_start* is given) *z_start* e.g. 0.1 - source redshift or 0 if src_name should be used *Npart* e.g. 100000 - number of particles to simulate *particle_type* - initial particle type, one of “gamma”,“electron” or “proton” *Emax* - maximal energy of particles emitted by the source in TeV *Emin* - minimal energy in TeV of secondary particles to trace in the simulation *EminSource* - minimal energy of particles emitted by the source in TeV. If *EminSourceTeV=EmaxTeV* fixed energy injection is assumed *Gamma* - injection spectrum power low index: dN/dE = E^{-gamma} *EGMF_fG* - amplitude of the intergalactic magnetic field in femtogauss. The Kolmogorov turbulence model is assumed for the magnetic field *lmaxEGMF_Mpc* - maximal scale of the magnetic field turbulence in Mpc *jet_half_size* - jet half size in degrees *jet_direction* - angle in degrees between the jet axis and the direction to the observer *psf* - observer instrument psf in degrees *EBL* - extragalactic background light model to use. Below is the list of models supported: - *Franceschini 2017*, see Ref. [2] - *Stecker 2016 lower limit* : lower limit model from Ref. [3] - *Stecker 2016 upper limit* : upper limit model from Ref. [3] - *Inoue 2012 Baseline* : baseline model from Ref. [4] - *Inoue 2012 lower limit* : lower limit model from Ref. [4] - *Inoue 2012 upper limit* : upper limit model from Ref. [4] - *zero* : CMB only References ---------- [1] O. Kalashev, A. Korochkin, A. Neronov, D. Semikoz, *Astron.Astrophys.* 675 (2023) A132 [2] Alberto Franceschini, Giulia Rodighiero, *Astron.Astrophys.* 603 (2017) A34 [3] Floyd W. Stecker, Sean T. Scully, Matthew A. Malkan, *Astrophys.J.* 827 (2016) [4] Yoshiyuki Inoue et al., *Astrophys.J.* 768 (2013) 197 </help> <citations> <citation type="bibtex">@misc{label, title = {Tool CRbeam}, url = {https://renkulab.io/projects/astronomy/mmoda/crbeam}, author = {Oleg Kalashev and Andrii Neronov}, year = {2024}, note = {} }</citation> </citations> </tool>