Mercurial > repos > astroteam > crbeam_astro_tool
diff crbeam_astro_tool.xml @ 0:f40d05521dca draft default tip
planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
| author | astroteam |
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| date | Fri, 25 Apr 2025 19:33:20 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crbeam_astro_tool.xml Fri Apr 25 19:33:20 2025 +0000 @@ -0,0 +1,260 @@ +<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> \ No newline at end of file