Mercurial > repos > astroteam > plot_tools_astro_tool
diff plot_tools_astro_tool.xml @ 0:2b1759ccaa8b draft default tip
planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
| author | astroteam |
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| date | Fri, 25 Apr 2025 21:48:27 +0000 (6 weeks ago) |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_tools_astro_tool.xml Fri Apr 25 21:48:27 2025 +0000 @@ -0,0 +1,270 @@ +<tool id="plot_tools_astro_tool" name="Plot Tools" version="0.0.1+galaxy0" profile="24.0"> + <requirements> + <requirement type="package" version="2.2.3">pandas</requirement> + <requirement type="package" version="3.9.2">matplotlib</requirement> + <requirement type="package" version="5.3">astropy</requirement> + <requirement type="package" version="1.2.37">oda-api</requirement> + <requirement type="package" version="1.2">gammapy</requirement> + <requirement type="package" version="9.1.0">ipython</requirement> + </requirements> + <command detect_errors="exit_code">python '$__tool_directory__/${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="light_curve" selected="true">light_curve</option> + <option value="spectrum" selected="false">spectrum</option> + <option value="sky_plot" selected="false">sky_plot</option> + </param> + <when value="light_curve"> + <param name="fn" type="data" label="fn" format="data" optional="false" /> + <param name="skiprows" type="integer" value="0" label="skiprows" optional="false" /> + <param name="sep" type="select" label="sep" optional="false"> + <option value="comma">comma</option> + <option value="semicolon">semicolon</option> + <option value="space">space</option> + <option value="tab">tab</option> + <option value="whitespace" selected="true">whitespace</option> + </param> + <param name="column" type="text" value="T" label="column" optional="false" /> + <param name="weight_col" type="text" value="" label="weight_col" optional="false" /> + <param name="binning" type="select" label="binning" optional="false"> + <option value="linear">linear</option> + <option value="logarithmic" selected="true">logarithmic</option> + </param> + <param name="minval" type="float" value="0" label="minval" optional="false" /> + <param name="maxval" type="float" value="0" label="maxval" optional="false" /> + <param name="use_quantile_values" type="boolean" label="use_quantile_values" optional="false" /> + <param name="nbins" type="integer" value="15" label="nbins" optional="false" /> + <param name="xlabel" type="text" value="time, s" label="xlabel" optional="false" /> + <param name="ylabel" type="text" value="Ncounts" label="ylabel" optional="false" /> + <param name="plot_mode" type="select" label="plot_mode" optional="false"> + <option value="counts">counts</option> + <option value="flux" selected="true">flux</option> + </param> + </when> + <when value="spectrum"> + <param name="fn" type="data" label="fn" format="data" optional="false" /> + <param name="skiprows" type="integer" value="0" label="skiprows" optional="false" /> + <param name="sep" type="select" label="sep" optional="false"> + <option value="auto">auto</option> + <option value="comma">comma</option> + <option value="semicolon">semicolon</option> + <option value="tab">tab</option> + <option value="whitespace" selected="true">whitespace</option> + </param> + <param name="column" type="text" value="c1" label="column" optional="false" /> + <param name="weight_col" type="text" value="" label="weight_col" optional="false" /> + <param name="binning" type="select" label="binning" optional="false"> + <option value="linear">linear</option> + <option value="logarithmic" selected="true">logarithmic</option> + </param> + <param name="minval" type="float" value="0" label="minval" optional="false" /> + <param name="maxval" type="float" value="0" label="maxval" optional="false" /> + <param name="nbins" type="integer" value="15" label="nbins" optional="false" /> + <param name="xlabel" type="text" value="Energy, [eV]" label="xlabel" optional="false" /> + <param name="ylabel" type="text" value="Flux E^2, [eV]" label="ylabel" optional="false" /> + <param name="spec_power" type="float" value="2.0" label="spec_power" optional="false" /> + </when> + <when value="sky_plot"> + <param name="fn" type="data" label="fn" format="data" optional="false" /> + <param name="skiprows" type="integer" value="0" label="skiprows" optional="false" /> + <param name="sep" type="select" label="sep" optional="false"> + <option value="auto">auto</option> + <option value="comma">comma</option> + <option value="semicolon">semicolon</option> + <option value="tab">tab</option> + <option value="whitespace" selected="true">whitespace</option> + </param> + <param name="ra_col" type="text" value="c3" label="ra_col" optional="false" /> + <param name="dec_col" type="text" value="c4" label="dec_col" optional="false" /> + <param name="weight_col" type="text" value="" label="weight_col" optional="false" /> + <param name="binsz" type="float" value="0.02" label="binsz" optional="false" /> + <param name="window_size_RA" type="float" value="2.0" label="window_size_RA" optional="false" /> + <param name="window_size_DEC" type="float" value="2.0" label="window_size_DEC" optional="false" /> + </when> + </conditional> + </inputs> + <outputs> + <data label="${tool.name} -> light_curve histogram_data" name="out_light_curve_histogram_data" format="auto" from_work_dir="histogram_data_galaxy.output"> + <filter>C_data_product_['DPselector_'] == 'light_curve'</filter> + </data> + <data label="${tool.name} -> light_curve histogram_picture" name="out_light_curve_histogram_picture" format="auto" from_work_dir="histogram_picture_galaxy.output"> + <filter>C_data_product_['DPselector_'] == 'light_curve'</filter> + </data> + <data label="${tool.name} -> spectrum histogram_data" name="out_spectrum_histogram_data" format="auto" from_work_dir="histogram_data_galaxy.output"> + <filter>C_data_product_['DPselector_'] == 'spectrum'</filter> + </data> + <data label="${tool.name} -> spectrum histogram_picture" name="out_spectrum_histogram_picture" format="auto" from_work_dir="histogram_picture_galaxy.output"> + <filter>C_data_product_['DPselector_'] == 'spectrum'</filter> + </data> + <data label="${tool.name} -> sky_plot plot" name="out_sky_plot_plot" format="auto" from_work_dir="plot_galaxy.output"> + <filter>C_data_product_['DPselector_'] == 'sky_plot'</filter> + </data> + <data label="${tool.name} -> sky_plot fits_image" name="out_sky_plot_fits_image" format="auto" from_work_dir="fits_image_galaxy.output"> + <filter>C_data_product_['DPselector_'] == 'sky_plot'</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="2"> + <conditional name="C_data_product_"> + <param name="DPselector_" value="light_curve" /> + <param name="fn" location="https://gitlab.renkulab.io/astronomy/mmoda/plot-tools/-/raw/57cc7b8180fa6c1a286114a9e7b903923f786631/data.tsv" /> + <param name="skiprows" value="0" /> + <param name="sep" value="whitespace" /> + <param name="column" value="T" /> + <param name="weight_col" value="" /> + <param name="binning" value="logarithmic" /> + <param name="minval" value="0" /> + <param name="maxval" value="0" /> + <param name="use_quantile_values" value="False" /> + <param name="nbins" value="15" /> + <param name="xlabel" value="time, s" /> + <param name="ylabel" value="Ncounts" /> + <param name="plot_mode" value="flux" /> + </conditional> + <assert_stdout> + <has_text text="*** Job finished successfully ***" /> + </assert_stdout> + </test> + <test expect_num_outputs="2"> + <conditional name="C_data_product_"> + <param name="DPselector_" value="spectrum" /> + <param name="fn" location="https://gitlab.renkulab.io/astronomy/mmoda/plot-tools/-/raw/57cc7b8180fa6c1a286114a9e7b903923f786631/data.tsv" /> + <param name="skiprows" value="0" /> + <param name="sep" value="whitespace" /> + <param name="column" value="c1" /> + <param name="weight_col" value="" /> + <param name="binning" value="logarithmic" /> + <param name="minval" value="0" /> + <param name="maxval" value="0" /> + <param name="nbins" value="15" /> + <param name="xlabel" value="Energy, [eV]" /> + <param name="ylabel" value="Flux E^2, [eV]" /> + <param name="spec_power" value="2.0" /> + </conditional> + <assert_stdout> + <has_text text="*** Job finished successfully ***" /> + </assert_stdout> + </test> + <test expect_num_outputs="2"> + <conditional name="C_data_product_"> + <param name="DPselector_" value="sky_plot" /> + <param name="fn" location="https://gitlab.renkulab.io/astronomy/mmoda/plot-tools/-/raw/57cc7b8180fa6c1a286114a9e7b903923f786631/data.tsv" /> + <param name="skiprows" value="0" /> + <param name="sep" value="whitespace" /> + <param name="ra_col" value="c3" /> + <param name="dec_col" value="c4" /> + <param name="weight_col" value="" /> + <param name="binsz" value="0.02" /> + <param name="window_size_RA" value="2.0" /> + <param name="window_size_DEC" value="2.0" /> + </conditional> + <assert_stdout> + <has_text text="*** Job finished successfully ***" /> + </assert_stdout> + </test> + </tests> + <help>Plot Tools +========== + +Set of tools for astronomical data visualization + +- sky_plot - visualize sky map using set of events as input +- light_cure - calculate and visualize light curve from a set of evebts +- spectrum - calculate energy spectrum using set of events as input + +Parameters +---------- + +common parameters +~~~~~~~~~~~~~~~~~ + +fn - input data file + +skiprows - number of rows to skip + +sep - separator value + +sky_plot parameters +~~~~~~~~~~~~~~~~~~~ + +ra_col - RA column (either column name of string cXX, where XX >= 1 is +column number) + +dec_col - DEC column (either column name of string cXX, where XX >= 1 is +column number) + +weight_col - weight column (either column name of string cXX, where XX +>= 1 is column number, or empty string if data doesn’t contain weights) + +binsz - bin size in degrees + +window_size_RA - size of window (RA) in degrees + +window_size_DEC - size of window (DEC) in degrees + +light_cure parameters +~~~~~~~~~~~~~~~~~~~~~ + +column - time column (either column name of string cXX, where XX >= 1 is +column number) + +weight_col - weight column (either column name of string cXX, where XX +>= 1 is column number, or empty string if data doesn’t contain weights) + +binning - binning type (‘logarithmic’ or “linear”) + +minval - minimal value (use 0 to infer from data) + +maxval - maximal value (use 0 to infer from data) + +use_quantile_values - interpret minval and maxval as quantiles + +nbins=15 - number of bins + +xlabel - plot x-label + +ylabel - plot y-label + +plot_mode - plotting mode (“counts” or “flux”) + +spectrum parameters +~~~~~~~~~~~~~~~~~~~ + +column - energy column (either column name of string cXX, where XX >= 1 +is column number) + +weight_col- weight column (either column name of string cXX, where XX >= +1 is column number, or empty string if data doesn’t contain weights) + +binning - binning type (‘logarithmic’ or “linear”) + +minval - minimal value (use 0 to infer from data) + +maxval - maximal value (use 0 to infer from data) + +nbins - number of bins + +xlabel - plot x-label + +ylabel - plot y-label + +spec_power - multiply spectrum by energy in this power on plot +</help> + <citations> + <citation type="bibtex">@misc{label, + title = {Tool repository}, + url = {https://renkulab.io/projects/astronomy/mmoda/plot-tools}, + author = {Oleg Kalashev}, + year = {2024}, + note = {} + }</citation> + </citations> +</tool> \ No newline at end of file