diff --git a/biobb_dna/backbone/bipopulations.py b/biobb_dna/backbone/bipopulations.py index 89a1fac5..d799be03 100755 --- a/biobb_dna/backbone/bipopulations.py +++ b/biobb_dna/backbone/bipopulations.py @@ -19,6 +19,7 @@ class BIPopulations(BiobbObject): """ | biobb_dna BIPopulations | Calculate BI/BII populations from epsilon and zeta parameters. + | Calculate BI/BII populations from epsilon and zeta parameters. Args: input_epsilC_path (str): Path to .ser file for helical parameter 'epsilC'. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/backbone/canonicalag.py b/biobb_dna/backbone/canonicalag.py index f0ca5a6f..8fcf7954 100755 --- a/biobb_dna/backbone/canonicalag.py +++ b/biobb_dna/backbone/canonicalag.py @@ -19,6 +19,7 @@ class CanonicalAG(BiobbObject): """ | biobb_dna CanonicalAG | Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters. + | Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters. Args: input_alphaC_path (str): Path to .ser file for helical parameter 'alphaC'. File type: input. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/backbone/puckering.py b/biobb_dna/backbone/puckering.py index f6c7c028..0e3237f3 100755 --- a/biobb_dna/backbone/puckering.py +++ b/biobb_dna/backbone/puckering.py @@ -19,6 +19,7 @@ class Puckering(BiobbObject): """ | biobb_dna Puckering | Calculate Puckering from phase parameters. + | Calculate North/East/West/South distribution of sugar puckering backbone torsions. Args: input_phaseC_path (str): Path to .ser file for helical parameter 'phaseC'. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/curvesplus/biobb_canal.py b/biobb_dna/curvesplus/biobb_canal.py index 16b2bb2a..f01c3f43 100755 --- a/biobb_dna/curvesplus/biobb_canal.py +++ b/biobb_dna/curvesplus/biobb_canal.py @@ -17,6 +17,7 @@ class Canal(BiobbObject): """ | biobb_dna Canal | Wrapper for the Canal executable that is part of the Curves+ software suite. + | The Canal program is used to analyze the curvature of DNA structures. Args: input_cda_file (str): Input cda file, from Cur+ output. File type: input. `Sample file `_. Accepted formats: cda (edam:format_2330). diff --git a/biobb_dna/curvesplus/biobb_canion.py b/biobb_dna/curvesplus/biobb_canion.py index ac8b1c2a..3f560b09 100755 --- a/biobb_dna/curvesplus/biobb_canion.py +++ b/biobb_dna/curvesplus/biobb_canion.py @@ -16,6 +16,7 @@ class Canion(BiobbObject): """ | biobb_dna Canion | Wrapper for the Canion executable that is part of the Curves+ software suite. + | Analyzes the trajectory of ions around a DNA molecule. Args: input_cdi_path (str): Trajectory input file. File type: input. `Sample file `_. Accepted formats: cdi (edam:format_2330). diff --git a/biobb_dna/curvesplus/biobb_curves.py b/biobb_dna/curvesplus/biobb_curves.py index 333868cc..1f091489 100755 --- a/biobb_dna/curvesplus/biobb_curves.py +++ b/biobb_dna/curvesplus/biobb_curves.py @@ -16,6 +16,7 @@ class Curves(BiobbObject): """ | biobb_dna Curves | Wrapper for the Cur+ executable that is part of the Curves+ software suite. + | The Cur+ program is used to analyze the structure of nucleic acids and their complexes. Args: input_struc_path (str): Trajectory or PDB input file. File type: input. `Sample file `_. Accepted formats: trj (edam:format_3910), pdb (edam:format_1476), netcdf (edam:format_3650), nc (edam:format_3650). diff --git a/biobb_dna/dna/dna_averages.py b/biobb_dna/dna/dna_averages.py index 3a973f30..c0d9bd02 100755 --- a/biobb_dna/dna/dna_averages.py +++ b/biobb_dna/dna/dna_averages.py @@ -19,6 +19,7 @@ class HelParAverages(BiobbObject): """ | biobb_dna HelParAverages | Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one. + | Calculate average values for each base pair and save them in a .csv file. Args: input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/dna/dna_bimodality.py b/biobb_dna/dna/dna_bimodality.py index 1e660fcc..9ffa80bc 100755 --- a/biobb_dna/dna/dna_bimodality.py +++ b/biobb_dna/dna/dna_bimodality.py @@ -24,6 +24,7 @@ class HelParBimodality(BiobbObject): """ | biobb_dna HelParBimodality | Determine binormality/bimodality from a helical parameter series dataset. + | Determine binormality/bimodality from a helical parameter series dataset. Args: input_csv_file (str): Path to .csv file with helical parameter series. If `input_zip_file` is passed, this should be just the filename of the .csv file inside .zip. File type: input. `Sample file `_. Accepted formats: csv (edam:format_3752). diff --git a/biobb_dna/dna/dna_timeseries.py b/biobb_dna/dna/dna_timeseries.py index 16ada3c0..5e50928d 100755 --- a/biobb_dna/dna/dna_timeseries.py +++ b/biobb_dna/dna/dna_timeseries.py @@ -20,6 +20,7 @@ class HelParTimeSeries(BiobbObject): """ | biobb_dna HelParTimeSeries | Created time series and histogram plots for each base pair from a helical parameter series file. + | The helical parameter series file is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. Args: input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/interbp_correlations/interbpcorr.py b/biobb_dna/interbp_correlations/interbpcorr.py index 19a6c25c..9517a21f 100755 --- a/biobb_dna/interbp_correlations/interbpcorr.py +++ b/biobb_dna/interbp_correlations/interbpcorr.py @@ -21,6 +21,7 @@ class InterBasePairCorrelation(BiobbObject): """ | biobb_dna InterBasePairCorrelation | Calculate correlation between all base pairs of a single sequence and for a single helical parameter. + | Calculate correlation between neighboring base pairs and pairs of helical parameters. Args: input_filename_shift (str): Path to .ser file with data for helical parameter 'shift'. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/interbp_correlations/interhpcorr.py b/biobb_dna/interbp_correlations/interhpcorr.py index f4ac0efd..4980b7b0 100755 --- a/biobb_dna/interbp_correlations/interhpcorr.py +++ b/biobb_dna/interbp_correlations/interhpcorr.py @@ -18,6 +18,7 @@ class InterHelParCorrelation(BiobbObject): """ | biobb_dna InterHelParCorrelation | Calculate correlation between helical parameters for a single inter-base pair. + | Calculate correlation between helical parameters for a single inter-base pair. Args: input_filename_shift (str): Path to .csv file with data for helical parameter 'shift'. File type: input. `Sample file `_. Accepted formats: csv (edam:format_3752). diff --git a/biobb_dna/interbp_correlations/interseqcorr.py b/biobb_dna/interbp_correlations/interseqcorr.py index 9430ae6d..a5cb27a4 100755 --- a/biobb_dna/interbp_correlations/interseqcorr.py +++ b/biobb_dna/interbp_correlations/interseqcorr.py @@ -19,6 +19,7 @@ class InterSequenceCorrelation(BiobbObject): """ | biobb_dna InterSequenceCorrelation | Calculate correlation between all base pairs of a single sequence and for a single helical parameter. + | Calculate correlation between all base pairs of a single sequence and for a single helical parameter. Args: input_ser_path (str): Path to .ser file with data for single helical parameter. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/intrabp_correlations/intrabpcorr.py b/biobb_dna/intrabp_correlations/intrabpcorr.py index 0f8445c5..8856939d 100755 --- a/biobb_dna/intrabp_correlations/intrabpcorr.py +++ b/biobb_dna/intrabp_correlations/intrabpcorr.py @@ -21,6 +21,7 @@ class IntraBasePairCorrelation(BiobbObject): """ | biobb_dna IntraBasePairCorrelation | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter. + | Calculate correlation between neighboring base pairs and pairs of helical parameters. Args: input_filename_shear (str): Path to .ser file with data for helical parameter 'shear'. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/intrabp_correlations/intrahpcorr.py b/biobb_dna/intrabp_correlations/intrahpcorr.py index 55d3ae35..bdf6cd73 100755 --- a/biobb_dna/intrabp_correlations/intrahpcorr.py +++ b/biobb_dna/intrabp_correlations/intrahpcorr.py @@ -18,6 +18,7 @@ class IntraHelParCorrelation(BiobbObject): """ | biobb_dna IntraHelParCorrelation | Calculate correlation between helical parameters for a single intra-base pair. + | Calculate correlation between helical parameters for a single intra-base pair. Args: input_filename_shear (str): Path to .csv file with data for helical parameter 'shear'. File type: input. `Sample file `_. Accepted formats: csv (edam:format_3752). diff --git a/biobb_dna/intrabp_correlations/intraseqcorr.py b/biobb_dna/intrabp_correlations/intraseqcorr.py index 8d13dfb8..013d6753 100755 --- a/biobb_dna/intrabp_correlations/intraseqcorr.py +++ b/biobb_dna/intrabp_correlations/intraseqcorr.py @@ -19,6 +19,7 @@ class IntraSequenceCorrelation(BiobbObject): """ | biobb_dna IntraSequenceCorrelation | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter. + | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter. Args: input_ser_path (str): Path to .ser file with data for single helical parameter. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/json_schemas/average_stiffness.json b/biobb_dna/json_schemas/average_stiffness.json index aa21c5de..960f5be8 100644 --- a/biobb_dna/json_schemas/average_stiffness.json +++ b/biobb_dna/json_schemas/average_stiffness.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/average_stiffness", "name": "biobb_dna AverageStiffness", "title": "Calculate average stiffness constants for each base pair of a trajectory's series.", - "description": null, + "description": "Calculate the average stiffness constants for each base pair of a trajectory's series. The input is a .ser file with the helical parameter values for each base/basepair. The output is a .csv file with the average stiffness constants for each base pair and a .jpg file with a plot of the average stiffness constants for each base pair.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/basepair_stiffness.json b/biobb_dna/json_schemas/basepair_stiffness.json index d18ddd28..1213e3e6 100644 --- a/biobb_dna/json_schemas/basepair_stiffness.json +++ b/biobb_dna/json_schemas/basepair_stiffness.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/basepair_stiffness", "name": "biobb_dna BPStiffness", "title": "Calculate stiffness constants matrix between all six helical parameters for a single base pair step.", - "description": null, + "description": "Calculate stiffness constants matrix between all six helical parameters for a single base pair step.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/biobb_canal.json b/biobb_dna/json_schemas/biobb_canal.json index 4354b94f..46530871 100644 --- a/biobb_dna/json_schemas/biobb_canal.json +++ b/biobb_dna/json_schemas/biobb_canal.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/biobb_canal", "name": "biobb_dna Canal", "title": "Wrapper for the Canal executable that is part of the Curves+ software suite.", - "description": null, + "description": "The Canal program is used to analyze the curvature of DNA structures.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/biobb_canion.json b/biobb_dna/json_schemas/biobb_canion.json index 38694eea..dd50044a 100644 --- a/biobb_dna/json_schemas/biobb_canion.json +++ b/biobb_dna/json_schemas/biobb_canion.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/biobb_canion", "name": "biobb_dna Canion", "title": "Wrapper for the Canion executable that is part of the Curves+ software suite.", - "description": null, + "description": "Analyzes the trajectory of ions around a DNA molecule.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/biobb_curves.json b/biobb_dna/json_schemas/biobb_curves.json index 5f14d3f1..b056aaf2 100644 --- a/biobb_dna/json_schemas/biobb_curves.json +++ b/biobb_dna/json_schemas/biobb_curves.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/biobb_curves", "name": "biobb_dna Curves", "title": "Wrapper for the Cur+ executable that is part of the Curves+ software suite.", - "description": null, + "description": "The Cur+ program is used to analyze the structure of nucleic acids and their complexes.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/bipopulations.json b/biobb_dna/json_schemas/bipopulations.json index 5b59c3d1..7cc5580a 100644 --- a/biobb_dna/json_schemas/bipopulations.json +++ b/biobb_dna/json_schemas/bipopulations.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/bipopulations", "name": "biobb_dna BIPopulations", "title": "Calculate BI/BII populations from epsilon and zeta parameters.", - "description": null, + "description": "Calculate BI/BII populations from epsilon and zeta parameters.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/canonicalag.json b/biobb_dna/json_schemas/canonicalag.json index 230c45f8..2a740e29 100644 --- a/biobb_dna/json_schemas/canonicalag.json +++ b/biobb_dna/json_schemas/canonicalag.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/canonicalag", "name": "biobb_dna CanonicalAG", "title": "Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters.", - "description": null, + "description": "Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/dna_averages.json b/biobb_dna/json_schemas/dna_averages.json index 4d693dac..7b516b51 100644 --- a/biobb_dna/json_schemas/dna_averages.json +++ b/biobb_dna/json_schemas/dna_averages.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/dna_averages", "name": "biobb_dna HelParAverages", "title": "Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one.", - "description": null, + "description": "Calculate average values for each base pair and save them in a .csv file.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/dna_bimodality.json b/biobb_dna/json_schemas/dna_bimodality.json index 0ad7d1a7..72cdfd95 100644 --- a/biobb_dna/json_schemas/dna_bimodality.json +++ b/biobb_dna/json_schemas/dna_bimodality.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/dna_bimodality", "name": "biobb_dna HelParBimodality", "title": "Determine binormality/bimodality from a helical parameter series dataset.", - "description": null, + "description": "Determine binormality/bimodality from a helical parameter series dataset.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/dna_timeseries.json b/biobb_dna/json_schemas/dna_timeseries.json index 0e86da5b..37b7f33d 100644 --- a/biobb_dna/json_schemas/dna_timeseries.json +++ b/biobb_dna/json_schemas/dna_timeseries.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/dna_timeseries", "name": "biobb_dna HelParTimeSeries", "title": "Created time series and histogram plots for each base pair from a helical parameter series file.", - "description": null, + "description": "The helical parameter series file is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/interbpcorr.json b/biobb_dna/json_schemas/interbpcorr.json index 3b5edc6e..644b8760 100644 --- a/biobb_dna/json_schemas/interbpcorr.json +++ b/biobb_dna/json_schemas/interbpcorr.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/interbpcorr", "name": "biobb_dna InterBasePairCorrelation", "title": "Calculate correlation between all base pairs of a single sequence and for a single helical parameter.", - "description": null, + "description": "Calculate correlation between neighboring base pairs and pairs of helical parameters.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/interhpcorr.json b/biobb_dna/json_schemas/interhpcorr.json index 0d09dc82..4285afac 100644 --- a/biobb_dna/json_schemas/interhpcorr.json +++ b/biobb_dna/json_schemas/interhpcorr.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/interhpcorr", "name": "biobb_dna InterHelParCorrelation", "title": "Calculate correlation between helical parameters for a single inter-base pair.", - "description": null, + "description": "Calculate correlation between helical parameters for a single inter-base pair.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/interseqcorr.json b/biobb_dna/json_schemas/interseqcorr.json index 551158b5..f13533f5 100644 --- a/biobb_dna/json_schemas/interseqcorr.json +++ b/biobb_dna/json_schemas/interseqcorr.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/interseqcorr", "name": "biobb_dna InterSequenceCorrelation", "title": "Calculate correlation between all base pairs of a single sequence and for a single helical parameter.", - "description": null, + "description": "Calculate correlation between all base pairs of a single sequence and for a single helical parameter.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/intrabpcorr.json b/biobb_dna/json_schemas/intrabpcorr.json index 56606175..38163546 100644 --- a/biobb_dna/json_schemas/intrabpcorr.json +++ b/biobb_dna/json_schemas/intrabpcorr.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/intrabpcorr", "name": "biobb_dna IntraBasePairCorrelation", "title": "Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.", - "description": null, + "description": "Calculate correlation between neighboring base pairs and pairs of helical parameters.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/intrahpcorr.json b/biobb_dna/json_schemas/intrahpcorr.json index 7a3e814d..302871c2 100644 --- a/biobb_dna/json_schemas/intrahpcorr.json +++ b/biobb_dna/json_schemas/intrahpcorr.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/intrahpcorr", "name": "biobb_dna IntraHelParCorrelation", "title": "Calculate correlation between helical parameters for a single intra-base pair.", - "description": null, + "description": "Calculate correlation between helical parameters for a single intra-base pair.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/intraseqcorr.json b/biobb_dna/json_schemas/intraseqcorr.json index 1b303233..4c0bd265 100644 --- a/biobb_dna/json_schemas/intraseqcorr.json +++ b/biobb_dna/json_schemas/intraseqcorr.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/intraseqcorr", "name": "biobb_dna IntraSequenceCorrelation", "title": "Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.", - "description": null, + "description": "Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/json_schemas/puckering.json b/biobb_dna/json_schemas/puckering.json index 47c86ec0..6840ed0d 100644 --- a/biobb_dna/json_schemas/puckering.json +++ b/biobb_dna/json_schemas/puckering.json @@ -3,7 +3,7 @@ "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/puckering", "name": "biobb_dna Puckering", "title": "Calculate Puckering from phase parameters.", - "description": null, + "description": "Calculate North/East/West/South distribution of sugar puckering backbone torsions.", "type": "object", "info": { "wrapped_software": { diff --git a/biobb_dna/stiffness/average_stiffness.py b/biobb_dna/stiffness/average_stiffness.py index db99ee31..4e079570 100755 --- a/biobb_dna/stiffness/average_stiffness.py +++ b/biobb_dna/stiffness/average_stiffness.py @@ -20,6 +20,7 @@ class AverageStiffness(BiobbObject): """ | biobb_dna AverageStiffness | Calculate average stiffness constants for each base pair of a trajectory's series. + | Calculate the average stiffness constants for each base pair of a trajectory's series. The input is a .ser file with the helical parameter values for each base/basepair. The output is a .csv file with the average stiffness constants for each base pair and a .jpg file with a plot of the average stiffness constants for each base pair. Args: input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/stiffness/basepair_stiffness.py b/biobb_dna/stiffness/basepair_stiffness.py index 4310281e..1b43dba0 100755 --- a/biobb_dna/stiffness/basepair_stiffness.py +++ b/biobb_dna/stiffness/basepair_stiffness.py @@ -19,6 +19,7 @@ class BPStiffness(BiobbObject): """ | biobb_dna BPStiffness | Calculate stiffness constants matrix between all six helical parameters for a single base pair step. + | Calculate stiffness constants matrix between all six helical parameters for a single base pair step. Args: input_filename_shift (str): Path to csv file with data for helical parameter 'shift'. File type: input. `Sample file `_. Accepted formats: csv (edam:format_3752)