global_properties:
  working_dir_path: biobb_wf_dna_helparms
  can_write_console_log: False

step1_biobb_curves:
  tool: biobb_curves
  paths:
    input_struc_path: /data/trajectory.nc
    input_top_path: /data/topology.top
    output_lis_path: curves.out.lis
    output_cda_path: curves.out.cda
    output_zip_path: curves.out.zip
  properties:
    s1range: '1:12'

step2_biobb_canal:
  tool: biobb_canal
  paths:
    input_cda_file: dependency/step1_biobb_curves/output_cda_path
    input_lis_file: dependency/step1_biobb_curves/output_lis_path
    output_zip_path: canal.out.zip
  properties:
    series: true
    histo: true

step4_dna_averages_base_pair_step:
  tool: dna_averages
  paths:
    input_ser_path: input.ser
    output_csv_path: output.averages.csv
    output_jpg_path: output.averages.jpg
  properties:
    helpar_name: helpar 
    sequence: CGCGAATTCGCG

step5_dna_averages_base_pair:
  tool: dna_averages
  paths:
    input_ser_path: input.ser
    output_csv_path: output.averages.csv
    output_jpg_path: output.averages.jpg
  properties:
    helpar_name: helpar 
    sequence: CGCGAATTCGCG

step6_dna_averages_axis_base_pairs:
  tool: dna_averages
  paths:
    input_ser_path: input.ser
    output_csv_path: output.averages.csv
    output_jpg_path: output.averages.jpg
  properties:
    helpar_name: helpar 
    sequence: CGCGAATTCGCG

step7_dna_averages_grooves:
  tool: dna_averages
  paths:
    input_ser_path: input.ser
    output_csv_path: output.averages.csv
    output_jpg_path: output.averages.jpg
  properties:
    helpar_name: helpar 
    sequence: CGCGAATTCGCG

step8_puckering:
  tool: puckering
  paths:
    input_phaseC_path: input.ser 
    input_phaseW_path: input.ser 
    output_csv_path: puckering.averages.csv
    output_jpg_path: puckering.averages.jpg
  properties:
    sequence: CGCGAATTCGCG

step9_canonicalag:
  tool: canonicalag
  paths:
    input_alphaC_path: input.ser
    input_alphaW_path: input.ser
    input_gammaC_path: input.ser
    input_gammaW_path: input.ser
    output_csv_path: alphagamma.averages.csv
    output_jpg_path: alphagamma.averages.jpg
  properties:
    sequence: CGCGAATTCGCG

step10_bipopulations:
  tool: bipopulations
  paths:
    input_epsilC_path: input.ser
    input_epsilW_path: input.ser
    input_zetaC_path: input.ser
    input_zetaW_path: input.ser
    output_csv_path: bIbII.averages.csv
    output_jpg_path: bIbII.averages.jpg
  properties:
    sequence: CGCGAATTCGCG

step12_dna_timeseries_base_pair_step:
  tool: dna_timeseries
  paths:
    input_ser_path: input.ser
    output_zip_path: timeseries.zip
  properties:
    helpar_name: helpar
    sequence: CGCGAATTCGCG

step13_dna_timeseries_base_pair:
  tool: dna_timeseries
  paths:
    input_ser_path: input.ser
    output_zip_path: timeseries.zip
  properties:
    helpar_name: helpar
    sequence: CGCGAATTCGCG

step14_dna_timeseries_axis_base_pairs:
  tool: dna_timeseries
  paths:
    input_ser_path: input.ser
    output_zip_path: timeseries.zip
  properties:
    helpar_name: helpar
    sequence: CGCGAATTCGCG

step15_dna_timeseries_grooves:
  tool: dna_timeseries
  paths:
    input_ser_path: input.ser
    output_zip_path: timeseries.zip
  properties:
    helpar_name: helpar
    sequence: CGCGAATTCGCG

step16_dna_timeseries_backbone_torsions:
  tool: dna_timeseries
  paths:
    input_ser_path: input.ser
    output_zip_path: timeseries.zip
  properties:
    helpar_name: helpar
    sequence: CGCGAATTCGCG

step18_basepair_stiffness:
  tool: basepair_stiffness
  paths:
    input_filename_shift: series_shift.csv
    input_filename_slide: series_slide.csv
    input_filename_rise: series_rise.csv
    input_filename_tilt: series_tilt.csv
    input_filename_roll: series_roll.csv
    input_filename_twist: series_twist.csv
    output_csv_path: stiffness_bps.csv
    output_jpg_path: stiffness_bps.jpg

step19_dna_bimodality:
  tool: dna_bimodality
  paths:
    input_csv_file: series.csv
    output_csv_path: bimodality.csv
    output_jpg_path: bimodality.jpg
  properties:
    max_iter: 500

step20_intraseqcorr:
  tool: intraseqcorr
  paths:
    input_ser_path: input.ser
    output_csv_path: intrabp_correlation.csv
    output_jpg_path: intrabp_correlation.jpg
  properties:
    sequence: CGCGAATTCGCG

step21_interseqcorr:
  tool: interseqcorr
  paths:
    input_ser_path: input.ser
    output_csv_path: interbp_correlation.csv
    output_jpg_path: interbp_correlation.jpg
  properties:
    sequence: CGCGAATTCGCG

step22_intrahpcorr:
  tool: intrahpcorr
  paths:
    input_filename_shear: series_shear.csv
    input_filename_stretch: series_stretch.csv
    input_filename_stagger: series_stagger.csv
    input_filename_buckle: series_buckle.csv
    input_filename_propel: series_propel.csv
    input_filename_opening: series_opening.csv
    output_csv_path: helpar_bp_correlation.csv 
    output_jpg_path: helpar_bp_correlation.jpg 

step23_interhpcorr:
  tool: interhpcorr
  paths:
    input_filename_shift: series_shift.csv
    input_filename_slide: series_slide.csv
    input_filename_rise: series_rise.csv
    input_filename_tilt: series_tilt.csv
    input_filename_roll: series_roll.csv
    input_filename_twist: series_twist.csv
    output_csv_path: helpar_bps_correlation.csv 
    output_jpg_path: helpar_bps_correlation.jpg 

step24_intrabpcorr:
  tool: intrabpcorr
  paths:
    input_filename_shear: series_shear.csv
    input_filename_stretch: series_stretch.csv
    input_filename_stagger: series_stagger.csv
    input_filename_buckle: series_buckle.csv
    input_filename_propel: series_propel.csv
    input_filename_opening: series_opening.csv
    output_csv_path: bp_correlation.csv 
    output_jpg_path: bp_correlation.jpg 
  properties:
    sequence: CGCGAATTCGCG

step25_interbpcorr:
  tool: interbpcorr
  paths:
    input_filename_shift: series_shift.csv
    input_filename_slide: series_slide.csv
    input_filename_rise: series_rise.csv
    input_filename_tilt: series_tilt.csv
    input_filename_roll: series_roll.csv
    input_filename_twist: series_twist.csv
    output_csv_path: bps_correlation.csv 
    output_jpg_path: bps_correlation.jpg 
  properties:
    sequence: CGCGAATTCGCG