# HG changeset patch
# User galaxyp
# Date 1488381664 18000
# Node ID ae8e96c8f9a4b64d5e5be3eaffcc3137d37cb541
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
diff -r 000000000000 -r ae8e96c8f9a4 MSSimulator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MSSimulator.xml Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,940 @@
+
+
+
+
+ A highly configurable simulator for mass spectrometry experiments.
+
+ MSSimulator
+ macros.xml
+
+
+
+
+ MSSimulator
+
+-in
+ #for token in $param_in:
+ $token
+ #end for
+#if $param_out:
+ -out $param_out
+#end if
+#if $param_out_pm:
+ -out_pm $param_out_pm
+#end if
+#if $param_out_fm:
+ -out_fm $param_out_fm
+#end if
+#if $param_out_cm:
+ -out_cm $param_out_cm
+#end if
+#if $param_out_lcm:
+ -out_lcm $param_out_lcm
+#end if
+#if $param_out_cntm:
+ -out_cntm $param_out_cntm
+#end if
+#if $param_out_id:
+ -out_id $param_out_id
+#end if
+#if $param_algorithm_MSSim_Digestion_enzyme:
+ -algorithm:MSSim:Digestion:enzyme $param_algorithm_MSSim_Digestion_enzyme
+#end if
+#if $param_algorithm_MSSim_Digestion_model:
+ -algorithm:MSSim:Digestion:model $param_algorithm_MSSim_Digestion_model
+#end if
+#if $param_algorithm_MSSim_Digestion_min_peptide_length:
+ -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length
+#end if
+#if $param_algorithm_MSSim_Digestion_model_trained_threshold:
+ -algorithm:MSSim:Digestion:model_trained:threshold $param_algorithm_MSSim_Digestion_model_trained_threshold
+#end if
+#if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages:
+ -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages
+#end if
+#if $param_algorithm_MSSim_RT_rt_column:
+ -algorithm:MSSim:RT:rt_column $param_algorithm_MSSim_RT_rt_column
+#end if
+#if $param_algorithm_MSSim_RT_auto_scale:
+ -algorithm:MSSim:RT:auto_scale $param_algorithm_MSSim_RT_auto_scale
+#end if
+#if $param_algorithm_MSSim_RT_total_gradient_time:
+ -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time
+#end if
+#if $param_algorithm_MSSim_RT_sampling_rate:
+ -algorithm:MSSim:RT:sampling_rate $param_algorithm_MSSim_RT_sampling_rate
+#end if
+#if $param_algorithm_MSSim_RT_scan_window_min:
+ -algorithm:MSSim:RT:scan_window:min $param_algorithm_MSSim_RT_scan_window_min
+#end if
+#if $param_algorithm_MSSim_RT_scan_window_max:
+ -algorithm:MSSim:RT:scan_window:max $param_algorithm_MSSim_RT_scan_window_max
+#end if
+#if $param_algorithm_MSSim_RT_variation_feature_stddev:
+ -algorithm:MSSim:RT:variation:feature_stddev $param_algorithm_MSSim_RT_variation_feature_stddev
+#end if
+#if $param_algorithm_MSSim_RT_variation_affine_offset:
+ -algorithm:MSSim:RT:variation:affine_offset $param_algorithm_MSSim_RT_variation_affine_offset
+#end if
+#if $param_algorithm_MSSim_RT_variation_affine_scale:
+ -algorithm:MSSim:RT:variation:affine_scale $param_algorithm_MSSim_RT_variation_affine_scale
+#end if
+#if $param_algorithm_MSSim_RT_column_condition_distortion:
+ -algorithm:MSSim:RT:column_condition:distortion $param_algorithm_MSSim_RT_column_condition_distortion
+#end if
+#if $param_algorithm_MSSim_RT_profile_shape_width_value:
+ -algorithm:MSSim:RT:profile_shape:width:value $param_algorithm_MSSim_RT_profile_shape_width_value
+#end if
+#if $param_algorithm_MSSim_RT_profile_shape_width_variance:
+ -algorithm:MSSim:RT:profile_shape:width:variance $param_algorithm_MSSim_RT_profile_shape_width_variance
+#end if
+#if $param_algorithm_MSSim_RT_profile_shape_skewness_value:
+ -algorithm:MSSim:RT:profile_shape:skewness:value $param_algorithm_MSSim_RT_profile_shape_skewness_value
+#end if
+#if $param_algorithm_MSSim_RT_profile_shape_skewness_variance:
+ -algorithm:MSSim:RT:profile_shape:skewness:variance $param_algorithm_MSSim_RT_profile_shape_skewness_variance
+#end if
+#if $param_algorithm_MSSim_RT_HPLC_model_file:
+ -algorithm:MSSim:RT:HPLC:model_file "$param_algorithm_MSSim_RT_HPLC_model_file"
+#end if
+#if $param_algorithm_MSSim_RT_CE_pH:
+ -algorithm:MSSim:RT:CE:pH $param_algorithm_MSSim_RT_CE_pH
+#end if
+#if $param_algorithm_MSSim_RT_CE_alpha:
+ -algorithm:MSSim:RT:CE:alpha $param_algorithm_MSSim_RT_CE_alpha
+#end if
+#if $param_algorithm_MSSim_RT_CE_mu_eo:
+ -algorithm:MSSim:RT:CE:mu_eo $param_algorithm_MSSim_RT_CE_mu_eo
+#end if
+#if $param_algorithm_MSSim_RT_CE_lenght_d:
+ -algorithm:MSSim:RT:CE:lenght_d $param_algorithm_MSSim_RT_CE_lenght_d
+#end if
+#if $param_algorithm_MSSim_RT_CE_length_total:
+ -algorithm:MSSim:RT:CE:length_total $param_algorithm_MSSim_RT_CE_length_total
+#end if
+#if $param_algorithm_MSSim_RT_CE_voltage:
+ -algorithm:MSSim:RT:CE:voltage $param_algorithm_MSSim_RT_CE_voltage
+#end if
+#if $param_algorithm_MSSim_Detectability_dt_simulation_on:
+ -algorithm:MSSim:Detectability:dt_simulation_on
+#end if
+#if $param_algorithm_MSSim_Detectability_min_detect:
+ -algorithm:MSSim:Detectability:min_detect $param_algorithm_MSSim_Detectability_min_detect
+#end if
+#if $param_algorithm_MSSim_Detectability_dt_model_file:
+ -algorithm:MSSim:Detectability:dt_model_file "$param_algorithm_MSSim_Detectability_dt_model_file"
+#end if
+
+#if $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
+-algorithm:MSSim:Ionization:esi:ionized_residues
+ #for token in $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
+ #if " " in str(token):
+ "$token.param_algorithm_MSSim_Ionization_esi_ionized_residues"
+ #else
+ $token.param_algorithm_MSSim_Ionization_esi_ionized_residues
+ #end if
+ #end for
+#end if
+
+#if $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
+-algorithm:MSSim:Ionization:esi:charge_impurity
+ #for token in $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
+ #if " " in str(token):
+ "$token.param_algorithm_MSSim_Ionization_esi_charge_impurity"
+ #else
+ $token.param_algorithm_MSSim_Ionization_esi_charge_impurity
+ #end if
+ #end for
+#end if
+#if $param_algorithm_MSSim_Ionization_esi_ionization_probability:
+ -algorithm:MSSim:Ionization:esi:ionization_probability $param_algorithm_MSSim_Ionization_esi_ionization_probability
+#end if
+
+#if $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
+-algorithm:MSSim:Ionization:maldi:ionization_probabilities
+ #for token in $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
+ #if " " in str(token):
+ "$token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities"
+ #else
+ $token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities
+ #end if
+ #end for
+#end if
+#if $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit:
+ -algorithm:MSSim:Ionization:mz:lower_measurement_limit $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit
+#end if
+#if $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit:
+ -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit
+#end if
+#if $param_algorithm_MSSim_RawSignal_enabled:
+ -algorithm:MSSim:RawSignal:enabled $param_algorithm_MSSim_RawSignal_enabled
+#end if
+#if $param_algorithm_MSSim_RawSignal_peak_shape:
+ -algorithm:MSSim:RawSignal:peak_shape $param_algorithm_MSSim_RawSignal_peak_shape
+#end if
+#if $param_algorithm_MSSim_RawSignal_resolution_value:
+ -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value
+#end if
+#if $param_algorithm_MSSim_RawSignal_resolution_type:
+ -algorithm:MSSim:RawSignal:resolution:type $param_algorithm_MSSim_RawSignal_resolution_type
+#end if
+#if $param_algorithm_MSSim_RawSignal_baseline_scaling:
+ -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling
+#end if
+#if $param_algorithm_MSSim_RawSignal_baseline_shape:
+ -algorithm:MSSim:RawSignal:baseline:shape $param_algorithm_MSSim_RawSignal_baseline_shape
+#end if
+#if $param_algorithm_MSSim_RawSignal_mz_sampling_points:
+ -algorithm:MSSim:RawSignal:mz:sampling_points $param_algorithm_MSSim_RawSignal_mz_sampling_points
+#end if
+#if $param_algorithm_MSSim_RawSignal_contaminants_file:
+ -algorithm:MSSim:RawSignal:contaminants:file "$param_algorithm_MSSim_RawSignal_contaminants_file"
+#end if
+#if $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev:
+ -algorithm:MSSim:RawSignal:variation:mz:error_stddev $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev
+#end if
+#if $param_algorithm_MSSim_RawSignal_variation_mz_error_mean:
+ -algorithm:MSSim:RawSignal:variation:mz:error_mean $param_algorithm_MSSim_RawSignal_variation_mz_error_mean
+#end if
+#if $param_algorithm_MSSim_RawSignal_variation_intensity_scale:
+ -algorithm:MSSim:RawSignal:variation:intensity:scale $param_algorithm_MSSim_RawSignal_variation_intensity_scale
+#end if
+#if $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev:
+ -algorithm:MSSim:RawSignal:variation:intensity:scale_stddev $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev
+#end if
+#if $param_algorithm_MSSim_RawSignal_noise_shot_rate:
+ -algorithm:MSSim:RawSignal:noise:shot:rate $param_algorithm_MSSim_RawSignal_noise_shot_rate
+#end if
+#if $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean:
+ -algorithm:MSSim:RawSignal:noise:shot:intensity-mean $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean
+#end if
+#if $param_algorithm_MSSim_RawSignal_noise_white_mean:
+ -algorithm:MSSim:RawSignal:noise:white:mean $param_algorithm_MSSim_RawSignal_noise_white_mean
+#end if
+#if $param_algorithm_MSSim_RawSignal_noise_white_stddev:
+ -algorithm:MSSim:RawSignal:noise:white:stddev $param_algorithm_MSSim_RawSignal_noise_white_stddev
+#end if
+#if $param_algorithm_MSSim_RawSignal_noise_detector_mean:
+ -algorithm:MSSim:RawSignal:noise:detector:mean $param_algorithm_MSSim_RawSignal_noise_detector_mean
+#end if
+#if $param_algorithm_MSSim_RawSignal_noise_detector_stddev:
+ -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_status:
+ -algorithm:MSSim:RawTandemSignal:status $param_algorithm_MSSim_RawTandemSignal_status
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_tandem_mode:
+ -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file:
+ -algorithm:MSSim:RawTandemSignal:svm_model_set_file "$param_algorithm_MSSim_RawTandemSignal_svm_model_set_file"
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance:
+ -algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window:
+ -algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks:
+ -algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks
+#end if
+
+#if $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
+-algorithm:MSSim:RawTandemSignal:Precursor:charge_filter
+ #for token in $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
+ #if " " in str(token):
+ "$token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter"
+ #else
+ $token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter
+ #end if
+ #end for
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion:
+ -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time:
+ -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability:
+ -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra:
+ -algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity:
+ -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity
+#end if
+#if $param_algorithm_MSSim_Global_ionization_type:
+ -algorithm:MSSim:Global:ionization_type $param_algorithm_MSSim_Global_ionization_type
+#end if
+#if $param_algorithm_MSSim_Labeling_type:
+ -algorithm:MSSim:Labeling:type $param_algorithm_MSSim_Labeling_type
+#end if
+#if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift:
+ -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift
+#end if
+#if $param_algorithm_MSSim_Labeling_ICPL_label_proteins:
+ -algorithm:MSSim:Labeling:ICPL:label_proteins $param_algorithm_MSSim_Labeling_ICPL_label_proteins
+#end if
+#if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift:
+ -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift
+#end if
+#if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine:
+ -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine"
+#end if
+#if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine:
+ -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine"
+#end if
+#if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine:
+ -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine"
+#end if
+#if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine:
+ -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine"
+#end if
+#if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
+ -algorithm:MSSim:Labeling:itraq:iTRAQ $param_algorithm_MSSim_Labeling_itraq_iTRAQ
+#end if
+#if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift:
+ -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift
+#end if
+
+#if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
+-algorithm:MSSim:Labeling:itraq:channel_active_4plex
+ #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
+ #if " " in str(token):
+ "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex"
+ #else
+ $token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex
+ #end if
+ #end for
+#end if
+
+#if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
+-algorithm:MSSim:Labeling:itraq:channel_active_8plex
+ #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
+ #if " " in str(token):
+ "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex"
+ #else
+ $token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex
+ #end if
+ #end for
+#end if
+#if $param_algorithm_MSSim_Labeling_itraq_Y_contamination:
+ -algorithm:MSSim:Labeling:itraq:Y_contamination $param_algorithm_MSSim_Labeling_itraq_Y_contamination
+#end if
+#if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency:
+ -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency
+#end if
+#if $param_algorithm_RandomNumberGenerators_biological:
+ -algorithm:RandomNumberGenerators:biological $param_algorithm_RandomNumberGenerators_biological
+#end if
+#if $param_algorithm_RandomNumberGenerators_technical:
+ -algorithm:RandomNumberGenerators:technical $param_algorithm_RandomNumberGenerators_technical
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+ #if $adv_opts.param_force:
+ -force
+#end if
+ #if $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size:
+ -algorithm:MSSim:Ionization:esi:max_impurity_set_size $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size
+#end if
+ #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label:
+ -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label"
+#end if
+ #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label:
+ -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label"
+#end if
+ #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label:
+ -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label"
+#end if
+
+#if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
+-algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex
+ #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
+ #if " " in str(token):
+ "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex"
+ #else
+ $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex
+ #end if
+ #end for
+#end if
+
+#if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
+-algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex
+ #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
+ #if " " in str(token):
+ "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex"
+ #else
+ $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex
+ #end if
+ #end for
+#end if
+#end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A highly configurable simulator for mass spectrometry experiments.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html
+
diff -r 000000000000 -r ae8e96c8f9a4 SKIP_TOOLS_FILE.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SKIP_TOOLS_FILE.txt Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer
diff -r 000000000000 -r ae8e96c8f9a4 datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,33 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r ae8e96c8f9a4 filetypes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filetypes.txt Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,29 @@
+# CTD type # Galaxy type # Long Galaxy data type # Mimetype
+csv tabular galaxy.datatypes.tabular:Tabular
+fasta fasta galaxy.datatypes.sequence:Fasta
+FASTA fasta galaxy.datatypes.sequence:Fasta
+ini txt galaxy.datatypes.data:Text
+txt txt galaxy.datatypes.data:Text
+options txt galaxy.datatypes.data:Text
+grid grid galaxy.datatypes.data:Grid
+html html galaxy.datatypes.text:Html text/html
+HTML html galaxy.datatypes.text:Html text/html
+TraML traml galaxy.datatypes.proteomics:TraML application/xml
+traML traml galaxy.datatypes.proteomics:TraML application/xml
+XML xml galaxy.datatypes.xml:GenericXml application/xml
+consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml
+edta tabular galaxy.datatypes.tabular:Tabular
+featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml
+idXML idxml galaxy.datatypes.proteomics:IdXM application/xml
+mzML mzml galaxy.datatypes.proteomics:MzML application/xml
+mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml
+pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml
+qcML qcml galaxy.datatypes.xml:GenericXml application/xml
+trafoXML trafoxml galaxy.datatypes.xml:GenericXml application/xml
+tsv tabular galaxy.datatypes.tabular:Tabular
+xsd txt galaxy.datatypes.data:Text
+mzq mzq galaxy.datatypes.proteomics:MzQuantML application/xml
+msp msp galaxy.datatypes.proteomics:Msp
+mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml
+png png galaxy.datatypes.images:Png image/png
+mgf mgf galaxy.datatypes.proteomics:Mgf
\ No newline at end of file
diff -r 000000000000 -r ae8e96c8f9a4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,35 @@
+
+
+
+
+ openms
+ xtandem
+ fido
+ msgf_plus
+
+
+
+
+
+
+
+
+
+
+
+ doi:10.1186/1471-2105-9-163
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r ae8e96c8f9a4 readme.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.md Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,165 @@
+Galaxy wrapper for OpenMS
+=========================
+
+OpenMS is an open-source software C++ library for LC/MS data management and analyses.
+It offers an infrastructure for the rapid development of mass spectrometry related software.
+OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
+
+More informations are available at:
+
+ * https://github.com/OpenMS/OpenMS
+ * http://open-ms.sourceforge.net
+
+
+Generating OpenMS wrappers
+==========================
+
+ * install OpenMS (you can do this automatically through the Tool Shed)
+ * create a folder called CTD
+ * inside of your new installed openms/bin folder, execute the following command:
+
+ ```bash
+ for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
+ ```
+
+ * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
+
+ * clone or install CTDopts
+
+ ```bash
+ git clone https://github.com/genericworkflownodes/CTDopts
+ ```
+
+ * add CTDopts to your `$PYTHONPATH`
+
+ ```bash
+ export PYTHONPATH=/home/user/CTDopts/
+ ```
+
+ * clone or install CTD2Galaxy
+
+ ```bash
+ git clone https://github.com/blankclemens/CTD2Galaxy.git
+ ```
+
+ * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts.
+
+ ```bash
+ python generator.py \
+ -i /PATH/TO/YOUR/CTD/*.ctd \
+ -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
+ -d datatypes_conf.xml -g openms \
+ -b version log debug test no_progress threads \
+ in_type executable myrimatch_executable \
+ fido_executable fidocp_executable \
+ omssa_executable pepnovo_executable \
+ xtandem_executable param_model_directory \
+ java_executable java_memory java_permgen \
+ -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
+ -s PATH/TO/SKIP_TOOLS_FILES.txt
+ ```
+
+
+ * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
+
+ ```
+ sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml
+ sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml
+ sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
+ sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
+ sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
+ ```
+
+ * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
+
+ ```
+
+ ```
+ * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
+
+ -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
+
+ and change it to
+
+ -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
+
+ * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
+
+
+
+ * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.
+
+ ```
+
+
+
+
+
+
+ ```
+
+
+ * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`:
+ * SeedListGenerator
+ * SpecLibSearcher
+ * MapAlignerIdentification
+ * MapAlignerPoseClustering
+ * MapAlignerSpectrum
+ * MapAlignerRTTransformer
+
+ * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well:
+ * OMSSAAdapter
+ * MyrimatchAdapter
+
+ * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed:
+ * PepNovoAdapter
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
diff -r 000000000000 -r ae8e96c8f9a4 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,4 @@
+
+
+
+
diff -r 000000000000 -r ae8e96c8f9a4 test-data/DecoyDatabase_input.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DecoyDatabase_input.fasta Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,146 @@
+>12
+MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI
+STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL
+YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM
+VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR
+DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL
+MIIVPTDTQNIFFMSKVTNPKQA
+>18
+MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMK
+QLNIIQNAEAVHFFCNYEESRGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQ
+NASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLITMACGSCSNENALKTIFMWYR
+SKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS
+FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGG
+DNHASDDFFRKLRDIARKHGCAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMM
+TGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIKREDLLNNAAHAGKALLTGLL
+DLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF
+RDHHAHLFLNIFSDILADFK
+>88
+MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIE
+NIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAE
+EIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNIQNFHTSW
+KDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP
+DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRT
+IPWLENRTPEKTMQAMQKKLEDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAF
+MPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLEHLAEKFRQKASTHETWAYGK
+EQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN
+DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQ
+DMFIVHSIEEIQSLITAHEQFKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYS
+TVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRRQFAAQANAIGPWIQNKMEEI
+ARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI
+RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRA
+CLISMGYDLGEAEFARIMTLVDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILAS
+DKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALDYAAFSSALYGESDL
+>112
+MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGP
+PRCPWQDDAFIRRGGPGKGKELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWR
+RLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLVLLTAVLLAFHAAPARPQPAY
+VALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW
+CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTN
+VIGICTHYPAEVSQRQAFQETRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINT
+KKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHC
+LRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV
+HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNA
+YLKEQHIETFLILGASQKRKEEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFR
+QMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQLRKDHVRRFLLTFQREDLEKK
+YSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC
+GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLT
+PADITACHLQQLNYSLGLDAPLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLA
+MIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNETFDGLDCPAAGRVALKYMTPV
+ILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF
+LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIIS
+EERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNN
+FQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVLAAKG
+YQLECRGVVKVKGKGEMTTYFLNGGPSS
+>114
+MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGS
+GSGGSGKASDPAGGGPNHHAPQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASG
+SGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNSFKSRDLERLYQRYFLGQRRK
+SEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT
+YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTS
+LLQVILQVVIPRLAVISINQVVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEAR
+LRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQHQFHRIYIHRYENVSILFADV
+KGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH
+CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKL
+ESGGIPGRIHISKATLDCLNGDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPED
+IVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHV
+QSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF
+IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINE
+TYLARNVIIFASILINFLGAILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTG
+VLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGLFLRYDNLNHSGEDFLGTKEV
+SLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA
+RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDE
+LLGEDRFQDIEKIKTIGSTYMAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKH
+SFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASRMDSTGVSGRIQVPEETYLIL
+KDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV
+QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP
+>143
+MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQ
+LNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCP
+DSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSR
+DCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL
+ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGI
+LLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVC
+ETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRV
+NETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD
+SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVT
+TDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQL
+PDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFP
+LDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN
+LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTK
+QSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYL
+PRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIAL
+HALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL
+SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCG
+AGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFL
+NDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGI
+LHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK
+EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSED
+FEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILA
+PAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQS
+ASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS
+LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCL
+LEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDE
+IVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGR
+ECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE
+GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG
+>213
+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
+AASQAALGL
+>230
+MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYR
+QVLFSADDRVKKCIGGVIFFHETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTD
+GETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPSALAILENANVLARYASICQQ
+NGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC
+PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTF
+SYGRALQASALNAWRGQRDNAGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIA
+NHAY
+>231
+MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQ
+EKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGK
+EFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKP
+AVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK
+HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCA
+LLSCTSHKDYPFHEEF
+>242
+MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQD
+LGELIIIRLHKERYAFFPKDPWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKT
+TADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIPSYRPPVRRHRNPNRPEWNGY
+IPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR
+KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGE
+GTCLQAELEKGNIYLADYRIMEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQ
+TPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLLETHLIAEAFCLALLRNLPMC
+HPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY
+LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEI
+FKECLLGRESSGFPRCLRTVPELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMR
+NPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPDDRRPLGHFPDIHFVEEAPRR
+SIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI
diff -r 000000000000 -r ae8e96c8f9a4 test-data/DecoyDatabase_output.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DecoyDatabase_output.fasta Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,228 @@
+>12
+MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI
+STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL
+YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM
+VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR
+DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL
+MIIVPTDTQNIFFMSKVTNPKQA
+>18
+MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMKQLNIIQNAEAVHFFCNYEES
+RGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLIT
+MACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS
+FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHG
+CAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMMTGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIK
+REDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF
+RDHHAHLFLNIFSDILADFK
+>88
+MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVIS
+GERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLW
+CQRKTAPYRNVNIQNFHTSWKDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP
+DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRTIPWLENRTPEKTMQAMQKKL
+EDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAFMPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLE
+HLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN
+DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQDMFIVHSIEEIQSLITAHEQ
+FKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRR
+QFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI
+RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRACLISMGYDLGEAEFARIMTL
+VDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALD
+YAAFSSALYGESDL
+>112
+MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGPPRCPWQDDAFIRRGGPGKGK
+ELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWRRLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLV
+LLTAVLLAFHAAPARPQPAYVALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW
+CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTNVIGICTHYPAEVSQRQAFQE
+TRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINTKKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQEL
+VMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV
+HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLILGASQKRK
+EEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFRQMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQL
+RKDHVRRFLLTFQREDLEKKYSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC
+GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLTPADITACHLQQLNYSLGLDA
+PLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLAMIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNET
+FDGLDCPAAGRVALKYMTPVILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF
+LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAA
+SGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDST
+GVPDRIQVTTDLYQVLAAKGYQLECRGVVKVKGKGEMTTYFLNGGPSS
+>114
+MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGSGSGGSGKASDPAGGGPNHHA
+PQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASGSGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNS
+FKSRDLERLYQRYFLGQRRKSEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT
+YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTSLLQVILQVVIPRLAVISINQ
+VVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQH
+QFHRIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH
+CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKATLDCLN
+GDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPEDIVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLA
+ALTRNSINLLPNHLAQALHVQSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF
+IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINETYLARNVIIFASILINFLGA
+ILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTGVLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGL
+FLRYDNLNHSGEDFLGTKEVSLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA
+RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDELLGEDRFQDIEKIKTIGSTY
+MAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKHSFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASR
+MDSTGVSGRIQVPEETYLILKDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV
+QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP
+>143
+MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQLNSIQKNHVHIANPDFIWKS
+IREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCPDSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKV
+GMEGGQEAVVVELQCSRDSRDCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL
+ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGILLLVKAALKNGETAEQLQKM
+MTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVCETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVL
+QNHHSKSPVDVLQIFRVGRVNETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD
+SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVTTDFEDDEFVVYKTNQVKMKY
+IIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQLPDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVI
+VFQTYTNKSHVPIEAKYIFPLDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN
+LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTKQSFSLTMSIEMPYVIEFIFS
+DTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYLPRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIIC
+LDCSSSMEGVTFLQAKQIALHALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL
+SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCGAGVFEYFNAKSKHSWRKQIE
+DQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFLNDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTT
+GTMIHKLAARALIRDYEDGILHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK
+EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSEDFEEDGLGVLPAFTSNLERGG
+VEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILAPAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFD
+ASQFSQGPVPGTCADWIPQSASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS
+LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCLLEESVGSLEGSRCPVFAFQS
+SDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDEIVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNT
+NGLHSFLKQKGIQSLGVKGRECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE
+GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG
+>213
+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVAD
+ESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLK
+KYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVEND
+EMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDE
+FKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHK
+PKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL
+>230
+MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYRQVLFSADDRVKKCIGGVIFF
+HETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTDGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPS
+ALAILENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC
+PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTFSYGRALQASALNAWRGQRDN
+AGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIANHAY
+>231
+MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLW
+CTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGIS
+NFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK
+HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
+>242
+MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQDLGELIIIRLHKERYAFFPKD
+PWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKTTADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIP
+SYRPPVRRHRNPNRPEWNGYIPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR
+KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGEGTCLQAELEKGNIYLADYRI
+MEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQTPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLL
+ETHLIAEAFCLALLRNLPMCHPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY
+LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEIFKECLLGRESSGFPRCLRTV
+PELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMRNPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPD
+DRRPLGHFPDIHFVEEAPRRSIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI
+>DECOY_12
+AQKPNTVKSMFFINQTDTPVIIMLFPRNFRVITRTEVLASLLTIKVATAASAETGEEFVDLVAKHVVQSVALNRAGTIGS
+LDAKSTFAEEIGLQLLIDNLNYDRSISFKPLYLEGIERFELSDRWRKLTEPLLMAEVEEMKDQDPLIFLASANGTYKLEV
+VTCSLEEDRFYPITLHHLSMMPVMVWKKKSLYFRSQHTDQPDFPMEWKAKFFIYNVLVMMTQSDLDKILDTIKGRTGNKV
+YDNILKKAAASDQFDTAFAESGYLRKADETFRDLLSLQEKVFMANGMSLQLEDSSQNLTRLLHQFSQHIEAESTETLNFK
+LGKLIETLTTNHAGLSLFALATSISLPSFIVNKDPAKLVLQKYLSFAFDVNASALGLDVHTGRDQNEQTLNEEDLPSNPH
+CLVAPCFGAALLGLALLPLMREM
+>DECOY_18
+KFDALIDSFINLFLHAHHDRFVLTPRFRISKDGCGGLVVGKNRAILILKNRISDDPTDFSCFTGRGRVRSIFQPYRAQLD
+LLGTLLAKGAHAANNLLDERKIINIVEALLLNKSPDGLWTNFIRYPANPRFEEKHFFGGTMMKKSFTMVDAPDDLGWHEH
+AWFKGTCGGGTQVEDVLFACGHKRAIDRLKRFFDDSAHNDGGESQIPEVIIGAVTKKKKRYKVILDEVEELCRAEEQQNE
+KVFEELPYKLRPFPAIPWDFSPIDIKHIAKSHTTALCGMTRGHFAGMFSLISYDPCGPAQNIMCTELEEQSFGRQGREKS
+RYWMFITKLANENSCSGCAMTILQSMGKPAVSLLSQRLKEVFNEPPLIGLAPRNVFMSANQPQQILKLLAPHSYGIPVSS
+IQSYLDLMRNGDVDVLYNGRSEEYNCFFHVAEANQIINLQKMLEQSRPGPVETKMLPGDYDFEVDVKAAAQSIHRSGPVL
+LRYSHQFSCALRQALLMSAM
+>DECOY_88
+LDSEGYLASSFAAYDLAGPVSGPGSYAPMRKICYQAQDPPLERRLEEALIYPKDSALIRFSAIVQEATDTDATERTMFDI
+FSQFTVTGQGNPDVLTMIRAFEAEGLDYGMSILCARFDEHDMLGNKRRDFHNFSARFENMQEQTIGKADRTLIQTEVENI
+TRAITTLLLEWGVRIHEMTYNTHKNDFVLAEQILQHDGELKDINNKYNIINHEYQKLQNMQDELAGTIQISSRAIEEMKN
+QIWPGIANAQAAFQRRLRENAHQRALEEQLSQDRIPVLQKVKDWKTRLEDMTVTSYPNSSSIRINYSQIVKEVENQIAMI
+SQREGDAEPLTAKFQEHATILSQIEEISHVIFMDQLDEMAGEMWNNFPAARKAFELHLQDITELLKEMRELAERRKQTLT
+GLRDWQDCIKQCRDNVNVADHYDLENLEQAIAAIQEVRDQHAALDSEFAEHKRLLARVETLSASEYDKQLLIQEKGYAWT
+EHTSAKQRFKEALHELRELRRIENLLWEEYGKEAQELRQWAGAIDSVMKGESPMFAPRNSIRLKTQLTNFNIELQCKEQV
+KPPKHKRRYDRFDELKKQMAQMTKEPTRNELWPITRRIWELLESALREYEEMLRENEQNVALVKCIRNAATEAQEAGAFA
+HYFCSVYTMIAREDPKPTNVIDEADLMKPIDLHKEAIEMALNINGIPDDKNLKSYDILDPRHRHILACLGLGDKWSTHFN
+QINVNRYPATKRQCWLLLGEKASTEEVSIDQIAFRLIITWIMGLTMKVNGDVIEEAGISVLKVGKSAIYDLAKNVNAIKH
+FRMKGRDPKPLREGSIVELLLMLKLGNRFDEEINEIQTGAKRLHSNCWATFTKRQQKEWAPDLLLDRDWEEEQIMYEDED
+YVYNYQVGPEIQNM
+>DECOY_112
+SSPGGNLFYTTMEGKGKVKVVGRCELQYGKAALVQYLDTTVQIRDPVGTSDMRSSVNVTNGWIDYQPKRAGIVGAVVPGM
+NLGIKMQFNNFSHENIHKMQEMLRMAYDALATIHSRGVQDYTSANLGSAAMYTSGITKIKELQRFREESIIEDFDAIIEN
+LLRLCEVGENNAELEVYFESFNAISAFMVAVCECSQYYLEDNRRERALFHAAVDKPLINHLLRRNYAQLEEMEEKEGTAQ
+LKWLFDLRATSEVQQAHLYLALAFVLLIVPTMYKLAVRGAAPCDLGDFTENSSALGHVGLLLDYNDFITAPPGLLLLVLY
+ILGLVFIMALKGISSIHLFVSSALLSLLMNGIFYEPFSCTPMTGECLPADLGLSYNLQQLHCATIDAPTLNLMRAACSRI
+PTHNCTFMNAIASTFVLLVSFIGVATSHARSRVISRSLRQLAKPFLSGCSYVACILVTILLLLFISAYIGLMLTSHPFIL
+LQIFCIFCFVLLACAVYAGFRPDVKRSYKKELDERQFTLLFRRVHDKRLQDISRADIARSLFEDVEDEPNLADQTGRNDK
+SSDDIGMQRFAKSDKTRSFARDPVWRPMLGEMSNARTRQLKALMAKEEKRKQSAGLILFTEIHQEKLYANREGGRGPEVE
+YDGNLYQLTARTIHIRGARGGAEMHNALTVDNSWVDFQWKRLGLVGCHVRGSHIGVRMNVNVGTVERVLSIAEIMDVGME
+VCCHAHDARAEPLGSVCYYCDGLIKIRLCHNEAALKDFRAFLENLTMVLEQATCQSALSTFGEIDAFLISVNDHKQIYIK
+HFMMDEKKTNIDEKMEMAVHQPLVSLLLREQQRNEHQLHLRAQIYGRTEQFAQRQSVEAPYHTCIGIVNTCLFLLVNAGL
+QKWLFADGRNLQWALILHLTSLGLGSLVAARMRIPLLTYAIYVFFVPCWLGASPSRPDAALAGGVQVAALIGLVVYSVVW
+MSDQRFSHRNCVVMLGVFLAAACALLAVYAPQPRAPAAHFALLVATLLVLVAMLLTLSSQNMQFFYRQYLRELKASRFQK
+SQFVQVLRRWCSRGSRPVADPAVEATGGATTTVETDEFGLAVARLGLEKGKGPGGRRIFADDQWPCRPPGAPTPSPPEAD
+RLCSMYRPTCFGGARTGRRRSRKQGNREGWATKREDVKPVLLGSFWSM
+>DECOY_114
+PLDSKDTGEAQAGPETGSPSLLTRRNYHGKIIGTNNNENLLQKQRQRNLSQVLGLVVAALSYQGPLRRPPLIFPNPQVRG
+LLFYTKIKGEQESIGKVYIEGRYDFAFGQDKLILYTEEPVQIRGSVGTSDMRSALNVTKGWIDYQPKKAGIVGAVVSGHS
+IGIRLEFNNFSHKNIEQISETLALSFDALACLHGWKDECQQKEPSLGSVAMYTSGITKIKEIDQFRDEGLLEDFDAIIEN
+LLRLCEVGQNNMETQSYFDAFGPISAFMVGVADYSQSYLEENDRDKELFHRAVHSPLINRLMNENHERLEKMENIEEKAQ
+VRWLFDLRATYELQQGHYFVALLFMAMLLLSVEKTGLFDEGSHNLNDYRLFLGAYVTETLLAYIAIMILLVALKLVSNLR
+LFVACTVMALVGTFVFYEPYSCIDTFVASSNFTLNKLPISKDFDCWLINLIAGLFNILISAFIIVNRALYTENIWCCTKR
+LILPLCKYDEATTILVLASHLMILISFQITMPMVRSSPLLSQIATIFLLVIFACVLNSKFVEDRMQSYKHELSSDKFMLS
+FPKIHERRLKDGSRLDITHEIRKNIEEPGSQVHLAQALHNPLLNISNRTLAALTNQKGVINDFPLEPSWSGETFTAGSNR
+RDSSSVSEKVIDEPLSLLSDEPQKILYTEINHKRLFENREKGHGEEVNYDGNLCDLTAKSIHIRGPIGGSELKNAIDVDW
+SWVDFQWKRLGLVGCLVSGSHIGIRMDVDHKTRSRVYRITKIMSLGMEVCCHAHDQRPEPLGSVCYYCDGLIKIRLCHHE
+HALRDFRAFLENLMRVLEQASLTTSLNTFGKVDAFLISVNEYRHIYIRHFQHQLHEDEVNTMDNIMELVVFRPLVSLVLR
+EQRQNETELRLRAEVCRRTELFAQRQARDSLYSIFIGATNMCMFLVAQAVVQNISIVALRPIVVQLIVQLLSTGLGALIA
+WTLPLPLMSYTAFLTFLVYGIGDGLLGYGLGAALIQTTMAVWTVVGSYQLYTHSTTDKRVVVLACIVVEIGTFFGLLIGK
+LPDMPASALSLHLVLLTLKTLVDLVNMVVESKRRQGLFYRQYLRELDRSKFSNRLTPFIVGRYSYGGNLFFDSNSPACDL
+HLFGLDGGGGSGSASGSGSREPFVKTGCTSHAREGPGLSYLPLASDGSLQPAHHNPGGGAPDSAKGSGGSGSGSGGRHGH
+IFRQETIHRVATQWLLRQPRSASRGDGAPPTPHITYLEESGTLCRVDSLEM
+>DECOY_143
+GQSYHLVRHLPSVTSIPQLGLLQKTASDWDNGLELRPCISPYQGETRRVWESAQKIAEFAWPINRSISADDMKMLSKFVI
+GEKELRTRIFQLVLMTAILDLLCERGKVGLSQIGKQKLFSHLGNTNLNLILGLEPTLKWFGDETQLSLLETWPVADQWHQ
+ICVIEDEEKVELFCLISDDKTDCKIQLFCSDQLVESLEDSETDSSQFAFVPCRSGELSGVSEELLCLDVPTTRSQSCLAE
+PLASAMPLRLNATLSAASPQFHFPSSASPHYSGFGRIPDPDTPLSFHLQPSDLEPFTGASPRTTFGGPHQLPASQASSLS
+SGSFVIGCYPSSPPNQPPGTPCSASQPIWDACTGPVPGQSFQSADFQRPPAASGFSAVQRYSAFSLSAPSHARATPPLYS
+GVAPALIPFFSSTSTEWPSVKKFLPETATPKCSETWSLDLLKEVGGRELNSTFAPLVGLGDEEFDESVEPQSLEMKRKSF
+PIKRHKRKSLRLEPWESSALLSQNRVAEQPEGQWSMYPLFDVDEKAILESVKPIDPFPSENEDRKEVAVFSTFQTILSNE
+KSLKIILSKLTQKKMEHSTENEHLIGDEYDRILARAALKHIMTGTTKQLETTSVMTRFEKEQILACLTAQTCHPIFGYVL
+LRDNLFLSPVQAPAQLAEPVDPNLQQWKVSVSHCSPSCLRTMQDEIQKRWSHKSKANFYEFVGAGCQSLIRLVHRNATSG
+IGCAFLRTHPRSRKVLQLTLSEDQLHGDSVLLINRSGRAPYLLSLYRLTKWFDTNGMTPTASMIFEAAMTNSTIHKPYSF
+LEKYGTGFQIINVKQKEGVLSLAHLAIQKAQLFTVGEMSSSCDLCIIVESESALDPLDVDLDPQFVLMCAESEKEPHKEV
+WMRPLYAASLGIHLSFGSSDLSSGEMTSIVAKCDTRKQKLEHTDSFIFEIVYPMEISMTLSFSQKTGIEKICIKEVTDQL
+NENLAKDQQWPAVTAPMFFVGVTGLISLETIYTIKILVKAKPPLNGVSVTFVDPADQSMLYAGHGQTVAELYEQQAEEKE
+KIEGVIHKGNIFAEFGCVAAKDDLPFIYKAEIPVHSKNTYTQFVIVQAVTDIIRGKIHVDELPVLNGSADQLGAKTSSST
+KADPLQYDEVKSFNSFEPRYEELETHDSPHFDKIQDGPMSFKIIYKMKVQNTKYVVFEDDEFDTTVSATQSVGHVSDYGP
+PAETLSFDKEHLDMCKGLAVDCILLLRTGDTEGPHSYKISTSLSDSFYIGSGLNGVDTRQVGRDEVVKPLLLGRCLIGVI
+NQVPSGHLLPRVNGLKSLFETTENVRGVRFIQLVDVPSKSHHNQLVEKRVRLFEETNQEVHEIKCRLARYKALSPPNPKS
+LNTECVNVMDRILQCLDAKKALLGLNVEKPMTGKHPILRYFETMMKQLQEATEGNKLAAKVLLLIGEAKSVDNLSIRNVP
+KLLMHELHGLAEAWIMEVLDSVEQSLTSSNMVEELLLAQLQESALQTAEPTFHERLLFGQKKLEEIYNEFYESADESTKK
+IAFQRRTEMGDDLLFHSSILFPCDRSDRSCQLEVVVAEQGGEMGVKELTNYKAVEFDQPLHPIEVNQMGFETLEVTDEEE
+TASDPCLGETKVESSSAKQDPPPTIDLPKYPDYNKVDLLRKERISKWIFDPNAIHVHNKQISNLQYQSLVDANDLIIHTC
+QPNLSFSFKGGNEKIDTQLKKKQQQPLYKVKLCFICNAFIGMVM
+>DECOY_213
+LGLAAQSAAVLKKGEEAFCTEKDDAKCCKEVFAAFDDMVAKLQEKTAKPKHKVLEVLATQKKIQREKESLTCIDAHFTFT
+EANFEKPVYTEDVELASFCPRRNVLSETCCKTVRDSVPTKEHLVCLQNLVVSLYDEACPMRKAEPHKCCKSGVKGLNRSV
+EVLTPTSVQPVKKTYRVLLANQFKYEGLQEFLECNQKILNQPEEVLPKFEDFVKAYCEHPDAAACCKELTTEYTKALRLL
+LVVSYDPHRRAYEYLFMGLFVDKAEAYNKCVDKSEVFDAALSPLDAPMEDNEVEAICHSKELLPKECCEKLKSSISDQNE
+CIYKALDARDDACELLDGHCCETHVKTLDTVLKSVEAFEAKPFRQSLRAVAWAKFAREGFKQLSACKLRQKASSAKGEDR
+LEDLKPLLCAAKDAAQCCETFAAKYRKAFFLLEPAYFYPHRRAIEYLYKKLFTEENDHFATCMVDVEPRVLRPLNPNDDK
+HQLFCENREPEQKACCDAMEGYTERLTAVTCLKDGFLTHLSKDCNEASEDAVCTKAFETVENVLKVHDEFPCQQLYQAFA
+ILVLAKFNEEGLDKFRHAVESKHADRRFVGRSYASSFLFLLSIFTVWKM
+>DECOY_230
+YAHNAIYLSQAAAGGDEGSGEYKGQAALGNVEARKIFEETAAGANDRQGRWANLASAQLARGYSFTLAWPRPLPCRNIAN
+LNFSAEEESQGGSLFTVGPVAPPVTRRLATVTAMAIEEPTYKIPCAHGPTVMNPKLLTGELYVHHDSLAKYVAALVKETV
+YQCRKLDHDGDPLIEPEVIPVIGNQQCISAYRALVNANELIALASPTRESIKLVCRWKAFDAGDKKYQACRESLGDLGQT
+TTEGDTGALPVVGKDVKIGVVIGKDQITRVFPVGNDDKQYLTEHFFIVGGICKKVRDDASFLVQRYLRRNEETNEVGIQS
+LRKAMSGVSEDAALIGKGPAVIRLAIDSLEKKQEASLAPYSHPM
+>DECOY_231
+FEEHFPYDKHSTCSLLACVRWNRNYSLLTTMDQSSLEFDFVKFNEAIREPTVSKPIVVLNRQMPFRILVQATTKNHKAAI
+AKIRPDELLSPDEPKAWPRDPSGLPSYATVVIGKSQCYQILKEQTLYPHCEIQNVAPKYKLGPKNLIMEVQLHNFNSIGI
+AKVLGEDVLEEMAAWTDLINTDSPVVNGSEDLPFFEKGPKFGTPWHILYLDLYDLKLDSLTKQCAGKVLGKEHYTCWLKS
+VIFLEERKVVQERLKEQIAVGVENENQYVHACDIHRYGVDIAVKVAETVQGPPSKWTGLGLIPMKAGNNLLLRSAM
+>DECOY_242
+ISISNEILVPDLYYYPIPLCKNRQRIDHSIQNLRQRFAEISRRPAEEVFHIDPFHGLPRRDDPERSLTWLVLLTICTTKV
+DPLTDMFTELTTLGKTQIPPNRMSAPFNPMWATFEMQGTNVAAHKASCTYIVITVYRILEPVTRLCRPFGSSERGLLCEK
+FIEQVWSQLEPDGEVAADSPYYYTIIETVYKELANWVALSDDRYYYGPLDQVGREVFDNPLYLSDYTLESLARVMVGAFG
+EVGLSMGKASLGGENLLVARGISNIQVTYRTHPILLKYLPHCMPLNRLLALCFAEAILHTELLHAIAEHSYFEAYRVWTK
+ALLWDWESDSPLFIPCDPGPTQSLQIAIPMMKGEPGFHLLCLPACHHQKRGSLEVTPIGEMIRYDALYINGKELEAQLCT
+GEGLFPAVMDDTVPFKDPIRTCRRILGPNVGNLYQYGFFTDEAWHEAVYESVVSKKGPFIKRIDKLRKWSHKCDLLGRVK
+FALAMPGLRVFFSATKLFSYRLNLNLFKTAKFNILIPFGPIYGNWEPRNPNRHRRVPPRYSPIHVYSPLGPLFVRWHYFD
+QKARIEEKRHELLVPLSDDATTKGTAERLALTEYGDMWQYAPFHYIRGNPACIQVYNCYWPDKPFFAYREKHLRIIILEG
+LDQPCQVTYQGVAGTAFDRGFHNLLQKHSEGQTGVITLSISDRTGSLLDTGTAVRVKYTAM
diff -r 000000000000 -r ae8e96c8f9a4 tool.conf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool.conf Wed Mar 01 10:21:04 2017 -0500
@@ -0,0 +1,162 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+