changeset 0:566046627ebf draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:16:05 -0500
parents
children 974dec16eb84
files OpenSwathRTNormalizer.xml SKIP_TOOLS_FILE.txt datatypes_conf.xml filetypes.txt macros.xml readme.md repository_dependencies.xml test-data/DecoyDatabase_input.fasta test-data/DecoyDatabase_output.fasta tool.conf
diffstat 10 files changed, 1194 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathRTNormalizer.xml	Wed Mar 01 12:16:05 2017 -0500
@@ -0,0 +1,383 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Targeted Experiments]-->
+<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.1.0">
+  <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathRTNormalizer
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_tr:
+  -tr $param_tr
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_rt_norm:
+  -rt_norm $param_rt_norm
+#end if
+#if $param_min_rsq:
+  -min_rsq $param_min_rsq
+#end if
+#if $param_min_coverage:
+  -min_coverage $param_min_coverage
+#end if
+#if $param_estimateBestPeptides:
+  -estimateBestPeptides
+#end if
+#if $param_algorithm_stop_report_after_feature:
+  -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
+#end if
+#if $param_algorithm_rt_extraction_window:
+  -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
+#end if
+#if $param_algorithm_rt_normalization_factor:
+  -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
+#end if
+#if $param_algorithm_uis_threshold_sn:
+  -algorithm:uis_threshold_sn $param_algorithm_uis_threshold_sn
+#end if
+#if $param_algorithm_uis_threshold_peak_area:
+  -algorithm:uis_threshold_peak_area $param_algorithm_uis_threshold_peak_area
+#end if
+#if $param_algorithm_TransitionGroupPicker_stop_after_feature:
+  -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
+#end if
+#if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
+  -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
+#end if
+#if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
+#end if
+#if $param_algorithm_DIAScoring_dia_extraction_window:
+  -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
+#end if
+#if $param_algorithm_DIAScoring_dia_centroided:
+  -algorithm:DIAScoring:dia_centroided
+#end if
+#if $param_algorithm_DIAScoring_dia_byseries_intensity_min:
+  -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min
+#end if
+#if $param_algorithm_DIAScoring_dia_byseries_ppm_diff:
+  -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff
+#end if
+#if $param_algorithm_DIAScoring_dia_nr_isotopes:
+  -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes
+#end if
+#if $param_algorithm_DIAScoring_dia_nr_charges:
+  -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges
+#end if
+#if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
+  -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
+#end if
+#if $param_outlierDetection_outlierMethod:
+  -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod
+#end if
+#if $param_outlierDetection_useIterativeChauvenet:
+  -outlierDetection:useIterativeChauvenet
+#end if
+#if $param_outlierDetection_RANSACMaxIterations:
+  -outlierDetection:RANSACMaxIterations $param_outlierDetection_RANSACMaxIterations
+#end if
+#if $param_outlierDetection_RANSACMaxPercentRTThreshold:
+  -outlierDetection:RANSACMaxPercentRTThreshold $param_outlierDetection_RANSACMaxPercentRTThreshold
+#end if
+#if $param_outlierDetection_RANSACSamplingSize:
+  -outlierDetection:RANSACSamplingSize $param_outlierDetection_RANSACSamplingSize
+#end if
+#if $param_peptideEstimation_InitialQualityCutoff:
+  -peptideEstimation:InitialQualityCutoff $param_peptideEstimation_InitialQualityCutoff
+#end if
+#if $param_peptideEstimation_OverallQualityCutoff:
+  -peptideEstimation:OverallQualityCutoff $param_peptideEstimation_OverallQualityCutoff
+#end if
+#if $param_peptideEstimation_NrRTBins:
+  -peptideEstimation:NrRTBins $param_peptideEstimation_NrRTBins
+#end if
+#if $param_peptideEstimation_MinPeptidesPerBin:
+  -peptideEstimation:MinPeptidesPerBin $param_peptideEstimation_MinPeptidesPerBin
+#end if
+#if $param_peptideEstimation_MinBinsFilled:
+  -peptideEstimation:MinBinsFilled $param_peptideEstimation_MinBinsFilled
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_quantification_cutoff:
+  -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
+#end if
+    #if $adv_opts.param_algorithm_write_convex_hull:
+  -algorithm:write_convex_hull
+#end if
+    #if $adv_opts.param_algorithm_add_up_spectra:
+  -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
+#end if
+    #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
+  -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
+#end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
+  -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
+#end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
+  -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
+#end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
+  -algorithm:TransitionGroupPicker:recalculate_peaks     "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
+#end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
+  -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
+#end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
+  -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
+#end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
+  -algorithm:TransitionGroupPicker:compute_peak_quality     "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality"
+#end if
+    #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
+  -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
+#end if
+    #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
+  -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
+#end if
+    #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
+  -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
+#end if
+    #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
+  -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
+#end if
+    #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
+  -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_shape_score:
+  -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_coelution_score:
+  -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_rt_score:
+  -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_library_score:
+  -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
+  -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_intensity_score:
+  -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
+  -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
+  -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_sn_score:
+  -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_dia_scores:
+  -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
+  -algorithm:Scores:use_ms1_correlation
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
+  -algorithm:Scores:use_ms1_fullscan
+#end if
+    #if $adv_opts.param_algorithm_Scores_use_uis_scores:
+  -algorithm:Scores:use_uis_scores
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file with the RT peptides ('TraML' or 'csv')" help="(-tr) "/>
+    <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) "/>
+    <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
+    <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
+    <param name="param_estimateBestPeptides" display="radio" type="boolean" truevalue="-estimateBestPeptides" falsevalue="" checked="false" optional="True" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization. Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (" help="(-estimateBestPeptides) e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
+    <param name="param_algorithm_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help="(-stop_report_after_feature) "/>
+    <param name="param_algorithm_rt_extraction_window" type="float" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="(-rt_extraction_window) For this to work, the TraML input file needs to contain normalized RT values"/>
+    <param name="param_algorithm_rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)"/>
+    <param name="param_algorithm_uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_sn) "/>
+    <param name="param_algorithm_uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_peak_area) "/>
+    <param name="param_algorithm_TransitionGroupPicker_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/>
+    <param name="param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" display="radio" type="select" optional="False" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
+      <option value="false">false</option>
+      <option value="true" selected="true">true</option>
+    </param>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="40.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help="(-write_sn_log_messages) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
+      <option value="legacy" selected="true">legacy</option>
+      <option value="corrected">corrected</option>
+      <option value="crawdad">crawdad</option>
+    </param>
+    <param name="param_algorithm_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/>
+    <param name="param_algorithm_DIAScoring_dia_centroided" display="radio" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
+    <param name="param_algorithm_DIAScoring_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to conside" help="(-dia_byseries_intensity_min) "/>
+    <param name="param_algorithm_DIAScoring_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help="(-dia_byseries_ppm_diff) "/>
+    <param name="param_algorithm_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/>
+    <param name="param_algorithm_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/>
+    <param name="param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff" type="float" min="0.0" optional="True" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help="(-peak_before_mono_max_ppm_diff) "/>
+    <param name="param_outlierDetection_outlierMethod" display="radio" type="select" optional="False" value="iter_residual" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="(-outlierMethod) Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
+      <option value="iter_residual" selected="true">iter_residual</option>
+      <option value="iter_jackknife">iter_jackknife</option>
+      <option value="ransac">ransac</option>
+      <option value="none">none</option>
+    </param>
+    <param name="param_outlierDetection_useIterativeChauvenet" display="radio" type="boolean" truevalue="-outlierDetection:useIterativeChauvenet" falsevalue="" checked="false" optional="True" label="Whether to use Chauvenet's criterion when using iterative methods" help="(-useIterativeChauvenet) This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
+    <param name="param_outlierDetection_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help="(-RANSACMaxIterations) "/>
+    <param name="param_outlierDetection_RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="(-RANSACMaxPercentRTThreshold) Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
+    <param name="param_outlierDetection_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help="(-RANSACSamplingSize) "/>
+    <param name="param_peptideEstimation_InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="(-InitialQualityCutoff) -2 to 2)"/>
+    <param name="param_peptideEstimation_OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="(-OverallQualityCutoff) 0 to 10)"/>
+    <param name="param_peptideEstimation_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="(-NrRTBins) This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
+    <param name="param_peptideEstimation_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin) "/>
+    <param name="param_peptideEstimation_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_algorithm_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff) "/>
+      <param name="param_algorithm_write_convex_hull" display="radio" type="boolean" truevalue="-algorithm:write_convex_hull" falsevalue="" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull) "/>
+      <param name="param_algorithm_add_up_spectra" type="integer" min="1" optional="True" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help="(-add_up_spectra) "/>
+      <param name="param_algorithm_spacing_for_spectra_resampling" type="float" min="0.0" optional="True" value="0.005" label="If spectra are to be added, use this spacing to add them up" help="(-spacing_for_spectra_resampling) "/>
+      <param name="param_algorithm_TransitionGroupPicker_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
+      <param name="param_algorithm_TransitionGroupPicker_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that">
+        <option value="none" selected="true">none</option>
+        <option value="smoothed">smoothed</option>
+        <option value="original">original</option>
+      </param>
+      <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
+      <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
+      <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/>
+      <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/>
+      <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
+      <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
+      <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>
+      <param name="param_algorithm_Scores_use_shape_score" display="radio" type="select" optional="False" value="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_coelution_score" display="radio" type="select" optional="False" value="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_rt_score" display="radio" type="select" optional="False" value="true" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_library_score" display="radio" type="select" optional="False" value="true" label="Use the library score" help="(-use_library_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_elution_model_score" display="radio" type="select" optional="False" value="true" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help="(-use_elution_model_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_intensity_score" display="radio" type="select" optional="False" value="true" label="Use the intensity score" help="(-use_intensity_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_nr_peaks_score" display="radio" type="select" optional="False" value="true" label="Use the number of peaks score" help="(-use_nr_peaks_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_total_xic_score" display="radio" type="select" optional="False" value="true" label="Use the total XIC score" help="(-use_total_xic_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_sn_score" display="radio" type="select" optional="False" value="true" label="Use the SN (signal to noise) score" help="(-use_sn_score) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) ">
+        <option value="true" selected="true">true</option>
+        <option value="false">false</option>
+      </param>
+      <param name="param_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
+      <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/>
+      <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="trafoxml"/>
+  </outputs>
+  <help>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html</help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SKIP_TOOLS_FILE.txt	Wed Mar 01 12:16:05 2017 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Wed Mar 01 12:16:05 2017 -0500
@@ -0,0 +1,33 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<datatypes>
+  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
+    <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml"/>
+    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
+    <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXM" mimetype="application/xml"/>
+    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
+    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
+    <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf"/>
+    <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml"/>
+    <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
+    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
+    <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp"/>
+    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
+    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
+    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
+    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
+    <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml"/>
+    <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
+    <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml"/>
+    <datatype extension="grid" type="galaxy.datatypes.data:Grid"/>
+    <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml"/>
+    <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
+    <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
+    <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml"/>
+    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
+    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
+    <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml"/>
+    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
+  </registration>
+</datatypes>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filetypes.txt	Wed Mar 01 12:16:05 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Mar 01 12:16:05 2017 -0500
@@ -0,0 +1,35 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.1">openms</requirement>
+      <requirement type="package" version="15.12.15.2">xtandem</requirement>
+      <requirement type="package" version="1.0">fido</requirement>
+      <requirement type="package" version="2016.10.26">msgf_plus</requirement>
+    </requirements>
+  </xml>
+  <xml name="stdio">
+    <stdio>
+      <exit_code range="1:"/>
+      <exit_code range=":-1"/>
+      <regex match="Exception:"/>
+    </stdio>
+  </xml>
+  <xml name="references">
+    <citations>
+      <citation type="doi">doi:10.1186/1471-2105-9-163</citation>
+    </citations>
+  </xml>
+  <xml name="advanced_options">
+    <conditional name="adv_opts">
+      <param name="adv_opts_selector" type="select" label="Advanced Options">
+        <option value="basic" selected="True">Hide Advanced Options</option>
+        <option value="advanced">Show Advanced Options</option>
+      </param>
+      <when value="basic"/>
+      <when value="advanced">
+        <yield/>
+      </when>
+    </conditional>
+  </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.md	Wed Mar 01 12:16:05 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):
+ 
+   ```
+    <command><![CDATA[
+
+    ## check input file type
+    #set $in_type = $param_in.ext
+
+    ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files
+    ln -s '$param_in' 'param_in.${in_type}' &&
+    ln -s '$param_database' param_database.fasta &&
+    ## find location of the MSGFPlus.jar file of the msgf_plus conda package
+    MSGF_JAR=\$(msgf_plus -get_jar_path) &&
+
+    MSGFPlusAdapter
+    -executable \$MSGF_JAR
+    #if $param_in:
+      -in 'param_in.${in_type}'
+    #end if
+    #if $param_out:
+      -out $param_out
+    #end if
+    #if $param_mzid_out:
+      -mzid_out $param_mzid_out
+    #end if
+    #if $param_database:
+      -database param_database.fasta
+    #end if
+    
+    [...]
+    ]]>
+    ```
+ * 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.:
+ 
+        <data name="param_out" metadata_source="param_in" auto_format="true"/>
+        
+ * 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.
+ 
+    ```
+       <tests>
+        <test>
+            <param name="param_in" value="DecoyDatabase_input.fasta"/>
+            <output name="param_out" file="DecoyDatabase_output.fasta"/>
+        </test>
+    </tests>
+    ```
+    
+
+ * 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.
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Wed Mar 01 12:16:05 2017 -0500
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Required proteomics dependencies.">
+  <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DecoyDatabase_input.fasta	Wed Mar 01 12:16:05 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DecoyDatabase_output.fasta	Wed Mar 01 12:16:05 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool.conf	Wed Mar 01 12:16:05 2017 -0500
@@ -0,0 +1,162 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<toolbox>
+  <section id="section-id-Peptidepropertyprediction" name="Peptide property prediction">
+    <tool file="openms/PTModel.xml"/>
+    <tool file="openms/PTPredict.xml"/>
+    <tool file="openms/RTModel.xml"/>
+    <tool file="openms/RTPredict.xml"/>
+  </section>
+  <section id="section-id-DEFAULT" name="DEFAULT">
+    <tool file="openms/OpenSwathFileSplitter.xml"/>
+    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
+  </section>
+  <section id="section-id-TargetedExperiments" name="Targeted Experiments">
+    <tool file="openms/ConvertTraMLToTSV.xml"/>
+    <tool file="openms/ConvertTSVToTraML.xml"/>
+    <tool file="openms/InclusionExclusionListCreator.xml"/>
+    <tool file="openms/MRMMapper.xml"/>
+    <tool file="openms/OpenSwathAnalyzer.xml"/>
+    <tool file="openms/OpenSwathAssayGenerator.xml"/>
+    <tool file="openms/OpenSwathChromatogramExtractor.xml"/>
+    <tool file="openms/OpenSwathConfidenceScoring.xml"/>
+    <tool file="openms/OpenSwathDecoyGenerator.xml"/>
+    <tool file="openms/OpenSwathDIAPreScoring.xml"/>
+    <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/>
+    <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/>
+    <tool file="openms/OpenSwathRTNormalizer.xml"/>
+    <tool file="openms/PrecursorIonSelector.xml"/>
+  </section>
+  <section id="section-id-Utilities" name="Utilities">
+    <tool file="openms/AccurateMassSearch.xml"/>
+    <tool file="openms/CVInspector.xml"/>
+    <tool file="openms/DecoyDatabase.xml"/>
+    <tool file="openms/DeMeanderize.xml"/>
+    <tool file="openms/Digestor.xml"/>
+    <tool file="openms/DigestorMotif.xml"/>
+    <tool file="openms/ERPairFinder.xml"/>
+    <tool file="openms/FFEval.xml"/>
+    <tool file="openms/FuzzyDiff.xml"/>
+    <tool file="openms/IDDecoyProbability.xml"/>
+    <tool file="openms/IDExtractor.xml"/>
+    <tool file="openms/IDMassAccuracy.xml"/>
+    <tool file="openms/IDScoreSwitcher.xml"/>
+    <tool file="openms/IDSplitter.xml"/>
+    <tool file="openms/LabeledEval.xml"/>
+    <tool file="openms/LowMemPeakPickerHiRes.xml"/>
+    <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/>
+    <tool file="openms/MapAlignmentEvaluation.xml"/>
+    <tool file="openms/MassCalculator.xml"/>
+    <tool file="openms/MetaboliteSpectralMatcher.xml"/>
+    <tool file="openms/MetaProSIP.xml"/>
+    <tool file="openms/MRMPairFinder.xml"/>
+    <tool file="openms/MRMTransitionGroupPicker.xml"/>
+    <tool file="openms/MSSimulator.xml"/>
+    <tool file="openms/MultiplexResolver.xml"/>
+    <tool file="openms/MzMLSplitter.xml"/>
+    <tool file="openms/OpenSwathWorkflow.xml"/>
+    <tool file="openms/QCCalculator.xml"/>
+    <tool file="openms/QCEmbedder.xml"/>
+    <tool file="openms/QCExporter.xml"/>
+    <tool file="openms/QCExtractor.xml"/>
+    <tool file="openms/QCImporter.xml"/>
+    <tool file="openms/QCMerger.xml"/>
+    <tool file="openms/QCShrinker.xml"/>
+    <tool file="openms/RNPxl.xml"/>
+    <tool file="openms/RNPxlXICFilter.xml"/>
+    <tool file="openms/RTEvaluation.xml"/>
+    <tool file="openms/SemanticValidator.xml"/>
+    <tool file="openms/SequenceCoverageCalculator.xml"/>
+    <tool file="openms/SimpleSearchEngine.xml"/>
+    <tool file="openms/SpecLibCreator.xml"/>
+    <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/>
+    <tool file="openms/TICCalculator.xml"/>
+    <tool file="openms/TopPerc.xml"/>
+    <tool file="openms/TransformationEvaluation.xml"/>
+    <tool file="openms/XMLValidator.xml"/>
+  </section>
+  <section id="section-id-MapAlignment" name="Map Alignment">
+    <tool file="openms/ConsensusMapNormalizer.xml"/>
+    <tool file="openms/FeatureLinkerLabeled.xml"/>
+    <tool file="openms/FeatureLinkerUnlabeled.xml"/>
+    <tool file="openms/FeatureLinkerUnlabeledQT.xml"/>
+    <tool file="openms/MapRTTransformer.xml"/>
+  </section>
+  <section id="section-id-IDProcessing" name="ID Processing">
+    <tool file="openms/ConsensusID.xml"/>
+    <tool file="openms/FalseDiscoveryRate.xml"/>
+    <tool file="openms/FidoAdapter.xml"/>
+    <tool file="openms/IDConflictResolver.xml"/>
+    <tool file="openms/IDFileConverter.xml"/>
+    <tool file="openms/IDFilter.xml"/>
+    <tool file="openms/IDMapper.xml"/>
+    <tool file="openms/IDPosteriorErrorProbability.xml"/>
+    <tool file="openms/IDRTCalibration.xml"/>
+    <tool file="openms/LuciphorAdapter.xml"/>
+    <tool file="openms/PeptideIndexer.xml"/>
+    <tool file="openms/PhosphoScoring.xml"/>
+  </section>
+  <section id="section-id-Signalprocessingandpreprocessing" name="Signal processing and preprocessing">
+    <tool file="openms/BaselineFilter.xml"/>
+    <tool file="openms/ExternalCalibration.xml"/>
+    <tool file="openms/HighResPrecursorMassCorrector.xml"/>
+    <tool file="openms/InternalCalibration.xml"/>
+    <tool file="openms/MapNormalizer.xml"/>
+    <tool file="openms/MassTraceExtractor.xml"/>
+    <tool file="openms/NoiseFilterGaussian.xml"/>
+    <tool file="openms/NoiseFilterSGolay.xml"/>
+    <tool file="openms/PeakPickerHiRes.xml"/>
+    <tool file="openms/PeakPickerIterative.xml"/>
+    <tool file="openms/PeakPickerWavelet.xml"/>
+    <tool file="openms/PrecursorMassCorrector.xml"/>
+    <tool file="openms/SpectraMerger.xml"/>
+    <tool file="openms/TOFCalibration.xml"/>
+  </section>
+  <section id="section-id-Identification" name="Identification">
+    <tool file="openms/CompNovoCID.xml"/>
+    <tool file="openms/CompNovo.xml"/>
+    <tool file="openms/InspectAdapter.xml"/>
+    <tool file="openms/MascotAdapter.xml"/>
+    <tool file="openms/MascotAdapterOnline.xml"/>
+    <tool file="openms/MSGFPlusAdapter.xml"/>
+    <tool file="openms/ProteinInference.xml"/>
+    <tool file="openms/SpectraFilterBernNorm.xml"/>
+    <tool file="openms/SpectraFilterMarkerMower.xml"/>
+    <tool file="openms/SpectraFilterNLargest.xml"/>
+    <tool file="openms/SpectraFilterNormalizer.xml"/>
+    <tool file="openms/SpectraFilterParentPeakMower.xml"/>
+    <tool file="openms/SpectraFilterScaler.xml"/>
+    <tool file="openms/SpectraFilterSqrtMower.xml"/>
+    <tool file="openms/SpectraFilterThresholdMower.xml"/>
+    <tool file="openms/SpectraFilterWindowMower.xml"/>
+    <tool file="openms/XTandemAdapter.xml"/>
+  </section>
+  <section id="section-id-FileHandling" name="File Handling">
+    <tool file="openms/DTAExtractor.xml"/>
+    <tool file="openms/FileConverter.xml"/>
+    <tool file="openms/FileFilter.xml"/>
+    <tool file="openms/FileInfo.xml"/>
+    <tool file="openms/FileMerger.xml"/>
+    <tool file="openms/IDMerger.xml"/>
+    <tool file="openms/IDRipper.xml"/>
+    <tool file="openms/MapStatistics.xml"/>
+    <tool file="openms/MzTabExporter.xml"/>
+    <tool file="openms/TextExporter.xml"/>
+  </section>
+  <section id="section-id-Quantitation" name="Quantitation">
+    <tool file="openms/AdditiveSeries.xml"/>
+    <tool file="openms/Decharger.xml"/>
+    <tool file="openms/EICExtractor.xml"/>
+    <tool file="openms/FeatureFinderCentroided.xml"/>
+    <tool file="openms/FeatureFinderIdentification.xml"/>
+    <tool file="openms/FeatureFinderIsotopeWavelet.xml"/>
+    <tool file="openms/FeatureFinderMetabo.xml"/>
+    <tool file="openms/FeatureFinderMRM.xml"/>
+    <tool file="openms/FeatureFinderMultiplex.xml"/>
+    <tool file="openms/FeatureFinderSuperHirn.xml"/>
+    <tool file="openms/IsobaricAnalyzer.xml"/>
+    <tool file="openms/ITRAQAnalyzer.xml"/>
+    <tool file="openms/ProteinQuantifier.xml"/>
+    <tool file="openms/ProteinResolver.xml"/>
+    <tool file="openms/TMTAnalyzer.xml"/>
+  </section>
+</toolbox>