Mercurial > repos > galaxyp > openms_openswathanalyzer
changeset 0:f9ead04f81ef draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:58:14 -0500 |
| parents | |
| children | 2473b7efa9d1 |
| files | OpenSwathAnalyzer.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, 1162 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OpenSwathAnalyzer.xml Wed Mar 01 12:58:14 2017 -0500 @@ -0,0 +1,351 @@ +<?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="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.1.0"> + <description>Picks peaks and finds features in an SRM experiment.</description> + <macros> + <token name="@EXECUTABLE@">OpenSwathAnalyzer</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>OpenSwathAnalyzer + +#if $param_in: + -in $param_in +#end if +#if $param_tr: + -tr $param_tr +#end if +#if $param_rt_norm: + -rt_norm $param_rt_norm +#end if +#if $param_out: + -out $param_out +#end if +#if $param_no_strict: + -no-strict +#end if +-swath_files + #for token in $param_swath_files: + $token + #end for +#if $param_min_upper_edge_dist: + -min_upper_edge_dist $param_min_upper_edge_dist +#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 $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_model_type: + -model:type $adv_opts.param_model_type +#end if + #if $adv_opts.param_model_symmetric_regression: + -model:symmetric_regression +#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" optional="False" label="input file containing the chromatograms" help="(-in) "/> + <param name="param_tr" type="data" format="traml" optional="False" label="transition file" 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_no_strict" display="radio" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/> + <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be used"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_min_upper_edge_dist" type="float" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/> + <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) <br>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) "/> + <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_model_type" display="radio" type="select" optional="False" value="linear" label="Type of model" help="(-type) "> + <option value="linear" selected="true">linear</option> + <option value="b_spline">b_spline</option> + <option value="interpolated">interpolated</option> + <option value="lowess">lowess</option> + </param> + <param name="param_model_symmetric_regression" display="radio" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/> + <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="""/> + </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="""/> + </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="featurexml"/> + </outputs> + <help>Picks peaks and finds features in an SRM experiment. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SKIP_TOOLS_FILE.txt Wed Mar 01 12:58:14 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 12:58:14 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 12:58:14 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 12:58:14 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 12:58:14 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 12:58:14 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 12:58:14 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 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+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 12:58:14 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 12:58:14 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>