Mercurial > repos > galaxyp > openms_precursorionselector

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PrecursorIonSelector.xml	Wed Mar 01 12:20:14 2017 -0500
@@ -0,0 +1,336 @@
+<?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="PrecursorIonSelector" name="PrecursorIonSelector" version="2.1.0">
+  <description>PrecursorIonSelector</description>
+  <macros>
+    <token name="@EXECUTABLE@">PrecursorIonSelector</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PrecursorIonSelector
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_next_feat:
+  -next_feat $param_next_feat
+#end if
+#if $param_ids:
+  -ids $param_ids
+#end if
+#if $param_num_precursors:
+  -num_precursors $param_num_precursors
+#end if
+#if $param_raw_data:
+  -raw_data $param_raw_data
+#end if
+#if $param_load_preprocessing:
+  -load_preprocessing
+#end if
+#if $param_store_preprocessing:
+  -store_preprocessing
+#end if
+#if $param_simulation:
+  -simulation
+#end if
+#if $param_sim_results:
+  -sim_results     "$param_sim_results"
+#end if
+#if $param_db_path:
+  -db_path $param_db_path
+#end if
+#if $param_rt_model:
+  -rt_model     "$param_rt_model"
+#end if
+#if $param_dt_model:
+  -dt_model     "$param_dt_model"
+#end if
+
+#if $rep_param_fixed_modifications:
+-fixed_modifications
+  #for token in $rep_param_fixed_modifications:
+    #if " " in str(token):
+      "$token.param_fixed_modifications"
+    #else
+      $token.param_fixed_modifications
+    #end if
+  #end for
+#end if
+#if $param_algorithm_type:
+  -algorithm:type $param_algorithm_type
+#end if
+#if $param_algorithm_max_iteration:
+  -algorithm:max_iteration $param_algorithm_max_iteration
+#end if
+#if $param_algorithm_rt_bin_capacity:
+  -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity
+#end if
+#if $param_algorithm_step_size:
+  -algorithm:step_size $param_algorithm_step_size
+#end if
+#if $param_algorithm_peptide_min_prob:
+  -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob
+#end if
+#if $param_algorithm_sequential_spectrum_order:
+  -algorithm:sequential_spectrum_order
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_min_protein_probability:
+  -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability:
+  -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_min_pt_weight:
+  -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_min_mz:
+  -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_max_mz:
+  -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob:
+  -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_min_rt_weight:
+  -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule:
+  -algorithm:MIPFormulation:thresholds:use_peptide_rule
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids:
+  -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids
+#end if
+#if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability:
+  -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability
+#end if
+#if $param_algorithm_MIPFormulation_combined_ilp_k1:
+  -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1
+#end if
+#if $param_algorithm_MIPFormulation_combined_ilp_k2:
+  -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2
+#end if
+#if $param_algorithm_MIPFormulation_combined_ilp_k3:
+  -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
+#end if
+#if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
+  -algorithm:MIPFormulation:combined_ilp:scale_matching_probs $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs
+#end if
+#if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
+  -algorithm:MIPFormulation:feature_based:no_intensity_normalization
+#end if
+#if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature:
+  -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature
+#end if
+#if $param_algorithm_Preprocessing_precursor_mass_tolerance:
+  -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
+#end if
+#if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
+  -algorithm:Preprocessing:precursor_mass_tolerance_unit $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
+#end if
+#if $param_algorithm_Preprocessing_preprocessed_db_path:
+  -algorithm:Preprocessing:preprocessed_db_path     "$param_algorithm_Preprocessing_preprocessed_db_path"
+#end if
+#if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path:
+  -algorithm:Preprocessing:preprocessed_db_pred_rt_path     "$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path"
+#end if
+#if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path:
+  -algorithm:Preprocessing:preprocessed_db_pred_dt_path     "$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path"
+#end if
+#if $param_algorithm_Preprocessing_max_peptides_per_run:
+  -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run
+#end if
+#if $param_algorithm_Preprocessing_missed_cleavages:
+  -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages
+#end if
+#if $param_algorithm_Preprocessing_taxonomy:
+  -algorithm:Preprocessing:taxonomy     "$param_algorithm_Preprocessing_taxonomy"
+#end if
+#if $param_algorithm_Preprocessing_tmp_dir:
+  -algorithm:Preprocessing:tmp_dir     "$param_algorithm_Preprocessing_tmp_dir"
+#end if
+#if $param_algorithm_Preprocessing_store_peptide_sequences:
+  -algorithm:Preprocessing:store_peptide_sequences     "$param_algorithm_Preprocessing_store_peptide_sequences"
+#end if
+#if $param_algorithm_Preprocessing_rt_settings_min_rt:
+  -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt
+#end if
+#if $param_algorithm_Preprocessing_rt_settings_max_rt:
+  -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt
+#end if
+#if $param_algorithm_Preprocessing_rt_settings_rt_step_size:
+  -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size
+#end if
+#if $param_algorithm_Preprocessing_rt_settings_gauss_mean:
+  -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean
+#end if
+#if $param_algorithm_Preprocessing_rt_settings_gauss_sigma:
+  -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_solver:
+  -solver $adv_opts.param_solver
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="featurexml" optional="False" label="Input feature map file (featureXML)" help="(-in) "/>
+    <param name="param_ids" type="data" format="idxml" optional="False" label="file containing results of identification" help="(-ids) "/>
+    <param name="param_num_precursors" type="integer" value="1" label="number of precursors to be selected" help="(-num_precursors) "/>
+    <param name="param_raw_data" type="data" format="mzml" optional="True" label="Input profile data" help="(-raw_data) "/>
+    <param name="param_load_preprocessing" display="radio" type="boolean" truevalue="-load_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated" help="(-load_preprocessing) "/>
+    <param name="param_store_preprocessing" display="radio" type="boolean" truevalue="-store_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is stored" help="(-store_preprocessing) "/>
+    <param name="param_simulation" display="radio" type="boolean" truevalue="-simulation" falsevalue="" checked="false" optional="True" label="Simulate the whole LC-MS/MS run" help="(-simulation) "/>
+    <param name="param_sim_results" type="text" size="30" label="File containing the results of the simulation run" help="(-sim_results) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_db_path" type="data" format="fasta" optional="True" label="db file" help="(-db_path) "/>
+    <param name="param_rt_model" type="text" size="30" label="SVM Model for RTPredict" help="(-rt_model) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_dt_model" type="text" size="30" label="SVM Model for PTPredict" help="(-dt_model) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <repeat name="rep_param_fixed_modifications" min="0" max="1" title="param_fixed_modifications">
+      <param name="param_fixed_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_algorithm_type" type="select" optional="False" value="IPS" label="Strategy for precursor ion selection" help="(-type) ">
+      <option value="ILP_IPS">ILP_IPS</option>
+      <option value="IPS" selected="true">IPS</option>
+      <option value="SPS">SPS</option>
+      <option value="Upshift">Upshift</option>
+      <option value="Downshift">Downshift</option>
+      <option value="DEX">DEX</option>
+    </param>
+    <param name="param_algorithm_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations" help="(-max_iteration) "/>
+    <param name="param_algorithm_rt_bin_capacity" type="integer" min="1" optional="True" value="10" label="Maximal number of precursors per rt bin" help="(-rt_bin_capacity) "/>
+    <param name="param_algorithm_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration" help="(-step_size) "/>
+    <param name="param_algorithm_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability" help="(-peptide_min_prob) "/>
+    <param name="param_algorithm_sequential_spectrum_order" display="radio" type="boolean" truevalue="-algorithm:sequential_spectrum_order" falsevalue="" checked="false" optional="True" label="If true, precursors are selected sequentially with respect to their RT" help="(-sequential_spectrum_order) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_min_protein_probability" type="float" min="0.0" max="1.0" optional="True" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help="(-min_protein_probability) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified" help="(-min_protein_id_probability) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help="(-min_mz) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help="(-max_mz) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal predicted peptide probability of a precurso" help="(-min_pred_pep_prob) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_min_rt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal rt weight of a precurso" help="(-min_rt_weight) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_use_peptide_rule" display="radio" type="boolean" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule" falsevalue="" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids) "/>
+    <param name="param_algorithm_MIPFormulation_thresholds_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability) "/>
+    <param name="param_algorithm_MIPFormulation_combined_ilp_k1" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for z_i" help="(-k1) "/>
+    <param name="param_algorithm_MIPFormulation_combined_ilp_k2" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help="(-k2) "/>
+    <param name="param_algorithm_MIPFormulation_combined_ilp_k3" type="float" min="0.0" optional="True" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help="(-k3) "/>
+    <param name="param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" display="radio" type="select" optional="False" value="true" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_algorithm_MIPFormulation_feature_based_no_intensity_normalization" display="radio" type="boolean" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" falsevalue="" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]" help="(-no_intensity_normalization) This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1"/>
+    <param name="param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature" type="integer" min="1" optional="True" value="1" label="The maximal number of precursors per feature" help="(-max_number_precursors_per_feature) "/>
+    <param name="param_algorithm_Preprocessing_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help="(-precursor_mass_tolerance) "/>
+    <param name="param_algorithm_Preprocessing_precursor_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Precursor mass tolerance unit" help="(-precursor_mass_tolerance_unit) ">
+      <option value="ppm" selected="true">ppm</option>
+      <option value="Da">Da</option>
+    </param>
+    <param name="param_algorithm_Preprocessing_preprocessed_db_path" type="text" size="30" label="Path where the preprocessed database should be stored" help="(-preprocessed_db_path) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_rt_path) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_dt_path) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_Preprocessing_max_peptides_per_run" type="integer" min="1" optional="True" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help="(-max_peptides_per_run) "/>
+    <param name="param_algorithm_Preprocessing_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
+    <param name="param_algorithm_Preprocessing_taxonomy" type="text" size="30" label="Taxonomy" help="(-taxonomy) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_Preprocessing_tmp_dir" type="text" size="30" label="Absolute path to tmp data directory used to store files needed for rt and dt prediction" help="(-tmp_dir) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_Preprocessing_store_peptide_sequences" type="text" size="30" value="false" label="Flag if peptide sequences should be stored" help="(-store_peptide_sequences) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_Preprocessing_rt_settings_min_rt" type="float" min="1.0" optional="True" value="960.0" label="Minimal RT in the experiment (in seconds)" help="(-min_rt) "/>
+    <param name="param_algorithm_Preprocessing_rt_settings_max_rt" type="float" value="3840.0" label="Maximal RT in the experiment (in seconds)" help="(-max_rt) "/>
+    <param name="param_algorithm_Preprocessing_rt_settings_rt_step_size" type="float" value="30.0" label="Time between two consecutive spectra (in seconds)" help="(-rt_step_size) "/>
+    <param name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean) "/>
+    <param name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma) "/>
+    <expand macro="advanced_options">
+      <param name="param_solver" display="radio" type="select" optional="False" value="GLPK" label="LP solver type" help="(-solver) ">
+        <option value="GLPK" selected="true">GLPK</option>
+        <option value="COINOR">COINOR</option>
+      </param>
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="featurexml"/>
+    <data name="param_next_feat" format="featurexml"/>
+  </outputs>
+  <help>PrecursorIonSelector
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html</help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SKIP_TOOLS_FILE.txt	Wed Mar 01 12:20:14 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 12:20:14 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 12:20:14 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 12:20:14 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 12:20:14 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 12:20:14 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 12:20:14 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
+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 12:20:14 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 12:20:14 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>