--- /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>