--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PrecursorIonSelector.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,148 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="1.12.0">
+  <description>PrecursorIonSelector</description>
+  <macros>
+    <token name="@EXECUTABLE@">PrecursorIonSelector</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PrecursorIonSelector
+
+-in ${param_in}
+-out ${param_out}
+-next_feat ${param_next_feat}
+-ids ${param_ids}
+-num_precursors ${param_num_precursors}
+-raw_data ${param_raw_data}
+${param_load_preprocessing}
+${param_store_preprocessing}
+${param_simulation}
+-sim_results ${param_sim_results}
+-db_path ${param_db_path}
+-rt_model ${param_rt_model}
+-dt_model ${param_dt_model}
+-fixed_modifications ${param_fixed_modifications}
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:type ${param_type}
+-algorithm:max_iteration ${param_max_iteration}
+-algorithm:rt_bin_capacity ${param_rt_bin_capacity}
+-algorithm:step_size ${param_step_size}
+-algorithm:peptide_min_prob ${param_peptide_min_prob}
+${param_sequential_spectrum_order}
+-algorithm:MIPFormulation:thresholds:min_protein_probability ${param_min_protein_probability}
+-algorithm:MIPFormulation:thresholds:min_protein_id_probability ${param_min_protein_id_probability}
+-algorithm:MIPFormulation:thresholds:min_pt_weight ${param_min_pt_weight}
+-algorithm:MIPFormulation:thresholds:min_mz ${param_min_mz}
+-algorithm:MIPFormulation:thresholds:max_mz ${param_max_mz}
+-algorithm:MIPFormulation:thresholds:min_pred_pep_prob ${param_min_pred_pep_prob}
+-algorithm:MIPFormulation:thresholds:min_rt_weight ${param_min_rt_weight}
+${param_use_peptide_rule}
+-algorithm:MIPFormulation:thresholds:min_peptide_ids ${param_min_peptide_ids}
+-algorithm:MIPFormulation:thresholds:min_peptide_probability ${param_min_peptide_probability}
+-algorithm:MIPFormulation:combined_ilp:k1 ${param_k1}
+-algorithm:MIPFormulation:combined_ilp:k2 ${param_k2}
+-algorithm:MIPFormulation:combined_ilp:k3 ${param_k3}
+${param_scale_matching_probs}
+${param_no_intensity_normalization}
+-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature}
+-algorithm:Preprocessing:precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-algorithm:Preprocessing:precursor_mass_tolerance_unit ${param_precursor_mass_tolerance_unit}
+-algorithm:Preprocessing:preprocessed_db_path ${param_preprocessed_db_path}
+-algorithm:Preprocessing:preprocessed_db_pred_rt_path ${param_preprocessed_db_pred_rt_path}
+-algorithm:Preprocessing:preprocessed_db_pred_dt_path ${param_preprocessed_db_pred_dt_path}
+-algorithm:Preprocessing:max_peptides_per_run ${param_max_peptides_per_run}
+-algorithm:Preprocessing:missed_cleavages ${param_missed_cleavages}
+-algorithm:Preprocessing:taxonomy ${param_taxonomy}
+-algorithm:Preprocessing:tmp_dir ${param_tmp_dir}
+-algorithm:Preprocessing:store_peptide_sequences ${param_store_peptide_sequences}
+-algorithm:Preprocessing:rt_settings:min_rt ${param_min_rt}
+-algorithm:Preprocessing:rt_settings:max_rt ${param_max_rt}
+-algorithm:Preprocessing:rt_settings:rt_step_size ${param_rt_step_size}
+-algorithm:Preprocessing:rt_settings:gauss_mean ${param_gauss_mean}
+-algorithm:Preprocessing:rt_settings:gauss_sigma ${param_gauss_sigma}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -solver ${adv_opts.param_solver}
+#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="text" size="20" label="file containing results of identification (idXML)" 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" type="boolean" truevalue="-load_preprocessing true" falsevalue="-load_preprocessing false" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated." help="(-load_preprocessing)"/>
+    <param name="param_store_preprocessing" type="boolean" truevalue="-store_preprocessing true" falsevalue="-store_preprocessing false" checked="false" optional="True" label="The preprocessed db is stored." help="(-store_preprocessing)"/>
+    <param name="param_simulation" type="boolean" truevalue="-simulation true" falsevalue="-simulation false" checked="false" optional="True" label="Simulate the whole LC-MS/MS run." help="(-simulation)"/>
+    <param name="param_sim_results" type="text" size="20" label="File containing the results of the simulation run" help="(-sim_results)"/>
+    <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="20" label="SVM Model for RTPredict" help="(-rt_model)"/>
+    <param name="param_dt_model" type="text" size="20" label="SVM Model for PTPredict" help="(-dt_model)"/>
+    <param name="param_fixed_modifications" type="text" size="20" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications)"/>
+    <param name="param_type" type="select" optional="True" value="IPS" label="Strategy for precursor ion selection." help="(-type)">
+      <option value="ILP_IPS">ILP_IPS</option>
+      <option value="IPS">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_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations." help="(-max_iteration)"/>
+    <param name="param_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_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration." help="(-step_size)"/>
+    <param name="param_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability." help="(-peptide_min_prob)"/>
+    <param name="param_sequential_spectrum_order" type="boolean" truevalue="-algorithm:sequential_spectrum_order true" falsevalue="-algorithm:sequential_spectrum_order false" checked="false" optional="True" label="If true, precursors are selected sequentially with respect to their RT." help="(-sequential_spectrum_order)"/>
+    <param name="param_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_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_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precursor" help="(-min_pt_weight)"/>
+    <param name="param_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_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_min_pred_pep_prob" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal predicted peptide probability of a precursor" help="(-min_pred_pep_prob)"/>
+    <param name="param_min_rt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal rt weight of a precursor" help="(-min_rt_weight)"/>
+    <param name="param_use_peptide_rule" type="boolean" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule true" falsevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule false" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule)"/>
+    <param name="param_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_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_k1" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for z_i" help="(-k1)"/>
+    <param name="param_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_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_scale_matching_probs" type="boolean" truevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs true" falsevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs false" checked="true" optional="True" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs)"/>
+    <param name="param_no_intensity_normalization" type="boolean" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization true" falsevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization false" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]. This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1." help="(-no_intensity_normalization)"/>
+    <param name="param_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_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_precursor_mass_tolerance_unit" type="select" optional="True" value="ppm" label="Precursor mass tolerance unit." help="(-precursor_mass_tolerance_unit)">
+      <option value="ppm">ppm</option>
+      <option value="Da">Da</option>
+    </param>
+    <param name="param_preprocessed_db_path" type="text" size="20" label="Path where the preprocessed database should be stored" help="(-preprocessed_db_path)"/>
+    <param name="param_preprocessed_db_pred_rt_path" type="text" size="20" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_rt_path)"/>
+    <param name="param_preprocessed_db_pred_dt_path" type="text" size="20" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_dt_path)"/>
+    <param name="param_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_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages." help="(-missed_cleavages)"/>
+    <param name="param_taxonomy" type="text" size="20" label="Taxonomy" help="(-taxonomy)"/>
+    <param name="param_tmp_dir" type="text" size="20" label="Absolute path to tmp data directory used to store files needed for rt and dt prediction." help="(-tmp_dir)"/>
+    <param name="param_store_peptide_sequences" type="text" size="20" value="false" label="Flag if peptide sequences should be stored." help="(-store_peptide_sequences)"/>
+    <param name="param_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_max_rt" type="float" value="3840.0" label="Maximal RT in the experiment (in seconds)" help="(-max_rt)"/>
+    <param name="param_rt_step_size" type="float" value="30.0" label="Time between two consecutive spectra (in seconds)" help="(-rt_step_size)"/>
+    <param name="param_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean)"/>
+    <param name="param_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma)"/>
+    <expand macro="advanced_options">
+      <param name="param_solver" type="select" optional="True" value="GLPK" label="LP solver type" help="(-solver)">
+        <option value="GLPK">GLPK</option>
+        <option value="COINOR">COINOR</option>
+      </param>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="modified feature map" format="featureXML"/>
+    <data name="param_next_feat" label="feature map (featureXML) file with the selected precursors" format="featureXML"/>
+  </outputs>
+  <help>**What it does**
+
+PrecursorIonSelector
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html
+
+@REFERENCES@
+</help>
+</tool>