--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/InclusionExclusionListCreator.xml	Wed Mar 01 12:27:13 2017 -0500
@@ -0,0 +1,219 @@
+<?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="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.1.0">
+  <description>Creates inclusion and/or exclusion lists.</description>
+  <macros>
+    <token name="@EXECUTABLE@">InclusionExclusionListCreator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>InclusionExclusionListCreator
+
+#if $param_include:
+  -include $param_include
+#end if
+#if $param_exclude:
+  -exclude $param_exclude
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_rt_model:
+  -rt_model $param_rt_model
+#end if
+#if $param_pt_model:
+  -pt_model $param_pt_model
+#end if
+
+#if $rep_param_inclusion_charges:
+-inclusion_charges
+  #for token in $rep_param_inclusion_charges:
+    #if " " in str(token):
+      "$token.param_inclusion_charges"
+    #else
+      $token.param_inclusion_charges
+    #end if
+  #end for
+#end if
+#if $param_inclusion_strategy:
+  -inclusion_strategy $param_inclusion_strategy
+#end if
+
+#if $rep_param_exclusion_charges:
+-exclusion_charges
+  #for token in $rep_param_exclusion_charges:
+    #if " " in str(token):
+      "$token.param_exclusion_charges"
+    #else
+      $token.param_exclusion_charges
+    #end if
+  #end for
+#end if
+#if $param_raw_data:
+  -raw_data $param_raw_data
+#end if
+#if $param_algorithm_InclusionExclusionList_missed_cleavages:
+  -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages
+#end if
+#if $param_algorithm_InclusionExclusionList_RT_unit:
+  -algorithm:InclusionExclusionList:RT:unit $param_algorithm_InclusionExclusionList_RT_unit
+#end if
+#if $param_algorithm_InclusionExclusionList_RT_use_relative:
+  -algorithm:InclusionExclusionList:RT:use_relative $param_algorithm_InclusionExclusionList_RT_use_relative
+#end if
+#if $param_algorithm_InclusionExclusionList_RT_window_relative:
+  -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative
+#end if
+#if $param_algorithm_InclusionExclusionList_RT_window_absolute:
+  -algorithm:InclusionExclusionList:RT:window_absolute $param_algorithm_InclusionExclusionList_RT_window_absolute
+#end if
+#if $param_algorithm_InclusionExclusionList_merge_mz_tol:
+  -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol
+#end if
+#if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit:
+  -algorithm:InclusionExclusionList:merge:mz_tol_unit $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
+#end if
+#if $param_algorithm_InclusionExclusionList_merge_rt_tol:
+  -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
+#end if
+#if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin:
+  -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin
+#end if
+#if $param_algorithm_PrecursorSelection_exclude_overlapping_peaks:
+  -algorithm:PrecursorSelection:exclude_overlapping_peaks
+#end if
+#if $param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion:
+  -algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion
+#end if
+#if $param_algorithm_PrecursorSelection_Exclusion_exclusion_time:
+  -algorithm:PrecursorSelection:Exclusion:exclusion_time $param_algorithm_PrecursorSelection_Exclusion_exclusion_time
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids
+#end if
+#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability:
+  -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability
+#end if
+#if $param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization:
+  -algorithm:PrecursorSelection:feature_based:no_intensity_normalization
+#end if
+#if $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature:
+  -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_include" type="data" format="fasta,featurexml" optional="True" label="Inclusion list input file in FASTA or featureXML format" help="(-include) "/>
+    <param name="param_exclude" type="data" format="fasta,featurexml,idxml" optional="True" label="Exclusion list input file in featureXML, idXML or FASTA format" help="(-exclude) "/>
+    <param name="param_rt_model" type="data" format="txt" optional="True" label="RTModel file used for the rt prediction of peptides in FASTA files" help="(-rt_model) "/>
+    <param name="param_pt_model" type="data" format="txt" optional="True" label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)" help="(-pt_model) "/>
+    <repeat name="rep_param_inclusion_charges" min="0" max="1" title="param_inclusion_charges">
+      <param name="param_inclusion_charges" type="text" min="1" optional="True" size="30" value="1" label="List containing the charge states to be considered for the inclusion list compounds, space separated" help="(-inclusion_charges) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_inclusion_strategy" display="radio" type="select" optional="False" value="ALL" label="strategy to be used for selection" help="(-inclusion_strategy) ">
+      <option value="FeatureBased_LP">FeatureBased_LP</option>
+      <option value="ProteinBased_LP">ProteinBased_LP</option>
+      <option value="ALL" selected="true">ALL</option>
+    </param>
+    <repeat name="rep_param_exclusion_charges" min="0" max="1" title="param_exclusion_charges">
+      <param name="param_exclusion_charges" type="text" min="1" optional="True" size="30" value="1" label="List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated" help="(-exclusion_charges) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_raw_data" type="data" format="mzml" optional="True" label="File containing the raw data (only needed for FeatureBased_LP)" help="(-raw_data) "/>
+    <param name="param_algorithm_InclusionExclusionList_missed_cleavages" type="integer" value="0" label="Number of missed cleavages used for protein digestion" help="(-missed_cleavages) &lt;br&gt;"/>
+    <param name="param_algorithm_InclusionExclusionList_RT_unit" display="radio" type="select" optional="False" value="minutes" label="Create lists with units as seconds instead of minutes" help="(-unit) ">
+      <option value="minutes" selected="true">minutes</option>
+      <option value="seconds">seconds</option>
+    </param>
+    <param name="param_algorithm_InclusionExclusionList_RT_use_relative" display="radio" type="select" optional="False" value="true" label="Use relative RT window, which depends on RT of precurso" help="(-use_relative) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_algorithm_InclusionExclusionList_RT_window_relative" type="float" min="0.0" max="10.0" optional="True" value="0.05" label="[for RT:use_relative == true] The relative factor X for the RT exclusion window," help="(-window_relative) e.g. the window is calculated as [rt - rt*X, rt + rt*X]"/>
+    <param name="param_algorithm_InclusionExclusionList_RT_window_absolute" type="float" min="0.0" optional="True" value="90.0" label="[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec]," help="(-window_absolute) e.g. the window is calculated as [rt - X, rt + X]"/>
+    <param name="param_algorithm_InclusionExclusionList_merge_mz_tol" type="float" min="0.0" optional="True" value="10.0" label="Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance" help="(-mz_tol) Unit of this is defined in 'mz_tol_unit'"/>
+    <param name="param_algorithm_InclusionExclusionList_merge_mz_tol_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of 'mz_tol'" help="(-mz_tol_unit) ">
+      <option value="ppm" selected="true">ppm</option>
+      <option value="Da">Da</option>
+    </param>
+    <param name="param_algorithm_InclusionExclusionList_merge_rt_tol" type="float" min="0.0" optional="True" value="1.1" label="Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows)" help="(-rt_tol) Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds]"/>
+    <param name="param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin" type="integer" min="1" optional="True" value="5" label="Number of allowed MS/MS spectra in a retention time bin" help="(-ms2_spectra_per_rt_bin) "/>
+    <param name="param_algorithm_PrecursorSelection_exclude_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks" falsevalue="" checked="false" optional="True" label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" help="(-exclude_overlapping_peaks) "/>
+    <param name="param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion" display="radio" type="boolean" truevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion" falsevalue="" checked="false" optional="True" label="If true dynamic exclusion is applied" help="(-use_dynamic_exclusion) "/>
+    <param name="param_algorithm_PrecursorSelection_Exclusion_exclusion_time" type="float" min="0.0" optional="True" value="100.0" label="The time (in seconds) a feature is excluded" help="(-exclusion_time) "/>
+    <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size" type="integer" min="1" optional="True" value="1000" label="The maximal number of precursors in the inclusion list" help="(-max_list_size) "/>
+    <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds" help="(-min_rt) "/>
+    <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds" help="(-max_rt) "/>
+    <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size" type="float" min="1.0" optional="True" value="30.0" label="rt step size in seconds" help="(-rt_step_size) "/>
+    <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds" help="(-rt_window_size) "/>
+    <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_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_PrecursorSelection_ProteinBasedInclusion_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_PrecursorSelection_ProteinBasedInclusion_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_PrecursorSelection_ProteinBasedInclusion_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_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule" display="radio" type="boolean" truevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion: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_PrecursorSelection_ProteinBasedInclusion_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_PrecursorSelection_ProteinBasedInclusion_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_PrecursorSelection_feature_based_no_intensity_normalization" display="radio" type="boolean" truevalue="-algorithm:PrecursorSelection: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_PrecursorSelection_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) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="tabular"/>
+  </outputs>
+  <help>Creates inclusion and/or exclusion lists.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html</help>
+</tool>