--- a/IsobaricAnalyzer.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/IsobaricAnalyzer.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,161 +1,542 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="1.12.0">
-  <description>Calculates isobaric quantitative values for peptides</description>
-  <macros>
-    <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>IsobaricAnalyzer
+<?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: [Quantitation]-->
+  <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.0.0">
+    <description>Calculates isobaric quantitative values for peptides</description>
+    <macros>
+      <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>IsobaricAnalyzer
+
+#if $param_type:
+  -type
+  #if &quot; &quot; in str($param_type):
+    &quot;$param_type&quot;
+  #else
+    $param_type
+  #end if
+#end if
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_extraction_select_activation:
+  -extraction:select_activation
+  #if &quot; &quot; in str($param_extraction_select_activation):
+    &quot;$param_extraction_select_activation&quot;
+  #else
+    $param_extraction_select_activation
+  #end if
+#end if
+#if $param_extraction_reporter_mass_shift:
+  -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift
+#end if
+#if $param_extraction_min_precursor_intensity:
+  -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity
+#end if
+#if $param_extraction_keep_unannotated_precursor:
+  -extraction:keep_unannotated_precursor
+#end if
+#if $param_extraction_min_reporter_intensity:
+  -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity
+#end if
+#if $param_extraction_discard_low_intensity_quantifications:
+  -extraction:discard_low_intensity_quantifications
+#end if
+#if $param_extraction_min_precursor_purity:
+  -extraction:min_precursor_purity $param_extraction_min_precursor_purity
+#end if
+#if $param_itraq4plex_channel_114_description:
+  -itraq4plex:channel_114_description     &quot;$param_itraq4plex_channel_114_description&quot;
+#end if
+#if $param_itraq4plex_channel_115_description:
+  -itraq4plex:channel_115_description     &quot;$param_itraq4plex_channel_115_description&quot;
+#end if
+#if $param_itraq4plex_channel_116_description:
+  -itraq4plex:channel_116_description     &quot;$param_itraq4plex_channel_116_description&quot;
+#end if
+#if $param_itraq4plex_channel_117_description:
+  -itraq4plex:channel_117_description     &quot;$param_itraq4plex_channel_117_description&quot;
+#end if
+#if $param_itraq4plex_reference_channel:
+  -itraq4plex:reference_channel $param_itraq4plex_reference_channel
+#end if
 
--type ${param_type}
--in ${param_in}
--out ${param_out}
--threads \${GALAXY_SLOTS:-24} 
--id_pool ${param_id_pool}
--extraction:select_activation ${param_select_activation}
--extraction:reporter_mass_shift ${param_reporter_mass_shift}
--extraction:min_precursor_intensity ${param_min_precursor_intensity}
-${param_keep_unannotated_precursor}
--extraction:min_reporter_intensity ${param_min_reporter_intensity}
-${param_discard_low_intensity_quantifications}
--extraction:min_precursor_purity ${param_min_precursor_purity}
--itraq4plex:channel_114_description ${param_channel_114_description}
--itraq4plex:channel_115_description ${param_channel_115_description}
--itraq4plex:channel_116_description ${param_channel_116_description}
--itraq4plex:channel_117_description ${param_channel_117_description}
--itraq4plex:reference_channel ${param_reference_channel}
--itraq4plex:correction_matrix ${param_correction_matrix}
--itraq8plex:channel_113_description ${param_channel_113_description}
--itraq8plex:channel_114_description ${param_channel_114_description}
--itraq8plex:channel_115_description ${param_channel_115_description}
--itraq8plex:channel_116_description ${param_channel_116_description}
--itraq8plex:channel_117_description ${param_channel_117_description}
--itraq8plex:channel_118_description ${param_channel_118_description}
--itraq8plex:channel_119_description ${param_channel_119_description}
--itraq8plex:channel_121_description ${param_channel_121_description}
--itraq8plex:reference_channel ${param_reference_channel}
--itraq8plex:correction_matrix ${param_correction_matrix}
-${param_isotope_correction}
-${param_normalization}
--tmt10plex:channel_126_description ${param_channel_126_description}
--tmt10plex:channel_127N_description ${param_channel_127N_description}
--tmt10plex:channel_127C_description ${param_channel_127C_description}
--tmt10plex:channel_128N_description ${param_channel_128N_description}
--tmt10plex:channel_128C_description ${param_channel_128C_description}
--tmt10plex:channel_129N_description ${param_channel_129N_description}
--tmt10plex:channel_129C_description ${param_channel_129C_description}
--tmt10plex:channel_130N_description ${param_channel_130N_description}
--tmt10plex:channel_130C_description ${param_channel_130C_description}
--tmt10plex:channel_131_description ${param_channel_131_description}
--tmt10plex:reference_channel ${param_reference_channel}
--tmt10plex:correction_matrix ${param_correction_matrix}
--tmt6plex:channel_126_description ${param_channel_126_description}
--tmt6plex:channel_127_description ${param_channel_127_description}
--tmt6plex:channel_128_description ${param_channel_128_description}
--tmt6plex:channel_129_description ${param_channel_129_description}
--tmt6plex:channel_130_description ${param_channel_130_description}
--tmt6plex:channel_131_description ${param_channel_131_description}
--tmt6plex:reference_channel ${param_reference_channel}
--tmt6plex:correction_matrix ${param_correction_matrix}
+#if $rep_param_itraq4plex_correction_matrix:
+-itraq4plex:correction_matrix
+  #for token in $rep_param_itraq4plex_correction_matrix:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_itraq4plex_correction_matrix&quot;
+    #else
+      $token.param_itraq4plex_correction_matrix
+    #end if
+  #end for
+#end if
+#if $param_itraq8plex_channel_113_description:
+  -itraq8plex:channel_113_description     &quot;$param_itraq8plex_channel_113_description&quot;
+#end if
+#if $param_itraq8plex_channel_114_description:
+  -itraq8plex:channel_114_description     &quot;$param_itraq8plex_channel_114_description&quot;
+#end if
+#if $param_itraq8plex_channel_115_description:
+  -itraq8plex:channel_115_description     &quot;$param_itraq8plex_channel_115_description&quot;
+#end if
+#if $param_itraq8plex_channel_116_description:
+  -itraq8plex:channel_116_description     &quot;$param_itraq8plex_channel_116_description&quot;
+#end if
+#if $param_itraq8plex_channel_117_description:
+  -itraq8plex:channel_117_description     &quot;$param_itraq8plex_channel_117_description&quot;
+#end if
+#if $param_itraq8plex_channel_118_description:
+  -itraq8plex:channel_118_description     &quot;$param_itraq8plex_channel_118_description&quot;
+#end if
+#if $param_itraq8plex_channel_119_description:
+  -itraq8plex:channel_119_description     &quot;$param_itraq8plex_channel_119_description&quot;
+#end if
+#if $param_itraq8plex_channel_121_description:
+  -itraq8plex:channel_121_description     &quot;$param_itraq8plex_channel_121_description&quot;
+#end if
+#if $param_itraq8plex_reference_channel:
+  -itraq8plex:reference_channel $param_itraq8plex_reference_channel
+#end if
+
+#if $rep_param_itraq8plex_correction_matrix:
+-itraq8plex:correction_matrix
+  #for token in $rep_param_itraq8plex_correction_matrix:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_itraq8plex_correction_matrix&quot;
+    #else
+      $token.param_itraq8plex_correction_matrix
+    #end if
+  #end for
+#end if
+#if $param_quantification_isotope_correction:
+  -quantification:isotope_correction
+#end if
+#if $param_quantification_normalization:
+  -quantification:normalization
+#end if
+#if $param_tmt10plex_channel_126_description:
+  -tmt10plex:channel_126_description     &quot;$param_tmt10plex_channel_126_description&quot;
+#end if
+#if $param_tmt10plex_channel_127N_description:
+  -tmt10plex:channel_127N_description     &quot;$param_tmt10plex_channel_127N_description&quot;
+#end if
+#if $param_tmt10plex_channel_127C_description:
+  -tmt10plex:channel_127C_description     &quot;$param_tmt10plex_channel_127C_description&quot;
+#end if
+#if $param_tmt10plex_channel_128N_description:
+  -tmt10plex:channel_128N_description     &quot;$param_tmt10plex_channel_128N_description&quot;
+#end if
+#if $param_tmt10plex_channel_128C_description:
+  -tmt10plex:channel_128C_description     &quot;$param_tmt10plex_channel_128C_description&quot;
+#end if
+#if $param_tmt10plex_channel_129N_description:
+  -tmt10plex:channel_129N_description     &quot;$param_tmt10plex_channel_129N_description&quot;
+#end if
+#if $param_tmt10plex_channel_129C_description:
+  -tmt10plex:channel_129C_description     &quot;$param_tmt10plex_channel_129C_description&quot;
+#end if
+#if $param_tmt10plex_channel_130N_description:
+  -tmt10plex:channel_130N_description     &quot;$param_tmt10plex_channel_130N_description&quot;
+#end if
+#if $param_tmt10plex_channel_130C_description:
+  -tmt10plex:channel_130C_description     &quot;$param_tmt10plex_channel_130C_description&quot;
+#end if
+#if $param_tmt10plex_channel_131_description:
+  -tmt10plex:channel_131_description     &quot;$param_tmt10plex_channel_131_description&quot;
+#end if
+#if $param_tmt10plex_reference_channel:
+  -tmt10plex:reference_channel
+  #if &quot; &quot; in str($param_tmt10plex_reference_channel):
+    &quot;$param_tmt10plex_reference_channel&quot;
+  #else
+    $param_tmt10plex_reference_channel
+  #end if
+#end if
+
+#if $rep_param_tmt10plex_correction_matrix:
+-tmt10plex:correction_matrix
+  #for token in $rep_param_tmt10plex_correction_matrix:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_tmt10plex_correction_matrix&quot;
+    #else
+      $token.param_tmt10plex_correction_matrix
+    #end if
+  #end for
+#end if
+#if $param_tmt6plex_channel_126_description:
+  -tmt6plex:channel_126_description     &quot;$param_tmt6plex_channel_126_description&quot;
+#end if
+#if $param_tmt6plex_channel_127_description:
+  -tmt6plex:channel_127_description     &quot;$param_tmt6plex_channel_127_description&quot;
+#end if
+#if $param_tmt6plex_channel_128_description:
+  -tmt6plex:channel_128_description     &quot;$param_tmt6plex_channel_128_description&quot;
+#end if
+#if $param_tmt6plex_channel_129_description:
+  -tmt6plex:channel_129_description     &quot;$param_tmt6plex_channel_129_description&quot;
+#end if
+#if $param_tmt6plex_channel_130_description:
+  -tmt6plex:channel_130_description     &quot;$param_tmt6plex_channel_130_description&quot;
+#end if
+#if $param_tmt6plex_channel_131_description:
+  -tmt6plex:channel_131_description     &quot;$param_tmt6plex_channel_131_description&quot;
+#end if
+#if $param_tmt6plex_reference_channel:
+  -tmt6plex:reference_channel $param_tmt6plex_reference_channel
+#end if
+
+#if $rep_param_tmt6plex_correction_matrix:
+-tmt6plex:correction_matrix
+  #for token in $rep_param_tmt6plex_correction_matrix:
+    #if &quot; &quot; in str(token):
+      &quot;$token.param_tmt6plex_correction_matrix&quot;
+    #else
+      $token.param_tmt6plex_correction_matrix
+    #end if
+  #end for
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    -extraction:precursor_isotope_deviation ${adv_opts.param_precursor_isotope_deviation}
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_extraction_precursor_isotope_deviation:
+  -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation
+#end if
+    #if $adv_opts.param_extraction_purity_interpolation:
+  -extraction:purity_interpolation
+#end if
 #end if
 </command>
-  <inputs>
-    <param name="param_type" type="select" optional="True" value="itraq4plex" label="Isobaric Quantitation method used in the experiment." help="(-type)">
-      <option value="itraq4plex">itraq4plex</option>
-      <option value="itraq8plex">itraq8plex</option>
-      <option value="tmt10plex">tmt10plex</option>
-      <option value="tmt6plex">tmt6plex</option>
-    </param>
-    <param name="param_in" type="data" format="mzML" optional="False" label="input raw/picked data file " help="(-in)"/>
-    <param name="param_id_pool" type="text" size="20" label="ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use /home/thouwaar/Projects/OpenMS/share/OpenMS/IDPool/IDPool.txt)" help="(-id_pool)"/>
-    <param name="param_select_activation" type="select" optional="True" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering." help="(-select_activation)">
-      <option value="Collision-induced dissociation">Collision-induced dissociation</option>
-      <option value="Post-source decay">Post-source decay</option>
-      <option value="Plasma desorption">Plasma desorption</option>
-      <option value="Surface-induced dissociation">Surface-induced dissociation</option>
-      <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
-      <option value="Electron capture dissociation">Electron capture dissociation</option>
-      <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
-      <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
-      <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
-      <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
-      <option value="Photodissociation">Photodissociation</option>
-      <option value="Electron transfer dissociation">Electron transfer dissociation</option>
-      <option value=""></option>
-    </param>
-    <param name="param_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position." help="(-reporter_mass_shift)"/>
-    <param name="param_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted. MS/MS scans having a precursor with a lower intensity will not be considered for quantitation." help="(-min_precursor_intensity)"/>
-    <param name="param_keep_unannotated_precursor" type="boolean" truevalue="-extraction:keep_unannotated_precursor true" falsevalue="-extraction:keep_unannotated_precursor false" checked="true" optional="True" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not." help="(-keep_unannotated_precursor)"/>
-    <param name="param_min_reporter_intensity" type="float" min="0.0" optional="True" value="0.0" label="Minimum intenesity of the individual reporter ions to be used extracted." help="(-min_reporter_intensity)"/>
-    <param name="param_discard_low_intensity_quantifications" type="boolean" truevalue="-extraction:discard_low_intensity_quantifications true" falsevalue="-extraction:discard_low_intensity_quantifications false" checked="false" optional="True" label="Remove all reporter intensities if a single reporter is below the threshold given in min_reporter_intensity." help="(-discard_low_intensity_quantifications)"/>
-    <param name="param_min_precursor_purity" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precursor." help="(-min_precursor_purity)"/>
-    <param name="param_channel_114_description" type="text" size="20" label="Description for the content of the 114 channel." help="(-channel_114_description)"/>
-    <param name="param_channel_115_description" type="text" size="20" label="Description for the content of the 115 channel." help="(-channel_115_description)"/>
-    <param name="param_channel_116_description" type="text" size="20" label="Description for the content of the 116 channel." help="(-channel_116_description)"/>
-    <param name="param_channel_117_description" type="text" size="20" label="Description for the content of the 117 channel." help="(-channel_117_description)"/>
-    <param name="param_reference_channel" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117)." help="(-reference_channel)"/>
-    <param name="param_correction_matrix" type="text" size="20" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Override default values (see Documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'" help="(-correction_matrix)"/>
-    <param name="param_channel_113_description" type="text" size="20" label="Description for the content of the 113 channel." help="(-channel_113_description)"/>
-    <param name="param_channel_114_description" type="text" size="20" label="Description for the content of the 114 channel." help="(-channel_114_description)"/>
-    <param name="param_channel_115_description" type="text" size="20" label="Description for the content of the 115 channel." help="(-channel_115_description)"/>
-    <param name="param_channel_116_description" type="text" size="20" label="Description for the content of the 116 channel." help="(-channel_116_description)"/>
-    <param name="param_channel_117_description" type="text" size="20" label="Description for the content of the 117 channel." help="(-channel_117_description)"/>
-    <param name="param_channel_118_description" type="text" size="20" label="Description for the content of the 118 channel." help="(-channel_118_description)"/>
-    <param name="param_channel_119_description" type="text" size="20" label="Description for the content of the 119 channel." help="(-channel_119_description)"/>
-    <param name="param_channel_121_description" type="text" size="20" label="Description for the content of the 121 channel." help="(-channel_121_description)"/>
-    <param name="param_reference_channel" type="integer" min="113" max="121" optional="True" value="113" label="Number of the reference channel (113-121). Please note that 120 is not valid." help="(-reference_channel)"/>
-    <param name="param_correction_matrix" type="text" size="20" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Override default values (see Documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'" help="(-correction_matrix)"/>
-    <param name="param_isotope_correction" type="boolean" truevalue="-quantification:isotope_correction true" falsevalue="-quantification:isotope_correction false" checked="true" optional="True" label="Enable isotope correction (highly recommended). Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results." help="(-isotope_correction)"/>
-    <param name="param_normalization" type="boolean" truevalue="-quantification:normalization true" falsevalue="-quantification:normalization false" checked="false" optional="True" label="Enable normalization of channel intensities with respect to the reference channel. The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!" help="(-normalization)"/>
-    <param name="param_channel_126_description" type="text" size="20" label="Description for the content of the 126 channel." help="(-channel_126_description)"/>
-    <param name="param_channel_127N_description" type="text" size="20" label="Description for the content of the 127N channel." help="(-channel_127N_description)"/>
-    <param name="param_channel_127C_description" type="text" size="20" label="Description for the content of the 127C channel." help="(-channel_127C_description)"/>
-    <param name="param_channel_128N_description" type="text" size="20" label="Description for the content of the 128N channel." help="(-channel_128N_description)"/>
-    <param name="param_channel_128C_description" type="text" size="20" label="Description for the content of the 128C channel." help="(-channel_128C_description)"/>
-    <param name="param_channel_129N_description" type="text" size="20" label="Description for the content of the 129N channel." help="(-channel_129N_description)"/>
-    <param name="param_channel_129C_description" type="text" size="20" label="Description for the content of the 129C channel." help="(-channel_129C_description)"/>
-    <param name="param_channel_130N_description" type="text" size="20" label="Description for the content of the 130N channel." help="(-channel_130N_description)"/>
-    <param name="param_channel_130C_description" type="text" size="20" label="Description for the content of the 130C channel." help="(-channel_130C_description)"/>
-    <param name="param_channel_131_description" type="text" size="20" label="Description for the content of the 131 channel." help="(-channel_131_description)"/>
-    <param name="param_reference_channel" type="select" optional="True" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)." help="(-reference_channel)">
-      <option value="126">126</option>
-      <option value="127N">127N</option>
-      <option value="127C">127C</option>
-      <option value="128N">128N</option>
-      <option value="128C">128C</option>
-      <option value="129N">129N</option>
-      <option value="129C">129C</option>
-      <option value="130N">130N</option>
-      <option value="130C">130C</option>
-      <option value="131">131</option>
-    </param>
-    <param name="param_correction_matrix" type="text" size="20" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Override default values (see Documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'" help="(-correction_matrix)"/>
-    <param name="param_channel_126_description" type="text" size="20" label="Description for the content of the 126 channel." help="(-channel_126_description)"/>
-    <param name="param_channel_127_description" type="text" size="20" label="Description for the content of the 127 channel." help="(-channel_127_description)"/>
-    <param name="param_channel_128_description" type="text" size="20" label="Description for the content of the 128 channel." help="(-channel_128_description)"/>
-    <param name="param_channel_129_description" type="text" size="20" label="Description for the content of the 129 channel." help="(-channel_129_description)"/>
-    <param name="param_channel_130_description" type="text" size="20" label="Description for the content of the 130 channel." help="(-channel_130_description)"/>
-    <param name="param_channel_131_description" type="text" size="20" label="Description for the content of the 131 channel." help="(-channel_131_description)"/>
-    <param name="param_reference_channel" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)." help="(-reference_channel)"/>
-    <param name="param_correction_matrix" type="text" size="20" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Override default values (see Documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'" help="(-correction_matrix)"/>
-    <expand macro="advanced_options">
-      <param name="param_precursor_isotope_deviation" type="float" min="0.0" optional="True" value="0.02" label="Maximum allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor." help="(-precursor_isotope_deviation)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output consensusXML file with quantitative information" format="consensusXML"/>
-  </outputs>
-  <help>**What it does**
-
-Calculates isobaric quantitative values for peptides
+    <inputs>
+      <param help="(-type) " label="Isobaric Quantitation method used in the experiment" name="param_type" optional="True" type="select" value="itraq4plex">
+        <option value="itraq4plex">itraq4plex</option>
+        <option value="itraq8plex">itraq8plex</option>
+        <option value="tmt10plex">tmt10plex</option>
+        <option value="tmt6plex">tmt6plex</option>
+      </param>
+      <param format="mzml" help="(-in) " label="input raw/picked data file" name="param_in" optional="False" type="data"/>
+      <param help="(-select_activation) e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering" label="Operate only on MSn scans where any of its precursors features a certain activation method (" name="param_extraction_select_activation" optional="True" type="select" value="High-energy collision-induced dissociation">
+        <option value="Collision-induced dissociation">Collision-induced dissociation</option>
+        <option value="Post-source decay">Post-source decay</option>
+        <option value="Plasma desorption">Plasma desorption</option>
+        <option value="Surface-induced dissociation">Surface-induced dissociation</option>
+        <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
+        <option value="Electron capture dissociation">Electron capture dissociation</option>
+        <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
+        <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
+        <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
+        <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
+        <option value="Photodissociation">Photodissociation</option>
+        <option value="Electron transfer dissociation">Electron transfer dissociation</option>
+        <option value=""></option>
+      </param>
+      <param help="(-reporter_mass_shift) " label="Allowed shift (left to right) in Da from the expected position" max="0.5" min="1e-08" name="param_extraction_reporter_mass_shift" optional="True" type="float" value="0.1"/>
+      <param help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation" label="Minimum intensity of the precursor to be extracted" min="0.0" name="param_extraction_min_precursor_intensity" optional="True" type="float" value="1.0"/>
+      <param checked="true" falsevalue="" help="(-keep_unannotated_precursor) " label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" name="param_extraction_keep_unannotated_precursor" optional="True" truevalue="-extraction:keep_unannotated_precursor" type="boolean"/>
+      <param help="(-min_reporter_intensity) " label="Minimum intensity of the individual reporter ions to be extracted" min="0.0" name="param_extraction_min_reporter_intensity" optional="True" type="float" value="0.0"/>
+      <param checked="false" falsevalue="" help="(-discard_low_intensity_quantifications) " label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" name="param_extraction_discard_low_intensity_quantifications" optional="True" truevalue="-extraction:discard_low_intensity_quantifications" type="boolean"/>
+      <param help="(-min_precursor_purity) " label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" max="1.0" min="0.0" name="param_extraction_min_precursor_purity" optional="True" type="float" value="0.0"/>
+      <param help="(-channel_114_description) " label="Description for the content of the 114 channel" name="param_itraq4plex_channel_114_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_115_description) " label="Description for the content of the 115 channel" name="param_itraq4plex_channel_115_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_116_description) " label="Description for the content of the 116 channel" name="param_itraq4plex_channel_116_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_117_description) " label="Description for the content of the 117 channel" name="param_itraq4plex_channel_117_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-reference_channel) " label="Number of the reference channel (114-117)" max="117" min="114" name="param_itraq4plex_reference_channel" optional="True" type="integer" value="114"/>
+      <repeat max="1" min="0" name="rep_param_itraq4plex_correction_matrix" title="param_itraq4plex_correction_matrix">
+        <param help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" name="param_itraq4plex_correction_matrix" size="30" type="text" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param help="(-channel_113_description) " label="Description for the content of the 113 channel" name="param_itraq8plex_channel_113_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_114_description) " label="Description for the content of the 114 channel" name="param_itraq8plex_channel_114_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_115_description) " label="Description for the content of the 115 channel" name="param_itraq8plex_channel_115_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_116_description) " label="Description for the content of the 116 channel" name="param_itraq8plex_channel_116_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_117_description) " label="Description for the content of the 117 channel" name="param_itraq8plex_channel_117_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_118_description) " label="Description for the content of the 118 channel" name="param_itraq8plex_channel_118_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_119_description) " label="Description for the content of the 119 channel" name="param_itraq8plex_channel_119_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_121_description) " label="Description for the content of the 121 channel" name="param_itraq8plex_channel_121_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-reference_channel) Please note that 120 is not valid" label="Number of the reference channel (113-121)" max="121" min="113" name="param_itraq8plex_reference_channel" optional="True" type="integer" value="113"/>
+      <repeat max="1" min="0" name="rep_param_itraq8plex_correction_matrix" title="param_itraq8plex_correction_matrix">
+        <param help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" name="param_itraq8plex_correction_matrix" size="30" type="text" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param checked="true" falsevalue="" help="(-isotope_correction) Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results" label="Enable isotope correction (highly recommended)" name="param_quantification_isotope_correction" optional="True" truevalue="-quantification:isotope_correction" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-normalization) The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!" label="Enable normalization of channel intensities with respect to the reference channel" name="param_quantification_normalization" optional="True" truevalue="-quantification:normalization" type="boolean"/>
+      <param help="(-channel_126_description) " label="Description for the content of the 126 channel" name="param_tmt10plex_channel_126_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_127N_description) " label="Description for the content of the 127N channel" name="param_tmt10plex_channel_127N_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_127C_description) " label="Description for the content of the 127C channel" name="param_tmt10plex_channel_127C_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_128N_description) " label="Description for the content of the 128N channel" name="param_tmt10plex_channel_128N_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_128C_description) " label="Description for the content of the 128C channel" name="param_tmt10plex_channel_128C_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_129N_description) " label="Description for the content of the 129N channel" name="param_tmt10plex_channel_129N_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_129C_description) " label="Description for the content of the 129C channel" name="param_tmt10plex_channel_129C_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_130N_description) " label="Description for the content of the 130N channel" name="param_tmt10plex_channel_130N_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_130C_description) " label="Description for the content of the 130C channel" name="param_tmt10plex_channel_130C_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_131_description) " label="Description for the content of the 131 channel" name="param_tmt10plex_channel_131_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-reference_channel) " label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" name="param_tmt10plex_reference_channel" optional="True" type="select" value="126">
+        <option value="126">126</option>
+        <option value="127N">127N</option>
+        <option value="127C">127C</option>
+        <option value="128N">128N</option>
+        <option value="128C">128C</option>
+        <option value="129N">129N</option>
+        <option value="129C">129C</option>
+        <option value="130N">130N</option>
+        <option value="130C">130C</option>
+        <option value="131">131</option>
+      </param>
+      <repeat max="1" min="0" name="rep_param_tmt10plex_correction_matrix" title="param_tmt10plex_correction_matrix">
+        <param help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" name="param_tmt10plex_correction_matrix" size="30" type="text" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param help="(-channel_126_description) " label="Description for the content of the 126 channel" name="param_tmt6plex_channel_126_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_127_description) " label="Description for the content of the 127 channel" name="param_tmt6plex_channel_127_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_128_description) " label="Description for the content of the 128 channel" name="param_tmt6plex_channel_128_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_129_description) " label="Description for the content of the 129 channel" name="param_tmt6plex_channel_129_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_130_description) " label="Description for the content of the 130 channel" name="param_tmt6plex_channel_130_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-channel_131_description) " label="Description for the content of the 131 channel" name="param_tmt6plex_channel_131_description" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-reference_channel) " label="Number of the reference channel (126-131)" max="131" min="126" name="param_tmt6plex_reference_channel" optional="True" type="integer" value="126"/>
+      <repeat max="1" min="0" name="rep_param_tmt6plex_correction_matrix" title="param_tmt6plex_correction_matrix">
+        <param help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" name="param_tmt6plex_correction_matrix" size="30" type="text" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-precursor_isotope_deviation) " label="Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precurso" min="0.0" name="param_extraction_precursor_isotope_deviation" optional="True" type="float" value="10.0"/>
+        <param checked="true" falsevalue="" help="(-purity_interpolation) If set to false, only the precursor scan will be used" label="If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan" name="param_extraction_purity_interpolation" optional="True" truevalue="-extraction:purity_interpolation" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="consensusxml" name="param_out"/>
+    </outputs>
+    <help>Calculates isobaric quantitative values for peptides
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html</help>
+  </tool>