--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TMTAnalyzer.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,148 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="TMTAnalyzer" name="TMTAnalyzer" version="2.0.0">
+  <description>Calculates TMT quantitative values for peptides</description>
+  <macros>
+    <token name="@EXECUTABLE@">TMTAnalyzer</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>TMTAnalyzer
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_mzq:
+  -out_mzq $param_out_mzq
+#end if
+#if $param_out_stats:
+  -out_stats $param_out_stats
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_id_pool:
+  -id_pool     "$param_id_pool"
+#end if
+#if $param_algorithm_Extraction_select_activation:
+  -algorithm:Extraction:select_activation
+  #if " " in str($param_algorithm_Extraction_select_activation):
+    "$param_algorithm_Extraction_select_activation"
+  #else
+    $param_algorithm_Extraction_select_activation
+  #end if
+#end if
+#if $param_algorithm_Extraction_reporter_mass_shift:
+  -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift
+#end if
+
+#if $rep_param_algorithm_Extraction_channel_active:
+-algorithm:Extraction:channel_active
+  #for token in $rep_param_algorithm_Extraction_channel_active:
+    #if " " in str(token):
+      "$token.param_algorithm_Extraction_channel_active"
+    #else
+      $token.param_algorithm_Extraction_channel_active
+    #end if
+  #end for
+#end if
+#if $param_algorithm_Quantification_channel_reference:
+  -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    
+#if $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
+-algorithm:Quantification:isotope_correction:tmt-6plex
+  #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
+    #if " " in str(token):
+      "$token.param_algorithm_Quantification_isotope_correction_tmt_6plex"
+    #else
+      $token.param_algorithm_Quantification_isotope_correction_tmt_6plex
+    #end if
+  #end for
+#end if
+    #if $adv_opts.param_algorithm_Quantification_do_normalization:
+  -algorithm:Quantification:do_normalization
+#end if
+    #if $adv_opts.param_algorithm_MetaInformation_Program:
+  -algorithm:MetaInformation:Program     "$adv_opts.param_algorithm_MetaInformation_Program"
+#end if
+#end if
+</command>
+  <inputs>
+    <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="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/thouwaar/Downloads/openms-2.0-Linux-x86_64/share/OpenMS/IDPool/IDPool.txt)">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_Extraction_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 (usually HCD for iTRAQ)" help="(-select_activation) Set to empty string if you want to disable filtering">
+      <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_algorithm_Extraction_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) "/>
+    <repeat name="rep_param_algorithm_Extraction_channel_active" min="0" max="1" title="param_algorithm_Extraction_channel_active">
+      <param name="param_algorithm_Extraction_channel_active" type="text" size="30" value="126:liver 131:lung" label="Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format &lt;channel&gt;:&lt;name&gt;," help="(-channel_active) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_algorithm_Quantification_channel_reference" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)" help="(-channel_reference) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <repeat name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_tmt_6plex">
+        <param name="param_algorithm_Quantification_isotope_correction_tmt_6plex" type="text" size="30" value="126:0/0/0/0 127:0/0/0/0 128:0/0/0/0 129:0/0/0/0 130:0/0/0/0 131:0/0/0/0" label="Override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" help="(-tmt-6plex) e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'">
+          <sanitizer>
+            <valid initial="string.printable">
+              <remove value="'"/>
+              <remove value="&quot;"/>
+            </valid>
+          </sanitizer>
+        </param>
+      </repeat>
+      <param name="param_algorithm_Quantification_do_normalization" type="boolean" truevalue="-algorithm:Quantification:do_normalization" falsevalue="" checked="false" optional="True" label="Normalize channels?" help="(-do_normalization) 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!"/>
+      <param name="param_algorithm_MetaInformation_Program" type="text" size="30" value="OpenMS::TMTAnalyzer" label="" help="(-Program) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="consensusxml"/>
+    <data name="param_out_mzq" format="mzq"/>
+    <data name="param_out_stats" format="tabular"/>
+  </outputs>
+  <help>**What it does**
+
+Calculates TMT quantitative values for peptides
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html</help>
+  <expand macro="references"/>
+</tool>