--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TMTAnalyzer.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,69 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="TMTAnalyzer" name="TMTAnalyzer" version="1.12.0">
+  <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
+
+-in ${param_in}
+-out ${param_out}
+-out_stats ${param_out_stats}
+-threads \${GALAXY_SLOTS:-24} 
+-id_pool ${param_id_pool}
+-algorithm:Extraction:select_activation ${param_select_activation}
+-algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift}
+-algorithm:Extraction:channel_active ${param_channel_active}
+-algorithm:Quantification:channel_reference ${param_channel_reference}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -out_mzq ${adv_opts.param_out_mzq}
+    -algorithm:Quantification:isotope_correction:tmt-6plex ${adv_opts.param_tmt-6plex}
+    ${adv_opts.param_do_normalization}
+    -algorithm:MetaInformation:Program ${adv_opts.param_Program}
+#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="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 (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_channel_active" type="text" size="20" 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;, e.g. &quot;114:myref&quot;,&quot;115:liver&quot;." help="(-channel_active)"/>
+    <param name="param_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_tmt-6plex" type="text" size="20" 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; ; e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'." help="(-tmt-6plex)"/>
+      <param name="param_do_normalization" type="boolean" truevalue="-algorithm:Quantification:do_normalization true" falsevalue="-algorithm:Quantification:do_normalization false" checked="false" optional="True" label="Normalize channels? 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="(-do_normalization)"/>
+      <param name="param_Program" type="text" size="20" value="OpenMS::TMTAnalyzer" label="" help="(-Program)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output consensusXML file with quantitative information" format="consensusXML"/>
+    <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/>
+    <data name="param_out_stats" label="output statistics as tab-separated file (readable by R or Excel or ...)" format="data"/>
+  </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
+
+@REFERENCES@
+</help>
+</tool>