<tool id="isobaric_analyzer" version="0.1.0" name="SILACAnalyzer">
  <description>
    Extracts and normalizes iTRAQ/TMT information from an MS experiment.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    #set $label_type = str($type.label_type)
    #if $label_type == "tmt-6plex"
    #set $program = "TMTAnalyzer"
    #else
    #set $program = "ITRAQAnalyzer"
    #end if
    openms_wrapper.py 
    --executable '$program' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=$input1
out=$out
Extraction!reporter_mass_shift=$reporter_mass_shift
Extraction!select_activation=$select_activation
Quantification!isotope_correction=$isotope_correction
Quantification!do_normalization=$do_normalization
Quantification!channel_reference=$type.channel_reference
</configfile>
  </configfiles>
  <inputs>
    <param name="input1" type="data" format="mzml" label="Input peak list" />
    <conditional name="type">
      <param name="label_type" type="select" label="Labels">
        <option value="4plex">iTRAQ 4-Plex</option>
        <option value="8plex">iTRAQ 8-Plex</option>
        <option value="tmt-6plex">TMT 6-plex</option>
      </param>
      <when value="4plex">
        <param name="channel_reference" type="select" label="Reference Channel">
          <option value="114">114</option>
          <option value="115">115</option>          
          <option value="116">116</option>
          <option value="117">117</option>
        </param>
      </when>
      <when value="8plex">
        <param name="channel_reference" type="select" label="Reference Channel">
          <option value="113">113</option>
          <option value="114">114</option>
          <option value="115">115</option>          
          <option value="116">116</option>
          <option value="117">117</option>
          <option value="118">118</option>
          <option value="119">119</option>
          <option value="121">121</option>
        </param>
      </when>
      <when value="tmt-6plex">
        <param name="channel_reference" type="select" label="Reference Channel">
          <option value="126">126</option>
          <option value="127">127</option>
          <option value="128">128</option>
          <option value="129">129</option>
          <option value="130">130</option>
          <option value="131">131</option>
        </param>
      </when>
    </conditional>
    <param name="select_activation" type="select" label="Select Activation" help="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.">
      <option value="">(Leave empty,use all MSn.)</option>
      <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" selected="true">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>
    </param>    
    <param name="reporter_mass_shift" label="Reporter Mass Shift" value="0.1" type="float" />
    <param name="isotope_correction" type="boolean" label="Isotope Correctoin" help="" truevalue="true" falsevalue="false" />
    <param name="do_normalization" type="boolean" label="Normalize" help="" truevalue="true" falsevalue="false" />
  </inputs>
  <outputs>
    <data format="consensusxml" name="out" />
  </outputs>
  <help>
**What it does**

Extract the iTRAQ reporter ion intensities (4plex or 8plex) from raw MS2 data, does isotope corrections and stores the resulting quantitation as consensusXML, where each consensus centroid corresponds to one iTRAQ MS2 scan (e.g., HCD). The position of the centroid is the precursor position, its sub-elements are the channels (thus having m/z's of 113-121).

Isotope correction is done using non-negative least squares (NNLS), i.e.,

Minimize ||Ax - b||, subject to x >= 0, where b is the vector of observed reporter intensities (with 'contaminating' isotope species), A is a correction matrix (as supplied by the manufacturer AB Sciex) and x is the desired vector of corrected (real) reporter intensities. Other software solves this problem using an inverse matrix multiplication, but this can yield entries in x which are negative. In a real sample, this solution cannot possibly be true, so usually negative values (= negative reporter intensities) are set to 0. However, a negative result usually means, that noise was not accounted for thus we use NNLS to get a non-negative solution, without the need to truncate negative values. In (the usual) case that inverse matrix multiplication yields only positive values, our NNLS will give the exact same optimal solution.

The correction matrices can be found (and changed) in the INI file. However, these matrices for both 4plex and 8plex are now stable, and every kit delivered should have the same isotope correction values. Thus, there should be no need to change them, but feel free to compare the values in the INI file with your kit's Certificate.

After this quantitation step, you might want to annotate the consensus elements with the respective identifications, obtained from an identification pipeline. Note that quantification is solely on peptide level at this stage. In order to obtain protein quantifications, you can try TextExporter to obtain a simple text format which you can feed to other software tools (e.g., R), or you can try ProteinQuantifier.


**Citation**

For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``.

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
  </help>
</tool>