<tool id="ms2preproc" name="ms2preproc" version="0.1.0">
  <description>preprocess and filter MS/MS spectra</description>

  <command>
    #if $window:
    #set $window_arg = "-Z %s" % $window
    #else
    #set $window_arg = ""
    #end if
    ms2preproc --infile ${input} --outfile ${output} --informat mgf --top ${top} ${window_arg}; sed -i -e 's/,SCAN\(.*\)$/\nSCANS=\1/' ${output}
  </command>

  <inputs>
    <param format="mgf" name="input" type="data" label="Input MGF" />
    <param name="top" type="integer" label="Number of top peaks to keep" value="200" help="" />
    <param name="window" type="float" label="m/z Window" value="" optional="true" help="m/z Windows (+/-Z) around high-intensity peaks in which the number specified above are selected. (Optional)" />
  </inputs>
  <outputs>
    <data format="mgf" name="output" label="ms2preproc on ${on_string}"/>
  </outputs>

  <requirements>
    <requirement type="package">ms2preproc</requirement>  
  </requirements>

  <help>
**What it does**

ms2preproc is a software tool to preprocess MS/MS spectra, please see the citation below for more information.

**Inputs and Parameters**

ms2preproc is very specific about the formatting of the MGF file it parses. Therefore it is recommended that the MGF Formatter tool is used to create a MGF file specifically for ms2preproc prior to the use of this tool.

The authors of this software recommend running ms2preproc with the following settings:

  Mascot: 
    Select top 200 peaks globally. 

  Sequest: 
    Select top 6 peaks in windows of size 30 m/z.

  ProteinPilot: 
    Select top 6 peaks in windows of size 30 m/z.

------

**Citation**

For the underlying tool, please cite `Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J, Winter D, Steen JAJ, Hamprecht FA, Steen H. When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification, Proteomics (2009).`

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-ms2preproc
  </help>
</tool>