<tool id="mzxml2search" name="Search Formatter" version="0.1.0">
  <description>Use MzXML2Search to convert peak lists.</description>

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

  <command>
    ln -s ${input} input.${input.ext} ; 
    MzXML2Search -B${min_mhp_mass} -T${max_mhp_mass} -P${min_peak_count} -I${min_peak_intensity} -${output_type} input.${input.ext} ;
    mv input.${output_type} ${output}
  </command>

  <inputs>
    <param format="mzxml,mzml" name="input" type="data" label="Input Peak List" />
    <param name="output_type" label="Output Format" type="select">
      <option value="mgf">MGF</option>
      <option value="ms2">MS2</option>
    </param>
    <param name="min_mhp_mass" type="float" label="Minimum MH+ mass (daltons)" value="600.0" />
    <param name="max_mhp_mass" type="float" label="Maximum MH+ mass (daltons)" value="4200.0" />
    <param name="min_peak_count" type="integer" label="Minimum peak count" value="5" />
    <param name="min_peak_intensity" type="float" label="Minimum peak intensity" value="0.01" />
    <param name="use_hydrogen_mass" type="boolean" label="Use hydrogen mass for charge ion (default is proton mass)" truevalue=" -h " falsevalue="" />
  </inputs>

  <outputs>
    <data format="mgf" name="output" />
  </outputs>

  <help>
**What it does**

Converts mzML and mzXML peak lists into files formatted for search engines (MGF, MS2).

------

**Citation**

For the underlying tool, please cite `Proteomics. 2010 Mar;10(6):1150-9. A guided tour of the Trans-Proteomic Pipeline. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. PMID 20101611`

  </help>
</tool>