<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [ID Processing]-->
<tool id="PhosphoScoring" name="PhosphoScoring" version="2.2.0">
  <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
  <macros>
    <token name="@EXECUTABLE@">PhosphoScoring</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PhosphoScoring

#if $param_in:
  -in $param_in
#end if
#if $param_id:
  -id $param_id
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_fragment_mass_tolerance:
  -fragment_mass_tolerance $param_fragment_mass_tolerance
#end if
#if $param_fragment_mass_unit:
  -fragment_mass_unit
  #if " " in str($param_fragment_mass_unit):
    "$param_fragment_mass_unit"
  #else
    $param_fragment_mass_unit
  #end if
#end if
#if $param_max_peptide_length:
  -max_peptide_length $param_max_peptide_length
#end if
#if $param_max_num_perm:
  -max_num_perm $param_max_num_perm
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file with MS/MS spectra" help="(-in) "/>
    <param name="param_id" type="data" format="idxml" optional="False" label="Identification input file which contains a search against a concatenated sequence database" help="(-id) "/>
    <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/>
    <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) ">
      <option value="Da" selected="true">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <param name="param_max_peptide_length" type="integer" min="1" optional="True" value="40" label="Restrict scoring to peptides with a length shorter than this value" help="(-max_peptide_length) "/>
    <param name="param_max_num_perm" type="integer" min="1" optional="True" value="16384" label="Maximum number of permutations a sequence can have" help="(-max_num_perm) "/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="idxml"/>
  </outputs>
  <help>Scores potential phosphorylation sites in order to localize the most probable sites.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PhosphoScoring.html</help>
</tool>