<?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: [Utilities]-->
<tool id="QCCalculator" name="QCCalculator" version="2.2.0">
  <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description>
  <macros>
    <token name="@EXECUTABLE@">QCCalculator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>QCCalculator

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_id:
  -id $param_id
#end if
#if $param_feature:
  -feature $param_feature
#end if
#if $param_consensus:
  -consensus $param_consensus
#end if
#if $param_remove_duplicate_features:
  -remove_duplicate_features
#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="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help="(-in) "/>
    <param name="param_id" type="data" format="idxml" optional="True" label="Input idXML file containing the identifications" help="(-id) Your identifications will be exported in an easy-to-read format"/>
    <param name="param_feature" type="data" format="featurexml" optional="True" label="feature input file (this is relevant for most QC issues)" help="(-feature) "/>
    <param name="param_consensus" type="data" format="consensusxml" optional="True" label="consensus input file (this is only used for charge state deconvoluted output" help="(-consensus) Use the consensusXML output form the DeCharger)"/>
    <param name="param_remove_duplicate_features" display="radio" type="boolean" truevalue="-remove_duplicate_features" falsevalue="" checked="false" optional="True" label="This flag should be set, if you work with a set of merged features" help="(-remove_duplicate_features) "/>
    <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="qcml"/>
  </outputs>
  <help>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.


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