<?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: [Quantitation]-->
  <tool id="EICExtractor" name="EICExtractor" version="2.0.0">
    <description>Extracts intensities from dedicates positions in a LC/MS map</description>
    <macros>
      <token name="@EXECUTABLE@">EICExtractor</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>EICExtractor

-in
  #for token in $param_in:
    $token
  #end for
-in_header
  #for token in $param_in_header:
    $token
  #end for
#if $param_pos:
  -pos $param_pos
#end if
#if $param_rt_tol:
  -rt_tol $param_rt_tol
#end if
#if $param_mz_tol:
  -mz_tol $param_mz_tol
#end if
#if $param_rt_collect:
  -rt_collect $param_rt_collect
#end if
#if $param_out:
  -out $param_out
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_auto_rt_enabled:
  -auto_rt:enabled
#end if
#if $param_auto_rt_out_debug_TIC:
  -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_out_separator:
  -out_separator     &quot;$adv_opts.param_out_separator&quot;
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_auto_rt_FHWM:
  -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM
#end if
    #if $adv_opts.param_auto_rt_SNThreshold:
  -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold
#end if
#end if
</command>
    <inputs>
      <param format="mzml" help="(-in) " label="Input raw data file" multiple="true" name="param_in" optional="False" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param format="txt" help="(-in_header) Provide one for each raw input file" label="[for Waters data only] Read additional information from _HEADER.TXT" multiple="true" name="param_in_header" optional="True" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param format="tabular" help="(-pos) " label="Input config file stating where to find signal" name="param_pos" optional="False" type="data"/>
      <param help="(-rt_tol) " label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" name="param_rt_tol" type="float" value="3.0"/>
      <param help="(-mz_tol) " label="m/z tolerance in [ppm] for finding a peak" name="param_mz_tol" type="float" value="10.0"/>
      <param help="(-rt_collect) " label="# of scans up &amp; down in RT from highest point for ppm estimation in result" name="param_rt_collect" type="integer" value="1"/>
      <param checked="false" falsevalue="" help="(-enabled) " label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" name="param_auto_rt_enabled" optional="True" truevalue="-auto_rt:enabled" type="boolean"/>
      <expand macro="advanced_options">
        <param help="(-out_separator) " label="Separator character for output CSV file" name="param_out_separator" size="30" type="text" value=",">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC" label="Expected full width at half-maximum of each raw RT peak in [s]" name="param_auto_rt_FHWM" type="float" value="5.0"/>
        <param help="(-SNThreshold) Higher thesholds will result in less peaks" label="S/N threshold for a smoothed raw peak to pass peak picking" name="param_auto_rt_SNThreshold" type="float" value="5.0"/>
      </expand>
    </inputs>
    <outputs>
      <data format="tabular" name="param_out"/>
      <data format="mzml" name="param_auto_rt_out_debug_TIC"/>
    </outputs>
    <help>Extracts intensities from dedicates positions in a LC/MS map


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