<?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="2.2.0">
  <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
#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 $adv_opts.param_out_separator:
  -out_separator     "$adv_opts.param_out_separator"
#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 name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input raw data file" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_in_header" type="data" format="txt" multiple="true" optional="True" size="30" label="[for Waters data only] Read additional information from _HEADER.TXT" help="(-in_header) Provide one for each raw input file">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_pos" type="data" format="tabular" optional="False" label="Input config file stating where to find signal" help="(-pos) "/>
    <param name="param_rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/>
    <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/>
    <param name="param_rt_collect" type="integer" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help="(-rt_collect) "/>
    <param name="param_auto_rt_enabled" display="radio" type="boolean" truevalue="-auto_rt:enabled" falsevalue="" checked="false" optional="True" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help="(-enabled) "/>
    <expand macro="advanced_options">
      <param name="param_out_separator" type="text" size="30" value="," label="Separator character for output CSV file" help="(-out_separator) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_auto_rt_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC"/>
      <param name="param_auto_rt_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="(-SNThreshold) Higher thesholds will result in less peaks"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
    <data name="param_auto_rt_out_debug_TIC" format="mzml"/>
  </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>