view EICExtractor.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="EICExtractor" name="EICExtractor" version="1.12.0">
  <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="stdio"/>
  <expand macro="requirements"/>
  <command>EICExtractor

-in ${param_in}
-in_header ${param_in_header}
-pos ${param_pos}
-rt_tol ${param_rt_tol}
-mz_tol ${param_mz_tol}
-rt_collect ${param_rt_collect}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
${param_enabled}
#if $adv_opts.adv_opts_selector=='advanced':
    -out_separator ${adv_opts.param_out_separator}
    -auto_rt:FHWM ${adv_opts.param_FHWM}
    -auto_rt:SNThreshold ${adv_opts.param_SNThreshold}
    -auto_rt:out_debug_TIC ${adv_opts.param_out_debug_TIC}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input raw data file" help="(-in)"/>
    <param name="param_in_header" type="data" format="txt" optional="True" size="20" label="[for Waters data only] Read additional information from _HEADER.TXT. Provide one for each raw input file." help="(-in_header)"/>
    <param name="param_pos" type="data" format="" 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_enabled" type="boolean" truevalue="-auto_rt:enabled true" falsevalue="-auto_rt:enabled false" 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="20" value="," label="Separator character for output CSV file." help="(-out_separator)"/>
      <param name="param_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]. Gaussian smoothing filter with this width is applied to TIC." help="(-FHWM)"/>
      <param name="param_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking. Higher thesholds will result in less peaks." help="(-SNThreshold)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output quantitation file (multiple columns for each input compound)" format="tabular"/>
    <data name="param_out_debug_TIC" label="Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions" format="mzML"/>
  </outputs>
  <help>**What it does**

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

@REFERENCES@
</help>
</tool>