view OpenSwathChromatogramExtractor.xml @ 1:17e8c91b70d5 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="1.12.0">
  <description>Extract chromatograms (XIC) from a MS2 map file.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathChromatogramExtractor

-in ${param_in}
-tr ${param_tr}
-rt_norm ${param_rt_norm}
-out ${param_out}
-min_upper_edge_dist ${param_min_upper_edge_dist}
-mz_window ${param_mz_window}
-rt_window ${param_rt_window}
${param_is_swath}
${param_ppm}
${param_extract_MS1}
-extraction_function ${param_extraction_function}
-threads \${GALAXY_SLOTS:-24} 
-model:type ${param_type}
${param_symmetric_regression}
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
    <param name="param_tr" type="data" format="tabular" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr)"/>
    <param name="param_rt_norm" type="data" format="" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm)"/>
    <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist)"/>
    <param name="param_mz_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size, e.g. 100 ppm would extract 50 ppm on either side." help="(-mz_window)"/>
    <param name="param_rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side." help="(-rt_window)"/>
    <param name="param_is_swath" type="boolean" truevalue="-is_swath true" falsevalue="-is_swath false" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath)"/>
    <param name="param_ppm" type="boolean" truevalue="-ppm true" falsevalue="-ppm false" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm)"/>
    <param name="param_extract_MS1" type="boolean" truevalue="-extract_MS1 true" falsevalue="-extract_MS1 false" checked="false" optional="True" label="Extract the MS1 transitions based on the precursor values in the TraML file" help="(-extract_MS1)"/>
    <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function)">
      <option value="tophat">tophat</option>
      <option value="bartlett">bartlett</option>
    </param>
    <param name="param_type" type="select" optional="True" value="linear" label="Type of model" help="(-type)">
      <option value="linear">linear</option>
      <option value="b_spline">b_spline</option>
      <option value="interpolated">interpolated</option>
    </param>
    <param name="param_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression true" falsevalue="-model:symmetric_regression false" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file" format="mzML"/>
  </outputs>
  <help>**What it does**

Extract chromatograms (XIC) from a MS2 map file.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html

@REFERENCES@
</help>
</tool>