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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="1.12.0">
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3 <description>Extract chromatograms (XIC) from a MS2 map file.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>OpenSwathChromatogramExtractor
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11
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12 -in ${param_in}
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13 -tr ${param_tr}
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14 -rt_norm ${param_rt_norm}
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15 -out ${param_out}
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16 -min_upper_edge_dist ${param_min_upper_edge_dist}
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17 -mz_window ${param_mz_window}
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18 -rt_window ${param_rt_window}
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19 ${param_is_swath}
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20 ${param_ppm}
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21 ${param_extract_MS1}
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22 -extraction_function ${param_extraction_function}
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23 -threads \${GALAXY_SLOTS:-24}
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24 -model:type ${param_type}
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25 ${param_symmetric_regression}
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26 </command>
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27 <inputs>
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28 <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
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29 <param name="param_tr" type="data" format="tabular" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr)"/>
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30 <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)"/>
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31 <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)"/>
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32 <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)"/>
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33 <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)"/>
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34 <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)"/>
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35 <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)"/>
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36 <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)"/>
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37 <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function)">
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38 <option value="tophat">tophat</option>
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39 <option value="bartlett">bartlett</option>
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40 </param>
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41 <param name="param_type" type="select" optional="True" value="linear" label="Type of model" help="(-type)">
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42 <option value="linear">linear</option>
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43 <option value="b_spline">b_spline</option>
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44 <option value="interpolated">interpolated</option>
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45 </param>
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46 <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)"/>
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47 </inputs>
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48 <outputs>
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49 <data name="param_out" label="output file" format="mzML"/>
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50 </outputs>
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51 <help>**What it does**
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52
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53 Extract chromatograms (XIC) from a MS2 map file.
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54
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55
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56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html
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57
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58 @REFERENCES@
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59 </help>
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60 </tool>
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