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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="1.12.0">
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3 <description>Detects two-dimensional features in LC-MS data.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FeatureFinderMRM</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>FeatureFinderMRM
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -threads \${GALAXY_SLOTS:-24}
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15 -algorithm:min_rt_distance ${param_min_rt_distance}
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16 -algorithm:min_signal_to_noise_ratio ${param_min_signal_to_noise_ratio}
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17 #if $adv_opts.adv_opts_selector=='advanced':
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18 -algorithm:min_num_peaks_per_feature ${adv_opts.param_min_num_peaks_per_feature}
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19 ${adv_opts.param_write_debug_files}
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20 ${adv_opts.param_resample_traces}
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21 ${adv_opts.param_write_debuginfo}
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22 #end if
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23 </command>
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24 <inputs>
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25 <param name="param_in" type="data" format="mzML" optional="False" label="input file" help="(-in)"/>
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26 <param name="param_min_rt_distance" type="float" min="0.0" optional="True" value="10.0" label="Minimal distance of MRM features in seconds." help="(-min_rt_distance)"/>
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27 <param name="param_min_signal_to_noise_ratio" type="float" min="0.0" optional="True" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise." help="(-min_signal_to_noise_ratio)"/>
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28 <expand macro="advanced_options">
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29 <param name="param_min_num_peaks_per_feature" type="integer" min="1" optional="True" value="5" label="Minimal number of peaks which are needed for a single feature" help="(-min_num_peaks_per_feature)"/>
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30 <param name="param_write_debug_files" type="boolean" truevalue="-algorithm:write_debug_files true" falsevalue="-algorithm:write_debug_files false" checked="false" optional="True" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help="(-write_debug_files)"/>
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31 <param name="param_resample_traces" type="boolean" truevalue="-algorithm:resample_traces true" falsevalue="-algorithm:resample_traces false" checked="false" optional="True" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help="(-resample_traces)"/>
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32 <param name="param_write_debuginfo" type="boolean" truevalue="-algorithm:write_debuginfo true" falsevalue="-algorithm:write_debuginfo false" checked="false" optional="True" label="If set to true, debug messages are written, the output can be somewhat lengthy." help="(-write_debuginfo)"/>
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33 </expand>
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34 </inputs>
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35 <outputs>
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36 <data name="param_out" label="output file" format="featureXML"/>
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37 </outputs>
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38 <help>**What it does**
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39
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40 Detects two-dimensional features in LC-MS data.
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41
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42
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43 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html
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44
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45 @REFERENCES@
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46 </help>
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47 </tool>
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