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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="2.0.0">
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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 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 -threads \${GALAXY_SLOTS:-24}
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19 #if $param_algorithm_min_rt_distance:
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20 -algorithm:min_rt_distance $param_algorithm_min_rt_distance
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21 #end if
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22 #if $param_algorithm_min_signal_to_noise_ratio:
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23 -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio
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24 #end if
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25 #if $adv_opts.adv_opts_selector=='advanced':
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26 #if $adv_opts.param_force:
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27 -force
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28 #end if
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29 #if $adv_opts.param_algorithm_min_num_peaks_per_feature:
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30 -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature
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31 #end if
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32 #if $adv_opts.param_algorithm_write_debug_files:
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33 -algorithm:write_debug_files
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34 #end if
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35 #if $adv_opts.param_algorithm_resample_traces:
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36 -algorithm:resample_traces
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37 #end if
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38 #if $adv_opts.param_algorithm_write_debuginfo:
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39 -algorithm:write_debuginfo
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40 #end if
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41 #end if
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42 </command>
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43 <inputs>
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44 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
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45 <param name="param_algorithm_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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46 <param name="param_algorithm_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" help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise"/>
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47 <expand macro="advanced_options">
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48 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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49 <param name="param_algorithm_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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50 <param name="param_algorithm_write_debug_files" type="boolean" truevalue="-algorithm:write_debug_files" falsevalue="" 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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51 <param name="param_algorithm_resample_traces" type="boolean" truevalue="-algorithm:resample_traces" falsevalue="" 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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52 <param name="param_algorithm_write_debuginfo" type="boolean" truevalue="-algorithm:write_debuginfo" falsevalue="" 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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53 </expand>
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54 </inputs>
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55 <outputs>
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56 <data name="param_out" format="featurexml"/>
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57 </outputs>
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58 <help>**What it does**
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59
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60 Detects two-dimensional features in LC-MS data.
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61
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62
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63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html</help>
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64 <expand macro="references"/>
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65 </tool>
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