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annotate FeatureFinderMRM.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="2.0.0">
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5 <description>Detects two-dimensional features in LC-MS data.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderMRM</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FeatureFinderMRM
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 -threads \${GALAXY_SLOTS:-24}
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22 #if $param_algorithm_min_rt_distance:
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23 -algorithm:min_rt_distance $param_algorithm_min_rt_distance
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24 #end if
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25 #if $param_algorithm_min_signal_to_noise_ratio:
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26 -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio
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27 #end if
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28 #if $adv_opts.adv_opts_selector=='advanced':
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29 #if $adv_opts.param_force:
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30 -force
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31 #end if
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32 #if $adv_opts.param_algorithm_min_num_peaks_per_feature:
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33 -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature
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34 #end if
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35 #if $adv_opts.param_algorithm_write_debug_files:
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36 -algorithm:write_debug_files
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37 #end if
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38 #if $adv_opts.param_algorithm_resample_traces:
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39 -algorithm:resample_traces
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40 #end if
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41 #if $adv_opts.param_algorithm_write_debuginfo:
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42 -algorithm:write_debuginfo
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43 #end if
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44 #end if
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45 </command>
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46 <inputs>
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47 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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48 <param help="(-min_rt_distance) " label="Minimal distance of MRM features in seconds" min="0.0" name="param_algorithm_min_rt_distance" optional="True" type="float" value="10.0"/>
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49 <param help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise" label="Minimal S/N ratio a peak must have to be taken into account" min="0.0" name="param_algorithm_min_signal_to_noise_ratio" optional="True" type="float" value="2.0"/>
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50 <expand macro="advanced_options">
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51 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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52 <param help="(-min_num_peaks_per_feature) " label="Minimal number of peaks which are needed for a single feature" min="1" name="param_algorithm_min_num_peaks_per_feature" optional="True" type="integer" value="5"/>
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53 <param checked="false" falsevalue="" help="(-write_debug_files) " label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" name="param_algorithm_write_debug_files" optional="True" truevalue="-algorithm:write_debug_files" type="boolean"/>
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54 <param checked="false" falsevalue="" help="(-resample_traces) " 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" name="param_algorithm_resample_traces" optional="True" truevalue="-algorithm:resample_traces" type="boolean"/>
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55 <param checked="false" falsevalue="" help="(-write_debuginfo) " label="If set to true, debug messages are written, the output can be somewhat lengthy" name="param_algorithm_write_debuginfo" optional="True" truevalue="-algorithm:write_debuginfo" type="boolean"/>
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56 </expand>
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57 </inputs>
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58 <outputs>
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59 <data format="xml" name="param_out"/>
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60 </outputs>
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61 <help>Detects two-dimensional features in LC-MS data.
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63
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64 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html</help>
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65 </tool>