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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: [Identification]-->
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4 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="2.0.0">
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5 <description>Applies thresholdfilter to peak spectra.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</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>SpectraFilterParentPeakMower
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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_window_size:
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23 -algorithm:window_size $param_algorithm_window_size
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24 #end if
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25 #if $param_algorithm_default_charge:
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26 -algorithm:default_charge $param_algorithm_default_charge
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27 #end if
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28 #if $param_algorithm_consider_NH3_loss:
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29 -algorithm:consider_NH3_loss $param_algorithm_consider_NH3_loss
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30 #end if
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31 #if $param_algorithm_consider_H2O_loss:
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32 -algorithm:consider_H2O_loss $param_algorithm_consider_H2O_loss
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33 #end if
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34 #if $adv_opts.adv_opts_selector=='advanced':
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35 #if $adv_opts.param_force:
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36 -force
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37 #end if
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38 #if $adv_opts.param_algorithm_clean_all_charge_states:
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39 -algorithm:clean_all_charge_states $adv_opts.param_algorithm_clean_all_charge_states
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40 #end if
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41 #if $adv_opts.param_algorithm_reduce_by_factor:
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42 -algorithm:reduce_by_factor $adv_opts.param_algorithm_reduce_by_factor
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43 #end if
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44 #if $adv_opts.param_algorithm_factor:
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45 -algorithm:factor $adv_opts.param_algorithm_factor
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46 #end if
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47 #if $adv_opts.param_algorithm_set_to_zero:
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48 -algorithm:set_to_zero $adv_opts.param_algorithm_set_to_zero
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49 #end if
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50 #end if
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51 </command>
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52 <inputs>
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53 <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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54 <param help="(-window_size) " label="The size of the m/z window where the peaks are removed, +/- window_size" name="param_algorithm_window_size" type="float" value="2.0"/>
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55 <param help="(-default_charge) " label="If the precursor has no charge set, the default charge is assumed" name="param_algorithm_default_charge" type="integer" value="2"/>
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56 <param help="(-consider_NH3_loss) " label="Whether NH3 loss peaks from the precursor should be removed" name="param_algorithm_consider_NH3_loss" type="integer" value="1"/>
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57 <param help="(-consider_H2O_loss) " label="Whether H2O loss peaks from the precursor should be removed" name="param_algorithm_consider_H2O_loss" type="integer" value="1"/>
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58 <expand macro="advanced_options">
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59 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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60 <param help="(-clean_all_charge_states) " label="Set to 1 if precursor ions of all possible charge states should be removed" name="param_algorithm_clean_all_charge_states" type="integer" value="1"/>
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61 <param help="(-reduce_by_factor) " label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" name="param_algorithm_reduce_by_factor" type="integer" value="0"/>
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62 <param help="(-factor) " label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" name="param_algorithm_factor" type="float" value="1000.0"/>
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63 <param help="(-set_to_zero) " label="Reduce the intensities of the precursor and related ions to zero" name="param_algorithm_set_to_zero" type="integer" value="1"/>
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64 </expand>
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65 </inputs>
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66 <outputs>
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67 <data format="mzml" name="param_out"/>
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68 </outputs>
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69 <help>Applies thresholdfilter to peak spectra.
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71
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72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraFilterParentPeakMower.html</help>
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73 </tool>