Mercurial > repos > galaxyp > openms_peakpickeriterative

annotate PeakPickerIterative.xml @ 2:eaba7fc3bc1e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:39:49 -0400
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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: [Signal processing and preprocessing]-->
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4 <tool id="PeakPickerIterative" name="PeakPickerIterative" version="2.2.0">
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5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PeakPickerIterative</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>PeakPickerIterative
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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 #if $param_algorithm_signal_to_noise_:
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22 -algorithm:signal_to_noise_ $param_algorithm_signal_to_noise_
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23 #end if
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24 #if $param_algorithm_peak_width:
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25 -algorithm:peak_width $param_algorithm_peak_width
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26 #end if
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27 #if $param_algorithm_ms1_only:
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28 -algorithm:ms1_only
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29 #end if
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30 #if $param_algorithm_clear_meta_data:
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31 -algorithm:clear_meta_data
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32 #end if
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33 #if $adv_opts.adv_opts_selector=='advanced':
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34 #if $adv_opts.param_force:
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35 -force
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36 #end if
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37 #if $adv_opts.param_algorithm_spacing_difference:
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38 -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
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39 #end if
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40 #if $adv_opts.param_algorithm_sn_bin_count_:
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41 -algorithm:sn_bin_count_ $adv_opts.param_algorithm_sn_bin_count_
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42 #end if
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43 #if $adv_opts.param_algorithm_nr_iterations_:
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44 -algorithm:nr_iterations_ $adv_opts.param_algorithm_nr_iterations_
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45 #end if
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46 #if $adv_opts.param_algorithm_sn_win_len_:
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47 -algorithm:sn_win_len_ $adv_opts.param_algorithm_sn_win_len_
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48 #end if
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49 #if $adv_opts.param_algorithm_check_width_internally:
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50 -algorithm:check_width_internally
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51 #end if
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52 #end if
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53 </command>
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54 <inputs>
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55 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
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56 <param name="param_algorithm_signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help="(-signal_to_noise_) "/>
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57 <param name="param_algorithm_peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="(-peak_width) In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
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58 <param name="param_algorithm_ms1_only" display="radio" type="boolean" truevalue="-algorithm:ms1_only" falsevalue="" checked="false" optional="True" label="Only do MS1" help="(-ms1_only) "/>
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59 <param name="param_algorithm_clear_meta_data" display="radio" type="boolean" truevalue="-algorithm:clear_meta_data" falsevalue="" checked="false" optional="True" label="Delete meta data about peak width" help="(-clear_meta_data) "/>
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60 <expand macro="advanced_options">
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61 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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62 <param name="param_algorithm_spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="(-spacing_difference) The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
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63 <param name="param_algorithm_sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation" help="(-sn_bin_count_) "/>
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64 <param name="param_algorithm_nr_iterations_" type="integer" min="1" optional="True" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help="(-nr_iterations_) "/>
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65 <param name="param_algorithm_sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation" help="(-sn_win_len_) "/>
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66 <param name="param_algorithm_check_width_internally" display="radio" type="boolean" truevalue="-algorithm:check_width_internally" falsevalue="" checked="false" optional="True" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help="(-check_width_internally) "/>
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67 </expand>
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68 </inputs>
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69 <outputs>
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70 <data name="param_out" format="mzml"/>
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71 </outputs>
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72 <help>Finds mass spectrometric peaks in profile mass spectra.
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73
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74
1
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75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_PeakPickerIterative.html</help>
0
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76 </tool>