Mercurial > repos > galaxyp > openms_peakpickerhires

annotate PeakPickerHiRes.xml @ 5:d34c1a10e713 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:11:48 -0500
parents 94b97d2d98a4
children 3d8d4ada5405
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.3.0">
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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@">PeakPickerHiRes</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>PeakPickerHiRes
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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
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25 #if $rep_param_algorithm_ms_levels:
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26 -algorithm:ms_levels
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27 #for token in $rep_param_algorithm_ms_levels:
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28 #if " " in str(token):
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29 "$token.param_algorithm_ms_levels"
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30 #else
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31 $token.param_algorithm_ms_levels
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32 #end if
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33 #end for
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34 #end if
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35 #if $param_algorithm_report_FWHM:
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36 -algorithm:report_FWHM
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37 #end if
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38 #if $param_algorithm_report_FWHM_unit:
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39 -algorithm:report_FWHM_unit
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40 #if " " in str($param_algorithm_report_FWHM_unit):
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41 "$param_algorithm_report_FWHM_unit"
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42 #else
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43 $param_algorithm_report_FWHM_unit
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44 #end if
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45 #end if
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46 #if $param_algorithm_SignalToNoise_win_len:
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47 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
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48 #end if
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49 #if $param_algorithm_SignalToNoise_bin_count:
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50 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
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51 #end if
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52 #if $param_algorithm_SignalToNoise_min_required_elements:
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53 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
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54 #end if
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55 #if $param_algorithm_SignalToNoise_write_log_messages:
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56 -algorithm:SignalToNoise:write_log_messages
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57 #if " " in str($param_algorithm_SignalToNoise_write_log_messages):
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58 "$param_algorithm_SignalToNoise_write_log_messages"
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59 #else
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60 $param_algorithm_SignalToNoise_write_log_messages
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61 #end if
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62 #end if
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63 #if $adv_opts.adv_opts_selector=='advanced':
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64 #if $adv_opts.param_processOption:
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65 -processOption
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66 #if " " in str($adv_opts.param_processOption):
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67 "$adv_opts.param_processOption"
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68 #else
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69 $adv_opts.param_processOption
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70 #end if
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71 #end if
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72 #if $adv_opts.param_force:
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73 -force
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74 #end if
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75 #if $adv_opts.param_algorithm_spacing_difference_gap:
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76 -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap
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77 #end if
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78 #if $adv_opts.param_algorithm_spacing_difference:
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79 -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
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80 #end if
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81 #if $adv_opts.param_algorithm_missing:
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82 -algorithm:missing $adv_opts.param_algorithm_missing
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83 #end if
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84 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
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85 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
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86 #end if
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87 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
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88 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
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89 #end if
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90 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
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91 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
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92 #end if
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93 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
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94 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
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95 #end if
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96 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
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97 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
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98 #end if
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99 #end if
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100 </command>
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101 <inputs>
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102 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
1
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103 <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/>
0
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104 <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels">
1
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105 <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes">
0
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106 <sanitizer>
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107 <valid initial="string.printable">
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108 <remove value="'"/>
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109 <remove value="&quot;"/>
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110 </valid>
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111 </sanitizer>
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112 </param>
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113 </repeat>
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114 <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/>
1
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115 <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
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116 <option value="relative" selected="true">relative</option>
0
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117 <option value="absolute">absolute</option>
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118 </param>
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119 <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/>
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120 <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/>
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121 <param name="param_algorithm_SignalToNoise_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/>
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122 <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) ">
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123 <option value="true" selected="true">true</option>
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124 <option value="false">false</option>
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125 </param>
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126 <expand macro="advanced_options">
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127 <param name="param_processOption" display="radio" type="select" optional="False" value="inmemory" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="(-processOption) ">
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128 <option value="inmemory" selected="true">inmemory</option>
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129 <option value="lowmemory">lowmemory</option>
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130 </param>
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131 <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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132 <param name="param_algorithm_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="(-spacing_difference_gap) 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/>
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133 <param name="param_algorithm_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="(-spacing_difference) If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/>
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134 <param name="param_algorithm_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="(-missing) A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/>
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135 <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
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136 <param name="param_algorithm_SignalToNoise_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/>
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137 <param name="param_algorithm_SignalToNoise_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/>
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138 <param name="param_algorithm_SignalToNoise_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode) "/>
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139 <param name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/>
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140 </expand>
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141 </inputs>
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142 <outputs>
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143 <data name="param_out" format="mzml"/>
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144 </outputs>
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145 <help>Finds mass spectrometric peaks in profile mass spectra.
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146
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147
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148 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help>
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149 </tool>