Mercurial > repos > galaxyp > openms_spectramerger

annotate SpectraMerger.xml @ 5:5b8e882b9fdc 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 13:11:30 -0500
parents 4a91d040aa01
children 106130886208
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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="SpectraMerger" name="SpectraMerger" version="2.3.0">
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5 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SpectraMerger</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>SpectraMerger
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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 $param_merging_method:
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22 -merging_method
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23 #if " " in str($param_merging_method):
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24 "$param_merging_method"
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25 #else
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26 $param_merging_method
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27 #end if
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28 #end if
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29 #if $param_algorithm_average_gaussian_spectrum_type:
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30 -algorithm:average_gaussian:spectrum_type
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31 #if " " in str($param_algorithm_average_gaussian_spectrum_type):
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32 "$param_algorithm_average_gaussian_spectrum_type"
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33 #else
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34 $param_algorithm_average_gaussian_spectrum_type
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35 #end if
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36 #end if
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37 #if $param_algorithm_average_gaussian_ms_level:
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38 -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level
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39 #end if
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40 #if $param_algorithm_average_gaussian_rt_FWHM:
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41 -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM
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42 #end if
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43 #if $param_algorithm_average_tophat_spectrum_type:
1
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44 -algorithm:average_tophat:spectrum_type
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45 #if " " in str($param_algorithm_average_tophat_spectrum_type):
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46 "$param_algorithm_average_tophat_spectrum_type"
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47 #else
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48 $param_algorithm_average_tophat_spectrum_type
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49 #end if
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50 #end if
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51 #if $param_algorithm_average_tophat_ms_level:
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52 -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level
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53 #end if
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54 #if $param_algorithm_average_tophat_rt_range:
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55 -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range
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56 #end if
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57 #if $param_algorithm_average_tophat_rt_unit:
1
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58 -algorithm:average_tophat:rt_unit
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59 #if " " in str($param_algorithm_average_tophat_rt_unit):
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60 "$param_algorithm_average_tophat_rt_unit"
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61 #else
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62 $param_algorithm_average_tophat_rt_unit
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63 #end if
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64 #end if
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65
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66 #if $rep_param_algorithm_block_method_ms_levels:
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67 -algorithm:block_method:ms_levels
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68 #for token in $rep_param_algorithm_block_method_ms_levels:
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69 #if " " in str(token):
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70 "$token.param_algorithm_block_method_ms_levels"
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71 #else
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72 $token.param_algorithm_block_method_ms_levels
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73 #end if
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74 #end for
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75 #end if
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76 #if $param_algorithm_block_method_rt_block_size:
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77 -algorithm:block_method:rt_block_size $param_algorithm_block_method_rt_block_size
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78 #end if
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79 #if $param_algorithm_block_method_rt_max_length:
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80 -algorithm:block_method:rt_max_length $param_algorithm_block_method_rt_max_length
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81 #end if
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82 #if $param_algorithm_precursor_method_mz_tolerance:
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83 -algorithm:precursor_method:mz_tolerance $param_algorithm_precursor_method_mz_tolerance
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84 #end if
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85 #if $param_algorithm_precursor_method_rt_tolerance:
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86 -algorithm:precursor_method:rt_tolerance $param_algorithm_precursor_method_rt_tolerance
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87 #end if
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88 #if $adv_opts.adv_opts_selector=='advanced':
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89 #if $adv_opts.param_force:
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90 -force
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91 #end if
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92 #if $adv_opts.param_algorithm_mz_binning_width:
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93 -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
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94 #end if
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95 #if $adv_opts.param_algorithm_mz_binning_width_unit:
1
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96 -algorithm:mz_binning_width_unit
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97 #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit):
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98 "$adv_opts.param_algorithm_mz_binning_width_unit"
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99 #else
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100 $adv_opts.param_algorithm_mz_binning_width_unit
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101 #end if
0
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102 #end if
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103 #if $adv_opts.param_algorithm_sort_blocks:
1
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104 -algorithm:sort_blocks
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105 #if " " in str($adv_opts.param_algorithm_sort_blocks):
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106 "$adv_opts.param_algorithm_sort_blocks"
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107 #else
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108 $adv_opts.param_algorithm_sort_blocks
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109 #end if
0
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110 #end if
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111 #if $adv_opts.param_algorithm_average_gaussian_cutoff:
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112 -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff
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113 #end if
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114 #end if
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115 </command>
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116 <inputs>
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117 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file" help="(-in) "/>
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118 <param name="param_merging_method" display="radio" type="select" optional="False" value="average_gaussian" label="Method of merging which should be used" help="(-merging_method) ">
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119 <option value="average_gaussian" selected="true">average_gaussian</option>
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120 <option value="average_tophat">average_tophat</option>
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121 <option value="precursor_method">precursor_method</option>
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122 <option value="block_method">block_method</option>
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123 </param>
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124 <param name="param_algorithm_average_gaussian_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Spectrum type of the MS level to be averaged" help="(-spectrum_type) ">
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125 <option value="profile">profile</option>
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126 <option value="centroid">centroid</option>
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127 <option value="automatic" selected="true">automatic</option>
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128 </param>
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129 <param name="param_algorithm_average_gaussian_ms_level" type="integer" min="1" optional="True" value="1" label="Average spectra of this level" help="(-ms_level) All other spectra remain unchanged"/>
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130 <param name="param_algorithm_average_gaussian_rt_FWHM" type="float" min="0.0" max="1e+11" optional="True" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help="(-rt_FWHM) "/>
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131 <param name="param_algorithm_average_tophat_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Spectrum type of the MS level to be averaged" help="(-spectrum_type) ">
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132 <option value="profile">profile</option>
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133 <option value="centroid">centroid</option>
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134 <option value="automatic" selected="true">automatic</option>
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135 </param>
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136 <param name="param_algorithm_average_tophat_ms_level" type="integer" min="1" optional="True" value="1" label="Average spectra of this level" help="(-ms_level) All other spectra remain unchanged"/>
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137 <param name="param_algorithm_average_tophat_rt_range" type="float" min="0.0" max="1e+11" optional="True" value="5.0" label="RT range to be averaged over, i.e" help="(-rt_range) +/-(RT range)/2 from each spectrum"/>
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138 <param name="param_algorithm_average_tophat_rt_unit" display="radio" type="select" optional="False" value="scans" label="Unit for RT range" help="(-rt_unit) ">
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139 <option value="scans" selected="true">scans</option>
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140 <option value="seconds">seconds</option>
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141 </param>
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142 <repeat name="rep_param_algorithm_block_method_ms_levels" min="0" max="1" title="param_algorithm_block_method_ms_levels">
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143 <param name="param_algorithm_block_method_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="Merge spectra of this level" help="(-ms_levels) All spectra with other MS levels remain untouched">
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144 <sanitizer>
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145 <valid initial="string.printable">
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146 <remove value="'"/>
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147 <remove value="&quot;"/>
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148 </valid>
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149 </sanitizer>
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150 </param>
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151 </repeat>
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152 <param name="param_algorithm_block_method_rt_block_size" type="integer" min="1" optional="True" value="5" label="Maximum number of scans to be summed up" help="(-rt_block_size) "/>
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153 <param name="param_algorithm_block_method_rt_max_length" type="float" min="0.0" max="1e+11" optional="True" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help="(-rt_max_length) "/>
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154 <param name="param_algorithm_precursor_method_mz_tolerance" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help="(-mz_tolerance) "/>
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155 <param name="param_algorithm_precursor_method_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help="(-rt_tolerance) "/>
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156 <expand macro="advanced_options">
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157 <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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158 <param name="param_algorithm_mz_binning_width" type="float" min="0.0" optional="True" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="(-mz_binning_width) Closer data points or peaks will be merged"/>
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159 <param name="param_algorithm_mz_binning_width_unit" display="radio" type="select" optional="False" value="ppm" label="Unit in which the distance between two data points or peaks is given" help="(-mz_binning_width_unit) ">
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160 <option value="Da">Da</option>
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161 <option value="ppm" selected="true">ppm</option>
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162 </param>
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163 <param name="param_algorithm_sort_blocks" display="radio" type="select" optional="False" value="RT_ascending" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="(-sort_blocks) ">
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164 <option value="RT_ascending" selected="true">RT_ascending</option>
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165 <option value=" RT_descending"> RT_descending</option>
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166 </param>
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167 <param name="param_algorithm_average_gaussian_cutoff" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Intensity cutoff for Gaussian" help="(-cutoff) The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/>
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168 </expand>
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169 </inputs>
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170 <outputs>
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171 <data name="param_out" format="mzml"/>
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172 </outputs>
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173 <help>Merges spectra (each MS level separately), increasing S/N ratios.
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174
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175
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176 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html</help>
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177 </tool>