Mercurial > repos > galaxyp > openms_featurefindermetabo

annotate FeatureFinderMetabo.xml @ 6:e8f6b4cfe829 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
author galaxyp
date Thu, 11 Jan 2018 17:42:01 -0500
parents 514ecafed38f
children 1473223a9595
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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="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.2.0">
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5 <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderMetabo</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>FeatureFinderMetabo
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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_common_noise_threshold_int:
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22 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
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23 #end if
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24 #if $param_algorithm_common_chrom_peak_snr:
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25 -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
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26 #end if
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27 #if $param_algorithm_common_chrom_fwhm:
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28 -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
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29 #end if
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30 #if $param_algorithm_mtd_mass_error_ppm:
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31 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
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32 #end if
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33 #if $param_algorithm_mtd_reestimate_mt_sd:
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34 -algorithm:mtd:reestimate_mt_sd
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35 #if " " in str($param_algorithm_mtd_reestimate_mt_sd):
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36 "$param_algorithm_mtd_reestimate_mt_sd"
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37 #else
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38 $param_algorithm_mtd_reestimate_mt_sd
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39 #end if
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40 #end if
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41 #if $param_algorithm_mtd_quant_method:
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42 -algorithm:mtd:quant_method
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43 #if " " in str($param_algorithm_mtd_quant_method):
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44 "$param_algorithm_mtd_quant_method"
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45 #else
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46 $param_algorithm_mtd_quant_method
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47 #end if
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48 #end if
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49 #if $param_algorithm_epd_enabled:
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50 -algorithm:epd:enabled
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51 #if " " in str($param_algorithm_epd_enabled):
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52 "$param_algorithm_epd_enabled"
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53 #else
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54 $param_algorithm_epd_enabled
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55 #end if
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56 #end if
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57 #if $param_algorithm_epd_width_filtering:
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58 -algorithm:epd:width_filtering
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59 #if " " in str($param_algorithm_epd_width_filtering):
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60 "$param_algorithm_epd_width_filtering"
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61 #else
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62 $param_algorithm_epd_width_filtering
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63 #end if
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64 #end if
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65 #if $param_algorithm_ffm_charge_lower_bound:
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66 -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound
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67 #end if
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68 #if $param_algorithm_ffm_charge_upper_bound:
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69 -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound
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70 #end if
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71 #if $param_algorithm_ffm_enable_RT_filtering:
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72 -algorithm:ffm:enable_RT_filtering
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73 #if " " in str($param_algorithm_ffm_enable_RT_filtering):
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74 "$param_algorithm_ffm_enable_RT_filtering"
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75 #else
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76 $param_algorithm_ffm_enable_RT_filtering
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77 #end if
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78 #end if
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79 #if $param_algorithm_ffm_isotope_filtering_model:
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80 -algorithm:ffm:isotope_filtering_model
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81 #if " " in str($param_algorithm_ffm_isotope_filtering_model):
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82 "$param_algorithm_ffm_isotope_filtering_model"
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83 #else
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84 $param_algorithm_ffm_isotope_filtering_model
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85 #end if
0
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86 #end if
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87 #if $param_algorithm_ffm_mz_scoring_13C:
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88 -algorithm:ffm:mz_scoring_13C
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89 #end if
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90 #if $param_algorithm_ffm_report_convex_hulls:
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91 -algorithm:ffm:report_convex_hulls
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92 #end if
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93 #if $adv_opts.adv_opts_selector=='advanced':
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94 #if $adv_opts.param_force:
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95 -force
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96 #end if
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97 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
1
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98 -algorithm:mtd:trace_termination_criterion
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99 #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
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100 "$adv_opts.param_algorithm_mtd_trace_termination_criterion"
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101 #else
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102 $adv_opts.param_algorithm_mtd_trace_termination_criterion
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103 #end if
0
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104 #end if
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105 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
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106 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
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107 #end if
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108 #if $adv_opts.param_algorithm_mtd_min_sample_rate:
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109 -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
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110 #end if
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111 #if $adv_opts.param_algorithm_mtd_min_trace_length:
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112 -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
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113 #end if
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114 #if $adv_opts.param_algorithm_mtd_max_trace_length:
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115 -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
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116 #end if
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117 #if $adv_opts.param_algorithm_epd_min_fwhm:
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118 -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
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119 #end if
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120 #if $adv_opts.param_algorithm_epd_max_fwhm:
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121 -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
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122 #end if
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123 #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
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124 -algorithm:epd:masstrace_snr_filtering
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125 #end if
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126 #if $adv_opts.param_algorithm_ffm_local_rt_range:
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127 -algorithm:ffm:local_rt_range $adv_opts.param_algorithm_ffm_local_rt_range
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128 #end if
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129 #if $adv_opts.param_algorithm_ffm_local_mz_range:
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130 -algorithm:ffm:local_mz_range $adv_opts.param_algorithm_ffm_local_mz_range
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131 #end if
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132 #if $adv_opts.param_algorithm_ffm_report_summed_ints:
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133 -algorithm:ffm:report_summed_ints
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134 #end if
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135 #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities:
1
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136 -algorithm:ffm:use_smoothed_intensities
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137 #if " " in str($adv_opts.param_algorithm_ffm_use_smoothed_intensities):
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138 "$adv_opts.param_algorithm_ffm_use_smoothed_intensities"
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139 #else
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140 $adv_opts.param_algorithm_ffm_use_smoothed_intensities
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141 #end if
0
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142 #end if
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143 #end if
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144 </command>
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145 <inputs>
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146 <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/>
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147 <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/>
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148 <param name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help="(-chrom_peak_snr) "/>
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149 <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/>
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150 <param name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help="(-mass_error_ppm) "/>
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151 <param name="param_algorithm_mtd_reestimate_mt_sd" display="radio" type="select" optional="False" value="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help="(-reestimate_mt_sd) ">
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152 <option value="true" selected="true">true</option>
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153 <option value="false">false</option>
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154 </param>
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155 <param name="param_algorithm_mtd_quant_method" display="radio" type="select" optional="False" value="area" label="Method of quantification for mass traces" help="(-quant_method) For LC data 'area' is recommended, 'median' for direct injection data">
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156 <option value="area" selected="true">area</option>
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157 <option value="median">median</option>
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158 </param>
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159 <param name="param_algorithm_epd_enabled" display="radio" type="select" optional="False" value="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="(-enabled) Disable for direct injection">
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160 <option value="true" selected="true">true</option>
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161 <option value="false">false</option>
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162 </param>
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163 <param name="param_algorithm_epd_width_filtering" display="radio" type="select" optional="False" value="fixed" label="Enable filtering of unlikely peak widths" help="(-width_filtering) The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
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164 <option value="off">off</option>
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165 <option value="fixed" selected="true">fixed</option>
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166 <option value="auto">auto</option>
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167 </param>
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168 <param name="param_algorithm_ffm_charge_lower_bound" type="integer" value="1" label="Lowest charge state to conside" help="(-charge_lower_bound) "/>
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169 <param name="param_algorithm_ffm_charge_upper_bound" type="integer" value="3" label="Highest charge state to conside" help="(-charge_upper_bound) "/>
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170 <param name="param_algorithm_ffm_enable_RT_filtering" display="radio" type="select" optional="False" value="true" label="Require sufficient overlap in RT while assembling mass traces" help="(-enable_RT_filtering) Disable for direct injection data">
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171 <option value="false">false</option>
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172 <option value="true" selected="true">true</option>
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173 </param>
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174 <param name="param_algorithm_ffm_isotope_filtering_model" display="radio" type="select" optional="False" value="metabolites (5% RMS)" label="Remove/score candidate assemblies based on isotope intensities" help="(-isotope_filtering_model) SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
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175 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
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176 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
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177 <option value="peptides">peptides</option>
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178 <option value="none">none</option>
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179 </param>
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180 <param name="param_algorithm_ffm_mz_scoring_13C" display="radio" type="boolean" truevalue="-algorithm:ffm:mz_scoring_13C" falsevalue="" checked="false" optional="True" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="(-mz_scoring_13C) Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
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181 <param name="param_algorithm_ffm_report_convex_hulls" display="radio" type="boolean" truevalue="-algorithm:ffm:report_convex_hulls" falsevalue="" checked="false" optional="True" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help="(-report_convex_hulls) "/>
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182 <expand macro="advanced_options">
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183 <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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184 <param name="param_algorithm_mtd_trace_termination_criterion" display="radio" type="select" optional="False" value="outlier" label="Termination criterion for the extension of mass traces" help="(-trace_termination_criterion) In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
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185 <option value="outlier" selected="true">outlier</option>
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186 <option value="sample_rate">sample_rate</option>
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187 </param>
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188 <param name="param_algorithm_mtd_trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help="(-trace_termination_outliers) "/>
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189 <param name="param_algorithm_mtd_min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help="(-min_sample_rate) "/>
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190 <param name="param_algorithm_mtd_min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help="(-min_trace_length) "/>
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191 <param name="param_algorithm_mtd_max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="(-max_trace_length) Set to a negative value to disable maximal length check during mass trace detection"/>
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192 <param name="param_algorithm_epd_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-min_fwhm) Ignored if parameter width_filtering is off or auto"/>
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193 <param name="param_algorithm_epd_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-max_fwhm) Ignored if parameter width_filtering is off or auto"/>
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194 <param name="param_algorithm_epd_masstrace_snr_filtering" display="radio" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering" falsevalue="" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing" help="(-masstrace_snr_filtering) "/>
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195 <param name="param_algorithm_ffm_local_rt_range" type="float" value="10.0" label="RT range where to look for coeluting mass traces" help="(-local_rt_range) "/>
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196 <param name="param_algorithm_ffm_local_mz_range" type="float" value="6.5" label="MZ range where to look for isotopic mass traces" help="(-local_mz_range) "/>
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197 <param name="param_algorithm_ffm_report_summed_ints" display="radio" type="boolean" truevalue="-algorithm:ffm:report_summed_ints" falsevalue="" checked="false" optional="True" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help="(-report_summed_ints) "/>
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198 <param name="param_algorithm_ffm_use_smoothed_intensities" display="radio" type="select" optional="False" value="true" label="Use LOWESS intensities instead of raw intensities" help="(-use_smoothed_intensities) ">
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199 <option value="false">false</option>
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200 <option value="true" selected="true">true</option>
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201 </param>
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202 </expand>
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203 </inputs>
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204 <outputs>
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205 <data name="param_out" format="featurexml"/>
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206 </outputs>
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207 <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
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208
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209
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210 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help>
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211 </tool>