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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.0.0">
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3 <description>Assembles metabolite features from singleton mass traces.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FeatureFinderMetabo</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>FeatureFinderMetabo
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 -threads \${GALAXY_SLOTS:-24}
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19 #if $param_algorithm_common_noise_threshold_int:
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20 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
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21 #end if
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22 #if $param_algorithm_common_chrom_peak_snr:
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23 -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
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24 #end if
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25 #if $param_algorithm_common_chrom_fwhm:
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26 -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
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27 #end if
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28 #if $param_algorithm_mtd_mass_error_ppm:
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29 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
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30 #end if
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31 #if $param_algorithm_mtd_reestimate_mt_sd:
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32 -algorithm:mtd:reestimate_mt_sd
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33 #end if
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34 #if $param_algorithm_epd_enabled:
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35 -algorithm:epd:enabled
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36 #end if
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37 #if $param_algorithm_epd_width_filtering:
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38 -algorithm:epd:width_filtering
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39 #if " " in str($param_algorithm_epd_width_filtering):
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40 "$param_algorithm_epd_width_filtering"
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41 #else
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42 $param_algorithm_epd_width_filtering
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43 #end if
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44 #end if
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45 #if $param_algorithm_ffm_charge_lower_bound:
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46 -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound
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47 #end if
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48 #if $param_algorithm_ffm_charge_upper_bound:
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49 -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound
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50 #end if
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51 #if $adv_opts.adv_opts_selector=='advanced':
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52 #if $adv_opts.param_force:
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53 -force
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54 #end if
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55 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
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56 -algorithm:mtd:trace_termination_criterion
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57 #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
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58 "$adv_opts.param_algorithm_mtd_trace_termination_criterion"
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59 #else
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60 $adv_opts.param_algorithm_mtd_trace_termination_criterion
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61 #end if
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62 #end if
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63 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
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64 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
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65 #end if
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66 #if $adv_opts.param_algorithm_mtd_min_sample_rate:
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67 -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
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68 #end if
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69 #if $adv_opts.param_algorithm_mtd_min_trace_length:
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70 -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
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71 #end if
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72 #if $adv_opts.param_algorithm_mtd_max_trace_length:
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73 -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
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74 #end if
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75 #if $adv_opts.param_algorithm_epd_min_fwhm:
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76 -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
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77 #end if
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78 #if $adv_opts.param_algorithm_epd_max_fwhm:
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79 -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
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80 #end if
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81 #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
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82 -algorithm:epd:masstrace_snr_filtering
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83 #end if
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84 #if $adv_opts.param_algorithm_ffm_local_rt_range:
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85 -algorithm:ffm:local_rt_range $adv_opts.param_algorithm_ffm_local_rt_range
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86 #end if
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87 #if $adv_opts.param_algorithm_ffm_local_mz_range:
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88 -algorithm:ffm:local_mz_range $adv_opts.param_algorithm_ffm_local_mz_range
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89 #end if
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90 #if $adv_opts.param_algorithm_ffm_report_summed_ints:
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91 -algorithm:ffm:report_summed_ints
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92 #end if
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93 #if $adv_opts.param_algorithm_ffm_disable_isotope_filtering:
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94 -algorithm:ffm:disable_isotope_filtering
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95 #end if
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96 #if $adv_opts.param_algorithm_ffm_isotope_model:
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97 -algorithm:ffm:isotope_model
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98 #if " " in str($adv_opts.param_algorithm_ffm_isotope_model):
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99 "$adv_opts.param_algorithm_ffm_isotope_model"
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100 #else
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101 $adv_opts.param_algorithm_ffm_isotope_model
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102 #end if
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103 #end if
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104 #if $adv_opts.param_algorithm_ffm_isotope_noisemodel:
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105 -algorithm:ffm:isotope_noisemodel
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106 #if " " in str($adv_opts.param_algorithm_ffm_isotope_noisemodel):
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107 "$adv_opts.param_algorithm_ffm_isotope_noisemodel"
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108 #else
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109 $adv_opts.param_algorithm_ffm_isotope_noisemodel
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110 #end if
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111 #end if
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112 #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities:
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113 -algorithm:ffm:use_smoothed_intensities
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114 #end if
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115 #end if
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116 </command>
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117 <inputs>
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118 <param name="param_in" type="data" format="mzml" optional="False" label="input centroided mzML file" help="(-in) "/>
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119 <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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120 <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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121 <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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122 <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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123 <param name="param_algorithm_mtd_reestimate_mt_sd" type="boolean" truevalue="-algorithm:mtd:reestimate_mt_sd" falsevalue="" checked="true" optional="True" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help="(-reestimate_mt_sd) "/>
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124 <param name="param_algorithm_epd_enabled" type="boolean" truevalue="-algorithm:epd:enabled" falsevalue="" checked="true" optional="True" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="(-enabled) Disable for direct injection"/>
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125 <param name="param_algorithm_epd_width_filtering" type="select" optional="True" 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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126 <option value="off">off</option>
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127 <option value="fixed">fixed</option>
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128 <option value="auto">auto</option>
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129 </param>
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130 <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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131 <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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132 <expand macro="advanced_options">
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133 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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134 <param name="param_algorithm_mtd_trace_termination_criterion" type="select" optional="True" 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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135 <option value="outlier">outlier</option>
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136 <option value="sample_rate">sample_rate</option>
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137 </param>
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138 <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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139 <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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140 <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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141 <param name="param_algorithm_mtd_max_trace_length" type="float" value="300.0" label="Minimum expected length of a mass trace (in seconds)" help="(-max_trace_length) "/>
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142 <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 paramter width_filtering is off or auto"/>
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143 <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 paramter width_filtering is off or auto"/>
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144 <param name="param_algorithm_epd_masstrace_snr_filtering" 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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145 <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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146 <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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147 <param name="param_algorithm_ffm_report_summed_ints" 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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148 <param name="param_algorithm_ffm_disable_isotope_filtering" type="boolean" truevalue="-algorithm:ffm:disable_isotope_filtering" falsevalue="" checked="false" optional="True" label="Disable isotope filtering" help="(-disable_isotope_filtering) "/>
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149 <param name="param_algorithm_ffm_isotope_model" type="select" optional="True" value="metabolites" label="Change type of isotope model" help="(-isotope_model) ">
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150 <option value="metabolites">metabolites</option>
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151 <option value="peptides">peptides</option>
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152 </param>
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153 <param name="param_algorithm_ffm_isotope_noisemodel" type="select" optional="True" value="5%RMS" label="SVM isotope models were trained with either 2% or 5% RMS erro" help="(-isotope_noisemodel) Select the appropriate noise model according to the quality of measurement or MS device">
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154 <option value="5%RMS">5%RMS</option>
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155 <option value="2%RMS">2%RMS</option>
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156 </param>
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157 <param name="param_algorithm_ffm_use_smoothed_intensities" type="boolean" truevalue="-algorithm:ffm:use_smoothed_intensities" falsevalue="" checked="true" optional="True" label="Use LOWESS intensities instead of raw intensities" help="(-use_smoothed_intensities) "/>
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158 </expand>
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159 </inputs>
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160 <outputs>
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161 <data name="param_out" format="featurexml"/>
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162 </outputs>
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163 <help>**What it does**
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164
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165 Assembles metabolite features from singleton mass traces.
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166
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167
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168 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help>
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169 <expand macro="references"/>
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170 </tool>
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