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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="1.12.0">
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3 <description>Detects two-dimensional features in LC-MS data.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FeatureFinderCentroided</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>FeatureFinderCentroided
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -seeds ${param_seeds}
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15 -threads \${GALAXY_SLOTS:-24}
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16 -algorithm:intensity:bins ${param_bins}
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17 -algorithm:mass_trace:mz_tolerance ${param_mz_tolerance}
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18 -algorithm:mass_trace:min_spectra ${param_min_spectra}
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19 -algorithm:mass_trace:max_missing ${param_max_missing}
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20 -algorithm:mass_trace:slope_bound ${param_slope_bound}
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21 -algorithm:isotopic_pattern:charge_low ${param_charge_low}
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22 -algorithm:isotopic_pattern:charge_high ${param_charge_high}
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23 -algorithm:isotopic_pattern:mz_tolerance ${param_mz_tolerance}
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24 -algorithm:seed:min_score ${param_min_score}
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25 -algorithm:feature:min_score ${param_min_score}
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26 -algorithm:feature:reported_mz ${param_reported_mz}
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27 -algorithm:user-seed:rt_tolerance ${param_rt_tolerance}
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28 -algorithm:user-seed:mz_tolerance ${param_mz_tolerance}
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29 -algorithm:user-seed:min_score ${param_min_score}
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30 #if $adv_opts.adv_opts_selector=='advanced':
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31 -out_mzq ${adv_opts.param_out_mzq}
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32 -algorithm:debug:pseudo_rt_shift ${adv_opts.param_pseudo_rt_shift}
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33 -algorithm:isotopic_pattern:intensity_percentage ${adv_opts.param_intensity_percentage}
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34 -algorithm:isotopic_pattern:intensity_percentage_optional ${adv_opts.param_intensity_percentage_optional}
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35 -algorithm:isotopic_pattern:optional_fit_improvement ${adv_opts.param_optional_fit_improvement}
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36 -algorithm:isotopic_pattern:mass_window_width ${adv_opts.param_mass_window_width}
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37 -algorithm:isotopic_pattern:abundance_12C ${adv_opts.param_abundance_12C}
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38 -algorithm:isotopic_pattern:abundance_14N ${adv_opts.param_abundance_14N}
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39 -algorithm:fit:max_iterations ${adv_opts.param_max_iterations}
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40 -algorithm:feature:min_isotope_fit ${adv_opts.param_min_isotope_fit}
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41 -algorithm:feature:min_trace_score ${adv_opts.param_min_trace_score}
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42 -algorithm:feature:min_rt_span ${adv_opts.param_min_rt_span}
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43 -algorithm:feature:max_rt_span ${adv_opts.param_max_rt_span}
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44 -algorithm:feature:rt_shape ${adv_opts.param_rt_shape}
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45 -algorithm:feature:max_intersection ${adv_opts.param_max_intersection}
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46 #end if
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47 </command>
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48 <inputs>
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49 <param name="param_in" type="data" format="mzML" optional="False" label="input file" help="(-in)"/>
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50 <param name="param_seeds" type="data" format="featureXML" optional="True" label="User specified seed list" help="(-seeds)"/>
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51 <param name="param_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map." help="(-bins)"/>
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52 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!" help="(-mz_tolerance)"/>
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53 <param name="param_min_spectra" type="integer" min="1" optional="True" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace." help="(-min_spectra)"/>
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54 <param name="param_max_missing" type="integer" min="0" optional="True" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below 'min_spectra'!" help="(-max_missing)"/>
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55 <param name="param_slope_bound" type="float" min="0.0" optional="True" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to seperate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot." help="(-slope_bound)"/>
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56 <param name="param_charge_low" type="integer" min="1" optional="True" value="1" label="Lowest charge to search for." help="(-charge_low)"/>
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57 <param name="param_charge_high" type="integer" min="1" optional="True" value="4" label="Highest charge to search for." help="(-charge_high)"/>
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58 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!" help="(-mz_tolerance)"/>
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59 <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum seed score a peak has to reach to be used as seed.#br#The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.#br#If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score." help="(-min_score)"/>
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60 <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="Feature score threshold for a feature to be reported.#br#The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks." help="(-min_score)"/>
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61 <param name="param_reported_mz" type="select" optional="True" value="monoisotopic" label="The mass type that is reported for features.#br#'maximum' returns the m/z value of the highest mass trace.#br#'average' returns the intensity-weighted average m/z value of all contained peaks.#br#'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model." help="(-reported_mz)">
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62 <option value="maximum">maximum</option>
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63 <option value="average">average</option>
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64 <option value="monoisotopic">monoisotopic</option>
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65 </param>
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66 <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position." help="(-rt_tolerance)"/>
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67 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position." help="(-mz_tolerance)"/>
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68 <param name="param_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case." help="(-min_score)"/>
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69 <expand macro="advanced_options">
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70 <param name="param_pseudo_rt_shift" type="float" min="1.0" optional="True" value="500.0" label="Pseudo RT shift used when ." help="(-pseudo_rt_shift)"/>
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71 <param name="param_intensity_percentage" type="float" min="0.0" max="100.0" optional="True" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present." help="(-intensity_percentage)"/>
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72 <param name="param_intensity_percentage_optional" type="float" min="0.0" max="100.0" optional="True" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing." help="(-intensity_percentage_optional)"/>
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73 <param name="param_optional_fit_improvement" type="float" min="0.0" max="100.0" optional="True" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak." help="(-optional_fit_improvement)"/>
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74 <param name="param_mass_window_width" type="float" min="1.0" max="200.0" optional="True" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions." help="(-mass_window_width)"/>
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75 <param name="param_abundance_12C" type="float" min="0.0" max="100.0" optional="True" value="98.93" label="Rel. abundance of the light carbon. Modify if labeled." help="(-abundance_12C)"/>
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76 <param name="param_abundance_14N" type="float" min="0.0" max="100.0" optional="True" value="99.632" label="Rel. abundance of the light nitrogen. Modify if labeled." help="(-abundance_14N)"/>
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77 <param name="param_max_iterations" type="integer" min="1" optional="True" value="500" label="Maximum number of iterations of the fit." help="(-max_iterations)"/>
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78 <param name="param_min_isotope_fit" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum isotope fit of the feature before model fitting." help="(-min_isotope_fit)"/>
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79 <param name="param_min_trace_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Trace score threshold.#br#Traces below this threshold are removed after the model fitting.#br#This parameter is important for features that overlap in m/z dimension." help="(-min_trace_score)"/>
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80 <param name="param_min_rt_span" type="float" min="0.0" max="1.0" optional="True" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting." help="(-min_rt_span)"/>
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81 <param name="param_max_rt_span" type="float" min="0.5" optional="True" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have." help="(-max_rt_span)"/>
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82 <param name="param_rt_shape" type="select" optional="True" value="symmetric" label="Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used." help="(-rt_shape)">
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83 <option value="symmetric">symmetric</option>
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84 <option value="asymmetric">asymmetric</option>
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85 </param>
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86 <param name="param_max_intersection" type="float" min="0.0" max="1.0" optional="True" value="0.35" label="Maximum allowed intersection of features." help="(-max_intersection)"/>
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87 </expand>
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88 </inputs>
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89 <outputs>
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90 <data name="param_out" label="output file" format="featureXML"/>
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91 <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/>
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92 </outputs>
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93 <help>**What it does**
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94
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95 Detects two-dimensional features in LC-MS data.
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96
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97
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98 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html
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99
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100 @REFERENCES@
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101 </help>
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102 </tool>
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