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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.0.0">
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3 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">PeakPickerHiRes</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>PeakPickerHiRes
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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_signal_to_noise:
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20 -algorithm:signal_to_noise $param_algorithm_signal_to_noise
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21 #end if
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22
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23 #if $rep_param_algorithm_ms_levels:
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24 -algorithm:ms_levels
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25 #for token in $rep_param_algorithm_ms_levels:
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26 #if " " in str(token):
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27 "$token.param_algorithm_ms_levels"
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28 #else
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29 $token.param_algorithm_ms_levels
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30 #end if
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31 #end for
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32 #end if
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33 #if $param_algorithm_SignalToNoise_win_len:
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34 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
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35 #end if
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36 #if $param_algorithm_SignalToNoise_bin_count:
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37 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
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38 #end if
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39 #if $param_algorithm_SignalToNoise_min_required_elements:
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40 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
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41 #end if
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42 #if $adv_opts.adv_opts_selector=='advanced':
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43 #if $adv_opts.param_processOption:
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44 -processOption
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45 #if " " in str($adv_opts.param_processOption):
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46 "$adv_opts.param_processOption"
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47 #else
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48 $adv_opts.param_processOption
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49 #end if
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50 #end if
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51 #if $adv_opts.param_force:
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52 -force
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53 #end if
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54 #if $adv_opts.param_algorithm_spacing_difference_gap:
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55 -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap
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56 #end if
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57 #if $adv_opts.param_algorithm_spacing_difference:
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58 -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
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59 #end if
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60 #if $adv_opts.param_algorithm_missing:
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61 -algorithm:missing $adv_opts.param_algorithm_missing
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62 #end if
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63 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
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64 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
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65 #end if
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66 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
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67 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
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68 #end if
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69 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
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70 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
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71 #end if
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72 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
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73 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
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74 #end if
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75 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
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76 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
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77 #end if
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78 #end if
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79 </command>
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80 <inputs>
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81 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
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82 <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/>
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83 <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels">
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84 <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1 2" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes">
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85 <sanitizer>
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86 <valid initial="string.printable">
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87 <remove value="'"/>
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88 <remove value="""/>
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89 </valid>
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90 </sanitizer>
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91 </param>
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92 </repeat>
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93 <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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94 <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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95 <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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96 <expand macro="advanced_options">
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97 <param name="param_processOption" type="select" optional="True" 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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98 <option value="inmemory">inmemory</option>
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99 <option value="lowmemory">lowmemory</option>
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100 </param>
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101 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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102 <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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103 <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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104 <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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105 <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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106 <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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107 <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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108 <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 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode) "/>
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109 <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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110 </expand>
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111 </inputs>
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112 <outputs>
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113 <data name="param_out" format="mzml"/>
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114 </outputs>
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115 <help>**What it does**
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116
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117 Finds mass spectrometric peaks in profile mass spectra.
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118
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119
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120 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help>
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121 <expand macro="references"/>
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122 </tool>
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