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annotate PeakPickerHiRes.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
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4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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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: [Signal processing and preprocessing]-->
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4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.0.0">
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5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PeakPickerHiRes</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>PeakPickerHiRes
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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 -threads \${GALAXY_SLOTS:-24}
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22 #if $param_algorithm_signal_to_noise:
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23 -algorithm:signal_to_noise $param_algorithm_signal_to_noise
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24 #end if
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25
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26 #if $rep_param_algorithm_ms_levels:
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27 -algorithm:ms_levels
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28 #for token in $rep_param_algorithm_ms_levels:
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29 #if &quot; &quot; in str(token):
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30 &quot;$token.param_algorithm_ms_levels&quot;
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31 #else
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32 $token.param_algorithm_ms_levels
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33 #end if
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34 #end for
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35 #end if
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36 #if $param_algorithm_SignalToNoise_win_len:
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37 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
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38 #end if
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39 #if $param_algorithm_SignalToNoise_bin_count:
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40 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
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41 #end if
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42 #if $param_algorithm_SignalToNoise_min_required_elements:
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43 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
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44 #end if
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45 #if $param_algorithm_SignalToNoise_write_log_messages:
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46 -algorithm:SignalToNoise:write_log_messages
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47 #end if
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48 #if $adv_opts.adv_opts_selector=='advanced':
4
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49 #if $adv_opts.param_processOption:
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50 -processOption
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51 #if &quot; &quot; in str($adv_opts.param_processOption):
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52 &quot;$adv_opts.param_processOption&quot;
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53 #else
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54 $adv_opts.param_processOption
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55 #end if
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56 #end if
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57 #if $adv_opts.param_force:
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58 -force
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59 #end if
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60 #if $adv_opts.param_algorithm_spacing_difference_gap:
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61 -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap
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62 #end if
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63 #if $adv_opts.param_algorithm_spacing_difference:
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64 -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
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65 #end if
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66 #if $adv_opts.param_algorithm_missing:
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67 -algorithm:missing $adv_opts.param_algorithm_missing
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68 #end if
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69 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
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70 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
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71 #end if
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72 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
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73 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
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74 #end if
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75 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
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76 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
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77 #end if
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78 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
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79 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
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80 #end if
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81 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
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82 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
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83 #end if
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84 #end if
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85 </command>
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86 <inputs>
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87 <param format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/>
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88 <param help="(-signal_to_noise) " label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" min="0.0" name="param_algorithm_signal_to_noise" optional="True" type="float" value="1.0"/>
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89 <repeat max="1" min="0" name="rep_param_algorithm_ms_levels" title="param_algorithm_ms_levels">
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90 <param help="(-ms_levels) Other scans are copied to the output without changes" label="List of MS levels for which the peak picking is applied" min="1" name="param_algorithm_ms_levels" optional="True" size="30" type="text" value="1 2">
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91 <sanitizer>
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92 <valid initial="string.printable">
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93 <remove value="'"/>
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94 <remove value="&quot;"/>
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95 </valid>
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96 </sanitizer>
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97 </param>
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98 </repeat>
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99 <param help="(-win_len) " label="window length in Thomson" min="1.0" name="param_algorithm_SignalToNoise_win_len" optional="True" type="float" value="200.0"/>
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100 <param help="(-bin_count) " label="number of bins for intensity values" min="3" name="param_algorithm_SignalToNoise_bin_count" optional="True" type="integer" value="30"/>
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101 <param help="(-min_required_elements) " label="minimum number of elements required in a window (otherwise it is considered sparse)" min="1" name="param_algorithm_SignalToNoise_min_required_elements" optional="True" type="integer" value="10"/>
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102 <param checked="true" falsevalue="" help="(-write_log_messages) " label="Write out log messages in case of sparse windows or median in rightmost histogram bin" name="param_algorithm_SignalToNoise_write_log_messages" optional="True" truevalue="-algorithm:SignalToNoise:write_log_messages" type="boolean"/>
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103 <expand macro="advanced_options">
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104 <param help="(-processOption) " 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" name="param_processOption" optional="True" type="select" value="inmemory">
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105 <option value="inmemory">inmemory</option>
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106 <option value="lowmemory">lowmemory</option>
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107 </param>
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108 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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109 <param 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" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" min="0.0" name="param_algorithm_spacing_difference_gap" optional="True" type="float" value="4.0"/>
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110 <param 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" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" min="0.0" name="param_algorithm_spacing_difference" optional="True" type="float" value="1.5"/>
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111 <param 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" label="Maximum number of missing points allowed when extending a peak to the left or to the right" min="0" name="param_algorithm_missing" optional="True" type="integer" value="1"/>
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112 <param 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" label="maximal intensity considered for histogram construction" min="-1" name="param_algorithm_SignalToNoise_max_intensity" optional="True" type="integer" value="-1"/>
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113 <param help="(-auto_max_stdev_factor) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" max="999.0" min="0.0" name="param_algorithm_SignalToNoise_auto_max_stdev_factor" optional="True" type="float" value="3.0"/>
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114 <param help="(-auto_max_percentile) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" max="100" min="0" name="param_algorithm_SignalToNoise_auto_max_percentile" optional="True" type="integer" value="95"/>
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115 <param help="(-auto_mode) " label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" max="1" min="-1" name="param_algorithm_SignalToNoise_auto_mode" optional="True" type="integer" value="0"/>
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116 <param help="(-noise_for_empty_window) " label="noise value used for sparse windows" name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20"/>
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117 </expand>
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118 </inputs>
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119 <outputs>
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120 <data format="mzml" name="param_out"/>
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121 </outputs>
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122 <help>Finds mass spectrometric peaks in profile mass spectra.
0
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123
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124
4
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125 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help>
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126 </tool>