Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker

annotate MRMTransitionGroupPicker.xml @ 5:7dca11634139 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:01:09 -0500
parents 289009115eb2
children d88d659e7d2c
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2c8729a286ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.3.0">
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5 <description>Picks peaks in SRM/MRM chromatograms.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MRMTransitionGroupPicker</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>MRMTransitionGroupPicker
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14
2c8729a286ea planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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_tr:
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19 -tr $param_tr
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_algorithm_stop_after_feature:
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25 -algorithm:stop_after_feature $param_algorithm_stop_after_feature
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26 #end if
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27 #if $param_algorithm_stop_after_intensity_ratio:
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28 -algorithm:stop_after_intensity_ratio $param_algorithm_stop_after_intensity_ratio
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29 #end if
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30 #if $param_algorithm_PeakPickerMRM_sgolay_frame_length:
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31 -algorithm:PeakPickerMRM:sgolay_frame_length $param_algorithm_PeakPickerMRM_sgolay_frame_length
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32 #end if
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33 #if $param_algorithm_PeakPickerMRM_sgolay_polynomial_order:
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34 -algorithm:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_PeakPickerMRM_sgolay_polynomial_order
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35 #end if
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36 #if $param_algorithm_PeakPickerMRM_gauss_width:
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37 -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width
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38 #end if
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39 #if $param_algorithm_PeakPickerMRM_use_gauss:
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40 -algorithm:PeakPickerMRM:use_gauss
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41 #if " " in str($param_algorithm_PeakPickerMRM_use_gauss):
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42 "$param_algorithm_PeakPickerMRM_use_gauss"
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43 #else
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44 $param_algorithm_PeakPickerMRM_use_gauss
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45 #end if
0
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46 #end if
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47 #if $param_algorithm_PeakPickerMRM_peak_width:
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48 -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width
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49 #end if
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50 #if $param_algorithm_PeakPickerMRM_signal_to_noise:
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51 -algorithm:PeakPickerMRM:signal_to_noise $param_algorithm_PeakPickerMRM_signal_to_noise
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52 #end if
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53 #if $param_algorithm_PeakPickerMRM_sn_win_len:
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54 -algorithm:PeakPickerMRM:sn_win_len $param_algorithm_PeakPickerMRM_sn_win_len
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55 #end if
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56 #if $param_algorithm_PeakPickerMRM_sn_bin_count:
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57 -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count
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58 #end if
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59 #if $param_algorithm_PeakPickerMRM_write_sn_log_messages:
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60 -algorithm:PeakPickerMRM:write_sn_log_messages
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61 #if " " in str($param_algorithm_PeakPickerMRM_write_sn_log_messages):
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62 "$param_algorithm_PeakPickerMRM_write_sn_log_messages"
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63 #else
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64 $param_algorithm_PeakPickerMRM_write_sn_log_messages
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65 #end if
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66 #end if
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67 #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks:
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68 -algorithm:PeakPickerMRM:remove_overlapping_peaks
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69 #end if
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70 #if $param_algorithm_PeakPickerMRM_method:
1
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71 -algorithm:PeakPickerMRM:method
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72 #if " " in str($param_algorithm_PeakPickerMRM_method):
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73 "$param_algorithm_PeakPickerMRM_method"
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74 #else
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75 $param_algorithm_PeakPickerMRM_method
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76 #end if
0
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77 #end if
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78 #if $adv_opts.adv_opts_selector=='advanced':
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79 #if $adv_opts.param_force:
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80 -force
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81 #end if
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82 #if $adv_opts.param_algorithm_min_peak_width:
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83 -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width
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84 #end if
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85 #if $adv_opts.param_algorithm_background_subtraction:
1
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86 -algorithm:background_subtraction
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87 #if " " in str($adv_opts.param_algorithm_background_subtraction):
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88 "$adv_opts.param_algorithm_background_subtraction"
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89 #else
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90 $adv_opts.param_algorithm_background_subtraction
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91 #end if
0
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92 #end if
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93 #if $adv_opts.param_algorithm_recalculate_peaks:
1
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94 -algorithm:recalculate_peaks
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95 #end if
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96 #if $adv_opts.param_algorithm_use_precursors:
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97 -algorithm:use_precursors
0
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98 #end if
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99 #if $adv_opts.param_algorithm_recalculate_peaks_max_z:
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100 -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z
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101 #end if
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102 #if $adv_opts.param_algorithm_minimal_quality:
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103 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
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104 #end if
5
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105 #if $adv_opts.param_algorithm_resample_boundary:
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106 -algorithm:resample_boundary $adv_opts.param_algorithm_resample_boundary
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107 #end if
0
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108 #if $adv_opts.param_algorithm_compute_peak_quality:
1
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109 -algorithm:compute_peak_quality
0
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110 #end if
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111 #end if
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112 </command>
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113 <inputs>
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114 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
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115 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
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116 <param name="param_algorithm_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/>
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117 <param name="param_algorithm_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>
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118 <param name="param_algorithm_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/>
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119 <param name="param_algorithm_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
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120 <param name="param_algorithm_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
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121 <param name="param_algorithm_PeakPickerMRM_use_gauss" display="radio" type="select" optional="False" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
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122 <option value="false">false</option>
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123 <option value="true" selected="true">true</option>
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124 </param>
5
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125 <param name="param_algorithm_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
0
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126 <param name="param_algorithm_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
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127 <param name="param_algorithm_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
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128 <param name="param_algorithm_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
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129 <param name="param_algorithm_PeakPickerMRM_write_sn_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help="(-write_sn_log_messages) ">
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130 <option value="true" selected="true">true</option>
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131 <option value="false">false</option>
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132 </param>
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133 <param name="param_algorithm_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
5
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134 <param name="param_algorithm_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="(-method) ">
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135 <option value="legacy">legacy</option>
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136 <option value="corrected" selected="true">corrected</option>
0
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137 <option value="crawdad">crawdad</option>
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138 </param>
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139 <expand macro="advanced_options">
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140 <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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141 <param name="param_algorithm_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
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142 <param name="param_algorithm_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that">
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143 <option value="none" selected="true">none</option>
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144 <option value="smoothed">smoothed</option>
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145 <option value="original">original</option>
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146 </param>
1
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147 <param name="param_algorithm_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/>
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148 <param name="param_algorithm_use_precursors" display="radio" type="boolean" truevalue="-algorithm:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
0
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149 <param name="param_algorithm_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
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150 <param name="param_algorithm_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
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151 <param name="param_algorithm_resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help="(-resample_boundary) "/>
1
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152 <param name="param_algorithm_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
0
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153 </expand>
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154 </inputs>
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155 <outputs>
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156 <data name="param_out" format="featurexml"/>
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157 </outputs>
1
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158 <help>Picks peaks in SRM/MRM chromatograms.
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161 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMTransitionGroupPicker.html</help>
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162 </tool>