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comparison peak_list_preprocessor.xml @ 2:cf0d72c7b482 draft

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author galaxyp
date Fri, 10 May 2013 17:31:05 -0400
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1:5c65f8116244 2:cf0d72c7b482
1 <tool id="openms_peak_list_preprocessor" version="0.1" name="Peak List Preprocessor">
2 <description>
3 Wizard to apply multiple OpenMS signal preprocessing tools for peak lists.
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio" />
9 <expand macro="requires" />
10 <configfiles>
11 <configfile name="setup_input">cp '$input' 'output.mzML'</configfile>
12 <configfile name="rename">mv 'output.mzML' 'input.mzML'</configfile>
13 <configfile name="copy_output">mv 'output.mzML' '$output'</configfile>
14 <configfile name="resampler_config">[simple_options]
15 #if $resample.do
16 in=input.mzML
17 out=output.mzML
18 sampling_rate=$resample.sampling_rate
19 #end if
20 </configfile>
21 <configfile name="noise_filter_config">[simple_options]
22 #set $noise_filter_type = str($noise.type)
23 in=input.mzML
24 out=output.mzML
25 #if $noise_filter_type == 'NoiseFilterGaussian'
26
27 #end if
28 #if $noise_filter_type == 'NoiseFilterSGolay'
29
30 #end if
31 </configfile>
32 <configfile name="baseline_config">[simple_options]
33 in=input.mzML
34 out=output.mzML
35 #if $baseline.do
36
37 #end if
38 </configfile>
39 <configfile name="peak_picker_config">[simple_options]
40 #set $peak_picker_type = str($peak_picker.type)
41 in=input.mzML
42 out=output.mzML
43 #if $peak_picker_type == 'PeakPickerHiRes'
44 algorithm!signal_to_noise=$peak_picker.signal_to_noise
45 algorithm!ms1_only=$peak_picker.ms1_only
46 #end if
47 #if $peak_picker_type == 'PeakPickerWavelet'
48 algorithm!signal_to_noise=$peak_picker.signal_to_noise
49 #if $peak_picker.peak_width.estimate
50 algorithm!estimate_peak_width=true
51 #else
52 algorithm!estimate_peak_width=false
53 algorithm!peak_width=$peak_picker.peak_width.peak_width
54 #end if
55 #end if
56 </configfile>
57 <configfile name="mass_corrector_config">[simple_options]
58 in=input.mzML
59 out=output.mzML
60 </configfile>
61 <configfile name="spectra_filter_config">[simple_options]
62 in=input.mzML
63 out=output.mzML
64 #set $spectra_filter_type = str($spectra_filter.type)
65 </configfile>
66 </configfiles>
67 <command interpreter="python">
68 openms_wrapper.py
69 --executable '__SHELL__' --config $setup_input
70 #if $resample.do
71 --executable '__SHELL__' --config $rename
72 --executable 'Resampler' --config $resampler_config
73 #end if
74 #set $noise_filter_type = str($noise.type)
75 #if $noise_filter_type != "none"
76 --executable '__SHELL__' --config $rename
77 --executable '$noise_filter_type' --config $noise_filter_config
78 #end if
79 #if $baseline.do
80 --executable '__SHELL__' --config $rename
81 --executable 'BaselineFilter' --config $baseline_config
82 #end if
83 #set $peak_picker_type = str($peak_picker.type)
84 #if $peak_picker_type != "none"
85 --executable '__SHELL__' --config $rename
86 --executable '$peak_picker_type' --config $peak_picker_config
87 #if $peak_picker_type == "PeakPickerHiRes"
88 #if $peak_picker.use_high_res_mass_corrector
89 --executable '__SHELL__' --config $rename
90 --executable 'HighResPrecursorMassCorrector' --config $mass_corrector_config
91 #end if
92 #end if
93 #end if
94 #set $spectra_filter_type = str($spectra_filter.type)
95 #if $spectra_filter_type != "none"
96 --executable '__SHELL__' --config $rename
97 --executable '$spectra_filter_type' --config $spectra_filter_config
98 #end if
99 --executable '__SHELL__' --config $copy_output
100 </command>
101 <inputs>
102 <!-- TODO: Maybe even have a conversion step here. -->
103 <param format="mzML" name="input" type="data" label="Input Peak List (mzML)"/>
104 <conditional name="resample">
105 <param name="do" type="boolean" label="Resample" help="If you want to use the Savitzky Golay filter, or Baseline filter with non equally spaced profile data, e.g. TOF data, you have should generate equally spaced data by resampling.">
106 </param>
107 <when value="false">
108 </when>
109 <when value="true">
110 <expand macro="sampling_rate_param" />
111 </when>
112 </conditional>
113 <conditional name="noise">
114 <param name="type" type="select" label="Noise Filter" help="">
115 <option value="none" select="true">None</option>
116 <option value="NoiseFilterGaussian">Gaussian</option>
117 <option value="NoiseFilterSGolay">Savitzky Golay</option>
118 </param>
119 <when value="none">
120 </when>
121 <when value="NoiseFilterGaussian">
122 </when>
123 <when value="NoiseFilterSGolay">
124 </when>
125 </conditional>
126 <conditional name="baseline">
127 <param name="do" type="boolean" label="Apply Baseline Filter" help="Executes the top-hat filter to remove the baseline of an MS experiment." />
128 <when value="false">
129 </when>
130 <when value="true">
131 </when>
132 </conditional>
133 <conditional name="peak_picker">
134 <param name="type" type="select" label="Peak Picker" help="">
135 <option value="none" select="true">None</option>
136 <option value="PeakPickerHiRes">High Resolution</option>
137 <option value="PeakPickerWavelet">Wavelet</option>
138 </param>
139 <when value="none">
140 </when>
141 <when value="PeakPickerHiRes">
142 <param name="signal_to_noise" label="Signal-to-noise Ratio" help="Minimal signal to noise ratio for a peak to be picked. (0.0 disables SNT estimation!)" value="1.0" type="float" />
143 <param name="ms1_only" type="boolean" label="MS1 Only" truevalue="true" falsevalue="false" />
144 <param name="use_high_res_mass_corrector" label="Correct precursor m/z on centroided high resolution data." checked="false" type="boolean" />
145 </when>
146 <when value="PeakPickerWavelet">
147 <param name="signal_to_noise" label="Signal-to-noise Ratio" help="Minimal signal to noise ratio for a peak to be picked." value="1.0" type="float" />
148 <conditional name="peak_width">
149 <param name="estimate" label="Estimate Peak Width" type="boolean" checked="false" />
150 <when value="true">
151 </when>
152 <when value="false">
153 <param name="peak_width" type="float" value="0.15" help="Approximate fwhm of the peaks." label="Peak Width" />
154 </when>
155 </conditional>
156 </when>
157 </conditional>
158 <conditional name="spectra_filter">
159 <param name="type" type="select" label="Apply Spectra Filter" help="">
160 <option value="none" select="true">None</option>
161 <option value="SpectraFilterNLargest">N Largest</option>
162 <option value="SpectraFilterNormalizer">Normalizer</option>
163 <option value="SpectraFilterScaler">Scaler</option>
164 <option value="SpectraFilterBernNorm">Bern et. al. normalization</option>
165 <option value="SpectraFilterMarkerMower">Marker Mower</option>
166 <option value="SpectraFilterParentPeakMower">Parent Peak Mower</option>
167 <option value="SpectraFilterSqrtMower">Square Root Mower</option>
168 <option value="SpectraFilterThresholdMower">Threshold Mower</option>
169 <option value="SpectraFilterWindowMower">Window Mower</option>
170 </param>
171 <when value="none">
172 </when>
173 <when value="SpectraFilterNLargest">
174 <!-- 1 param -->
175 </when>
176 <when value="SpectraFilterNormalizer">
177 <!-- 1 param -->
178 </when>
179 <when value="SpectraFilterScaler">
180 <!-- 3 params -->
181 </when>
182 <when value="SpectraFilterBernNorm">
183 </when>
184 <when value="SpectraFilterMarkerMower">
185 </when>
186 <when value="SpectraFilterParentPeakMower">
187 <!-- Tons of params -->
188 </when>
189 <when value="SpectraFilterSqrtMower">
190 </when>
191 <when value="SpectraFilterThresholdMower">
192 <!-- 1 param -->
193 </when>
194 <when value="SpectraFilterWindowMower">
195 <!-- 2 params -->
196 </when>
197 </conditional>
198 </inputs>
199 <outputs>
200 <data format="mzml" name="output" />
201 </outputs>
202 <help>
203 **What it does**
204
205 **Citation**
206
207 For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
208
209 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
210 </help>
211 </tool>