|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="PeakPickerIterative" name="PeakPickerIterative" version="1.12.0">
|
|
|
3 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">PeakPickerIterative</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>PeakPickerIterative
|
|
|
11
|
|
|
12 -in ${param_in}
|
|
|
13 -out ${param_out}
|
|
|
14 -threads \${GALAXY_SLOTS:-24}
|
|
|
15 -algorithm:signal_to_noise_ ${param_signal_to_noise_}
|
|
|
16 -algorithm:peak_width ${param_peak_width}
|
|
|
17 ${param_ms1_only}
|
|
|
18 ${param_clear_meta_data}
|
|
|
19 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
20 -algorithm:spacing_difference ${adv_opts.param_spacing_difference}
|
|
|
21 -algorithm:sn_bin_count_ ${adv_opts.param_sn_bin_count_}
|
|
|
22 -algorithm:nr_iterations_ ${adv_opts.param_nr_iterations_}
|
|
|
23 -algorithm:sn_win_len_ ${adv_opts.param_sn_win_len_}
|
|
|
24 ${adv_opts.param_check_width_internally}
|
|
|
25 #end if
|
|
|
26 </command>
|
|
|
27 <inputs>
|
|
|
28 <param name="param_in" type="data" format="mzML" optional="False" label="input file " help="(-in)"/>
|
|
|
29 <param name="param_signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help="(-signal_to_noise_)"/>
|
|
|
30 <param name="param_peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing). In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value." help="(-peak_width)"/>
|
|
|
31 <param name="param_ms1_only" type="boolean" truevalue="-algorithm:ms1_only true" falsevalue="-algorithm:ms1_only false" checked="false" optional="True" label="Only do MS1" help="(-ms1_only)"/>
|
|
|
32 <param name="param_clear_meta_data" type="boolean" truevalue="-algorithm:clear_meta_data true" falsevalue="-algorithm:clear_meta_data false" checked="false" optional="True" label="Delete meta data about peak width" help="(-clear_meta_data)"/>
|
|
|
33 <expand macro="advanced_options">
|
|
|
34 <param name="param_spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue. The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak." help="(-spacing_difference)"/>
|
|
|
35 <param name="param_sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation." help="(-sn_bin_count_)"/>
|
|
|
36 <param name="param_nr_iterations_" type="integer" min="1" optional="True" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)." help="(-nr_iterations_)"/>
|
|
|
37 <param name="param_sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation." help="(-sn_win_len_)"/>
|
|
|
38 <param name="param_check_width_internally" type="boolean" truevalue="-algorithm:check_width_internally true" falsevalue="-algorithm:check_width_internally false" checked="false" optional="True" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help="(-check_width_internally)"/>
|
|
|
39 </expand>
|
|
|
40 </inputs>
|
|
|
41 <outputs>
|
|
|
42 <data name="param_out" label="output file" format="mzML"/>
|
|
|
43 </outputs>
|
|
|
44 <help>**What it does**
|
|
|
45
|
|
|
46 Finds mass spectrometric peaks in profile mass spectra.
|
|
|
47
|
|
|
48
|
|
|
49 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_PeakPickerIterative.html
|
|
|
50
|
|
|
51 @REFERENCES@
|
|
|
52 </help>
|
|
|
53 </tool>
|
