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comparison PeakPickerHiRes.xml @ 0:5ae104d0da6e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:21:36 -0500
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children 94b97d2d98a4
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-1:000000000000 0:5ae104d0da6e
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.1.0">
5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
6 <macros>
7 <token name="@EXECUTABLE@">PeakPickerHiRes</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>PeakPickerHiRes
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_algorithm_signal_to_noise:
22 -algorithm:signal_to_noise $param_algorithm_signal_to_noise
23 #end if
24
25 #if $rep_param_algorithm_ms_levels:
26 -algorithm:ms_levels
27 #for token in $rep_param_algorithm_ms_levels:
28 #if " " in str(token):
29 "$token.param_algorithm_ms_levels"
30 #else
31 $token.param_algorithm_ms_levels
32 #end if
33 #end for
34 #end if
35 #if $param_algorithm_report_FWHM:
36 -algorithm:report_FWHM
37 #end if
38 #if $param_algorithm_report_FWHM_unit:
39 -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
40 #end if
41 #if $param_algorithm_SignalToNoise_win_len:
42 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
43 #end if
44 #if $param_algorithm_SignalToNoise_bin_count:
45 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
46 #end if
47 #if $param_algorithm_SignalToNoise_min_required_elements:
48 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
49 #end if
50 #if $param_algorithm_SignalToNoise_write_log_messages:
51 -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages
52 #end if
53 #if $adv_opts.adv_opts_selector=='advanced':
54 #if $adv_opts.param_processOption:
55 -processOption $adv_opts.param_processOption
56 #end if
57 #if $adv_opts.param_force:
58 -force
59 #end if
60 #if $adv_opts.param_algorithm_spacing_difference_gap:
61 -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap
62 #end if
63 #if $adv_opts.param_algorithm_spacing_difference:
64 -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
65 #end if
66 #if $adv_opts.param_algorithm_missing:
67 -algorithm:missing $adv_opts.param_algorithm_missing
68 #end if
69 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
70 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
71 #end if
72 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
73 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
74 #end if
75 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
76 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
77 #end if
78 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
79 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
80 #end if
81 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
82 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
83 #end if
84 #end if
85 </command>
86 <inputs>
87 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
88 <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) "/>
89 <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels">
90 <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">
91 <sanitizer>
92 <valid initial="string.printable">
93 <remove value="'"/>
94 <remove value="&quot;"/>
95 </valid>
96 </sanitizer>
97 </param>
98 </repeat>
99 <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/>
100 <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative(ppm)" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
101 <option value="absolute">absolute</option>
102 <option value="relative(ppm)" selected="true">relative(ppm)</option>
103 </param>
104 <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) "/>
105 <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) "/>
106 <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) "/>
107 <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) ">
108 <option value="true" selected="true">true</option>
109 <option value="false">false</option>
110 </param>
111 <expand macro="advanced_options">
112 <param name="param_processOption" display="radio" type="select" optional="False" 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) ">
113 <option value="inmemory" selected="true">inmemory</option>
114 <option value="lowmemory">lowmemory</option>
115 </param>
116 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
117 <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"/>
118 <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"/>
119 <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"/>
120 <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"/>
121 <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) "/>
122 <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) "/>
123 <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 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode) "/>
124 <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) "/>
125 </expand>
126 </inputs>
127 <outputs>
128 <data name="param_out" format="mzml"/>
129 </outputs>
130 <help>Finds mass spectrometric peaks in profile mass spectra.
131
132
133 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help>
134 </tool>