Mercurial > repos > galaxyp > openms_lowmempeakpickerhires

comparison LowMemPeakPickerHiRes.xml @ 1:c9c2a39c94de draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:53:58 -0400
parents f4f9fd3b177d
children afb20fdaec5e
comparison
equal deleted inserted replaced
0:f4f9fd3b177d 1:c9c2a39c94de
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="LowMemPeakPickerHiRes" name="LowMemPeakPickerHiRes" version="2.1.0"> 4 <tool id="LowMemPeakPickerHiRes" name="LowMemPeakPickerHiRes" version="2.2.0">
5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> 5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">LowMemPeakPickerHiRes</token> 7 <token name="@EXECUTABLE@">LowMemPeakPickerHiRes</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
34 #end if 34 #end if
35 #if $param_algorithm_report_FWHM: 35 #if $param_algorithm_report_FWHM:
36 -algorithm:report_FWHM 36 -algorithm:report_FWHM
37 #end if 37 #end if
38 #if $param_algorithm_report_FWHM_unit: 38 #if $param_algorithm_report_FWHM_unit:
39 -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit 39 -algorithm:report_FWHM_unit
40 #if " " in str($param_algorithm_report_FWHM_unit):
41 "$param_algorithm_report_FWHM_unit"
42 #else
43 $param_algorithm_report_FWHM_unit
44 #end if
40 #end if 45 #end if
41 #if $param_algorithm_SignalToNoise_win_len: 46 #if $param_algorithm_SignalToNoise_win_len:
42 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len 47 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
43 #end if 48 #end if
44 #if $param_algorithm_SignalToNoise_bin_count: 49 #if $param_algorithm_SignalToNoise_bin_count:
46 #end if 51 #end if
47 #if $param_algorithm_SignalToNoise_min_required_elements: 52 #if $param_algorithm_SignalToNoise_min_required_elements:
48 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements 53 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
49 #end if 54 #end if
50 #if $param_algorithm_SignalToNoise_write_log_messages: 55 #if $param_algorithm_SignalToNoise_write_log_messages:
51 -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages 56 -algorithm:SignalToNoise:write_log_messages
57 #if " " in str($param_algorithm_SignalToNoise_write_log_messages):
58 "$param_algorithm_SignalToNoise_write_log_messages"
59 #else
60 $param_algorithm_SignalToNoise_write_log_messages
61 #end if
52 #end if 62 #end if
53 #if $adv_opts.adv_opts_selector=='advanced': 63 #if $adv_opts.adv_opts_selector=='advanced':
54 #if $adv_opts.param_force: 64 #if $adv_opts.param_force:
55 -force 65 -force
56 #end if 66 #end if
80 #end if 90 #end if
81 #end if 91 #end if
82 </command> 92 </command>
83 <inputs> 93 <inputs>
84 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> 94 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
85 <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) "/> 95 <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/>
86 <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels"> 96 <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels">
87 <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"> 97 <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes">
88 <sanitizer> 98 <sanitizer>
89 <valid initial="string.printable"> 99 <valid initial="string.printable">
90 <remove value="'"/> 100 <remove value="'"/>
91 <remove value="&quot;"/> 101 <remove value="&quot;"/>
92 </valid> 102 </valid>
93 </sanitizer> 103 </sanitizer>
94 </param> 104 </param>
95 </repeat> 105 </repeat>
96 <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) "/> 106 <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) "/>
97 <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)"> 107 <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative" 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)">
108 <option value="relative" selected="true">relative</option>
98 <option value="absolute">absolute</option> 109 <option value="absolute">absolute</option>
99 <option value="relative(ppm)" selected="true">relative(ppm)</option>
100 </param> 110 </param>
101 <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) "/> 111 <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) "/>
102 <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) "/> 112 <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) "/>
103 <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) "/> 113 <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) "/>
104 <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) "> 114 <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) ">
121 <data name="param_out" format="mzml"/> 131 <data name="param_out" format="mzml"/>
122 </outputs> 132 </outputs>
123 <help>Finds mass spectrometric peaks in profile mass spectra. 133 <help>Finds mass spectrometric peaks in profile mass spectra.
124 134
125 135
126 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_LowMemPeakPickerHiRes.html</help> 136 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes.html</help>
127 </tool> 137 </tool>