Mercurial > repos > galaxyp > openms_lowmempeakpickerhires_randomaccess

comparison LowMemPeakPickerHiRes_RandomAccess.xml @ 3:46907ec93057 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
author galaxyp
date Fri, 14 Jul 2017 18:54:09 -0400
parents b31a2a0faed7
children
comparison
equal deleted inserted replaced
2:a164526e3a3e 3:46907ec93057
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_RandomAccess" name="LowMemPeakPickerHiRes_RandomAccess" version="2.1.0"> 4 <tool id="LowMemPeakPickerHiRes_RandomAccess" name="LowMemPeakPickerHiRes_RandomAccess" 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_RandomAccess</token> 7 <token name="@EXECUTABLE@">LowMemPeakPickerHiRes_RandomAccess</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
90 #end if 90 #end if
91 #end if 91 #end if
92 </command> 92 </command>
93 <inputs> 93 <inputs>
94 <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) "/>
95 <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) "/>
96 <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">
97 <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">
98 <sanitizer> 98 <sanitizer>
99 <valid initial="string.printable"> 99 <valid initial="string.printable">
100 <remove value="'"/> 100 <remove value="'"/>
101 <remove value="&quot;"/> 101 <remove value="&quot;"/>
102 </valid> 102 </valid>
103 </sanitizer> 103 </sanitizer>
104 </param> 104 </param>
105 </repeat> 105 </repeat>
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) "/> 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) "/>
107 <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>
108 <option value="absolute">absolute</option> 109 <option value="absolute">absolute</option>
109 <option value="relative(ppm)" selected="true">relative(ppm)</option>
110 </param> 110 </param>
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) "/> 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) "/>
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) "/> 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) "/>
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) "/> 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) "/>
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) "> 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) ">
131 <data name="param_out" format="mzml"/> 131 <data name="param_out" format="mzml"/>
132 </outputs> 132 </outputs>
133 <help>Finds mass spectrometric peaks in profile mass spectra. 133 <help>Finds mass spectrometric peaks in profile mass spectra.
134 134
135 135
136 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_LowMemPeakPickerHiRes_RandomAccess.html</help> 136 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes_RandomAccess.html</help>
137 </tool> 137 </tool>