Mercurial > repos > galaxyp > openms_peakpickerhires

comparison PeakPickerHiRes.xml @ 1:94b97d2d98a4 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 09:04:11 -0400
parents 5ae104d0da6e
children d34c1a10e713
comparison
equal deleted inserted replaced
0:5ae104d0da6e 1:94b97d2d98a4
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: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.1.0"> 4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" 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@">PeakPickerHiRes</token> 7 <token name="@EXECUTABLE@">PeakPickerHiRes</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_processOption: 64 #if $adv_opts.param_processOption:
55 -processOption $adv_opts.param_processOption 65 -processOption
66 #if " " in str($adv_opts.param_processOption):
67 "$adv_opts.param_processOption"
68 #else
69 $adv_opts.param_processOption
70 #end if
56 #end if 71 #end if
57 #if $adv_opts.param_force: 72 #if $adv_opts.param_force:
58 -force 73 -force
59 #end if 74 #end if
60 #if $adv_opts.param_algorithm_spacing_difference_gap: 75 #if $adv_opts.param_algorithm_spacing_difference_gap:
83 #end if 98 #end if
84 #end if 99 #end if
85 </command> 100 </command>
86 <inputs> 101 <inputs>
87 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> 102 <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) "/> 103 <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) "/>
89 <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels"> 104 <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"> 105 <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">
91 <sanitizer> 106 <sanitizer>
92 <valid initial="string.printable"> 107 <valid initial="string.printable">
93 <remove value="'"/> 108 <remove value="'"/>
94 <remove value="&quot;"/> 109 <remove value="&quot;"/>
95 </valid> 110 </valid>
96 </sanitizer> 111 </sanitizer>
97 </param> 112 </param>
98 </repeat> 113 </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) "/> 114 <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)"> 115 <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)">
116 <option value="relative" selected="true">relative</option>
101 <option value="absolute">absolute</option> 117 <option value="absolute">absolute</option>
102 <option value="relative(ppm)" selected="true">relative(ppm)</option>
103 </param> 118 </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) "/> 119 <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) "/> 120 <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) "/> 121 <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) "> 122 <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) ">