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comparison PeakPickerHiRes.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="1.12.0"> 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 <description>Finds mass spectrometric peaks in profile mass spectra.</description> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <macros> 4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.0.0">
5 <token name="@EXECUTABLE@">PeakPickerHiRes</token> 5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">PeakPickerHiRes</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>PeakPickerHiRes 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>PeakPickerHiRes
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -processOption inmemory 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_out:
16 -algorithm:signal_to_noise ${param_signal_to_noise} 19 -out $param_out
17 -algorithm:ms_levels ${param_ms_levels} 20 #end if
18 -algorithm:SignalToNoise:win_len ${param_win_len} 21 -threads \${GALAXY_SLOTS:-24}
19 -algorithm:SignalToNoise:bin_count ${param_bin_count} 22 #if $param_algorithm_signal_to_noise:
20 -algorithm:SignalToNoise:min_required_elements ${param_min_required_elements} 23 -algorithm:signal_to_noise $param_algorithm_signal_to_noise
24 #end if
25
26 #if $rep_param_algorithm_ms_levels:
27 -algorithm:ms_levels
28 #for token in $rep_param_algorithm_ms_levels:
29 #if &quot; &quot; in str(token):
30 &quot;$token.param_algorithm_ms_levels&quot;
31 #else
32 $token.param_algorithm_ms_levels
33 #end if
34 #end for
35 #end if
36 #if $param_algorithm_SignalToNoise_win_len:
37 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
38 #end if
39 #if $param_algorithm_SignalToNoise_bin_count:
40 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
41 #end if
42 #if $param_algorithm_SignalToNoise_min_required_elements:
43 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
44 #end if
45 #if $param_algorithm_SignalToNoise_write_log_messages:
46 -algorithm:SignalToNoise:write_log_messages
47 #end if
21 #if $adv_opts.adv_opts_selector=='advanced': 48 #if $adv_opts.adv_opts_selector=='advanced':
22 -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap} 49 #if $adv_opts.param_processOption:
23 -algorithm:spacing_difference ${adv_opts.param_spacing_difference} 50 -processOption
24 -algorithm:missing ${adv_opts.param_missing} 51 #if &quot; &quot; in str($adv_opts.param_processOption):
25 -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity} 52 &quot;$adv_opts.param_processOption&quot;
26 -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} 53 #else
27 -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile} 54 $adv_opts.param_processOption
28 -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode} 55 #end if
29 -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} 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
30 #end if 84 #end if
31 </command> 85 </command>
32 <inputs> 86 <inputs>
33 <param name="param_in" type="data" format="mzML" optional="False" label="input profile data file " help="(-in)"/> 87 <param format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/>
34 <param name="param_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)"/> 88 <param help="(-signal_to_noise) " label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" min="0.0" name="param_algorithm_signal_to_noise" optional="True" type="float" value="1.0"/>
35 <param name="param_ms_levels" type="text" min="1" optional="True" size="20" value="1 2" label="List of MS levels for which the peak picking is applied. Other scans are copied to the output without changes." help="(-ms_levels)"/> 89 <repeat max="1" min="0" name="rep_param_algorithm_ms_levels" title="param_algorithm_ms_levels">
36 <param name="param_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len)"/> 90 <param help="(-ms_levels) Other scans are copied to the output without changes" label="List of MS levels for which the peak picking is applied" min="1" name="param_algorithm_ms_levels" optional="True" size="30" type="text" value="1 2">
37 <param name="param_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count)"/> 91 <sanitizer>
38 <param name="param_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)"/> 92 <valid initial="string.printable">
39 <expand macro="advanced_options"> 93 <remove value="'"/>
40 <param name="param_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="Maximum allowed m/z distance between data points in multiples of the minimal difference, above which a data point no longer belongs to the peak." help="(-spacing_difference_gap)"/> 94 <remove value="&quot;"/>
41 <param name="param_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed distance between peaks in multiples of the minimal difference. A higher value is implies a less stringent peak definition since individual signals within the peaks are allowed to further apart. E.g. if the value is set to 1.5 and in a peak the minimal spacing between peaks is 10 mDa, then only signals at most 15 mDa apart will be added to the peak." help="(-spacing_difference)"/> 95 </valid>
42 <param name="param_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points." help="(-missing)"/> 96 </sanitizer>
43 <param name="param_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction. 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." help="(-max_intensity)"/> 97 </param>
44 <param name="param_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)"/> 98 </repeat>
45 <param name="param_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)"/> 99 <param help="(-win_len) " label="window length in Thomson" min="1.0" name="param_algorithm_SignalToNoise_win_len" optional="True" type="float" value="200.0"/>
46 <param name="param_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)"/> 100 <param help="(-bin_count) " label="number of bins for intensity values" min="3" name="param_algorithm_SignalToNoise_bin_count" optional="True" type="integer" value="30"/>
47 <param name="param_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window)"/> 101 <param help="(-min_required_elements) " label="minimum number of elements required in a window (otherwise it is considered sparse)" min="1" name="param_algorithm_SignalToNoise_min_required_elements" optional="True" type="integer" value="10"/>
48 </expand> 102 <param checked="true" falsevalue="" help="(-write_log_messages) " label="Write out log messages in case of sparse windows or median in rightmost histogram bin" name="param_algorithm_SignalToNoise_write_log_messages" optional="True" truevalue="-algorithm:SignalToNoise:write_log_messages" type="boolean"/>
49 </inputs> 103 <expand macro="advanced_options">
50 <outputs> 104 <param help="(-processOption) " 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" name="param_processOption" optional="True" type="select" value="inmemory">
51 <data name="param_out" label="output peak file " format="mzML"/> 105 <option value="inmemory">inmemory</option>
52 </outputs> 106 <option value="lowmemory">lowmemory</option>
53 <help>**What it does** 107 </param>
54 108 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
55 Finds mass spectrometric peaks in profile mass spectra. 109 <param 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" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" min="0.0" name="param_algorithm_spacing_difference_gap" optional="True" type="float" value="4.0"/>
110 <param 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" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" min="0.0" name="param_algorithm_spacing_difference" optional="True" type="float" value="1.5"/>
111 <param 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" label="Maximum number of missing points allowed when extending a peak to the left or to the right" min="0" name="param_algorithm_missing" optional="True" type="integer" value="1"/>
112 <param 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" label="maximal intensity considered for histogram construction" min="-1" name="param_algorithm_SignalToNoise_max_intensity" optional="True" type="integer" value="-1"/>
113 <param help="(-auto_max_stdev_factor) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" max="999.0" min="0.0" name="param_algorithm_SignalToNoise_auto_max_stdev_factor" optional="True" type="float" value="3.0"/>
114 <param help="(-auto_max_percentile) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" max="100" min="0" name="param_algorithm_SignalToNoise_auto_max_percentile" optional="True" type="integer" value="95"/>
115 <param help="(-auto_mode) " 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" max="1" min="-1" name="param_algorithm_SignalToNoise_auto_mode" optional="True" type="integer" value="0"/>
116 <param help="(-noise_for_empty_window) " label="noise value used for sparse windows" name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20"/>
117 </expand>
118 </inputs>
119 <outputs>
120 <data format="mzml" name="param_out"/>
121 </outputs>
122 <help>Finds mass spectrometric peaks in profile mass spectra.
56 123
57 124
58 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html 125 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help>
59 126 </tool>
60 @REFERENCES@
61 </help>
62 </tool>