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comparison PeakPickerHiRes.xml @ 8:146b59d2d3e5 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
author galaxyp
date Wed, 04 Nov 2020 13:04:26 +0000
parents 3d8d4ada5405
children 6b01678ec2fc
comparison
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7:3d8d4ada5405 8:146b59d2d3e5
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 CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.3.0"> 4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[PeakPickerHiRes 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir 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 22
25 #if $rep_param_algorithm_ms_levels: 23 ## Main program call
26 -algorithm:ms_levels 24
27 #for token in $rep_param_algorithm_ms_levels: 25 set -o pipefail &&
28 #if " " in str(token): 26 @EXECUTABLE@ -write_ctd ./ &&
29 "$token.param_algorithm_ms_levels" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
30 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
31 $token.param_algorithm_ms_levels 29 -in
32 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
33 #end for 31 -out
34 #end if 32 'out/output.${gxy2omsext("mzml")}'
35 #if $param_algorithm_report_FWHM: 33
36 -algorithm:report_FWHM 34 ## Postprocessing
37 #end if 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
38 #if $param_algorithm_report_FWHM_unit: 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
39 -algorithm:report_FWHM_unit 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
40 #if " " in str($param_algorithm_report_FWHM_unit): 38 #end if]]></command>
41 "$param_algorithm_report_FWHM_unit" 39 <configfiles>
42 #else 40 <inputs name="args_json" data_style="paths"/>
43 $param_algorithm_report_FWHM_unit 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
44 #end if 42 </configfiles>
45 #end if
46 #if $param_algorithm_SignalToNoise_win_len:
47 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
48 #end if
49 #if $param_algorithm_SignalToNoise_bin_count:
50 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
51 #end if
52 #if $param_algorithm_SignalToNoise_min_required_elements:
53 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
54 #end if
55 #if $param_algorithm_SignalToNoise_write_log_messages:
56 -algorithm:SignalToNoise:write_log_messages
57 #if " " in str($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
62 #end if
63 #if $adv_opts.adv_opts_selector=='advanced':
64 #if $adv_opts.param_processOption:
65 -processOption
66 #if " " in str($adv_opts.param_processOption):
67 "$adv_opts.param_processOption"
68 #else
69 $adv_opts.param_processOption
70 #end if
71 #end if
72 #if $adv_opts.param_force:
73 -force
74 #end if
75 #if $adv_opts.param_algorithm_spacing_difference_gap:
76 -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap
77 #end if
78 #if $adv_opts.param_algorithm_spacing_difference:
79 -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
80 #end if
81 #if $adv_opts.param_algorithm_missing:
82 -algorithm:missing $adv_opts.param_algorithm_missing
83 #end if
84 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
85 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
86 #end if
87 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
88 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
89 #end if
90 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
91 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
92 #end if
93 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
94 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
95 #end if
96 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
97 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
98 #end if
99 #end if
100 ]]></command>
101 <inputs> 43 <inputs>
102 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/>
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) "/> 45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
104 <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels"> 46 <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help=""/>
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"> 47 <param name="spacing_difference_gap" argument="-algorithm:spacing_difference_gap" type="float" optional="true" min="0.0" 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="'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"/>
106 <sanitizer> 48 <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" optional="true" min="0.0" 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="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"/>
107 <valid initial="string.printable"> 49 <param name="missing" argument="-algorithm:missing" type="integer" optional="true" min="0" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="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"/>
108 <remove value="'"/> 50 <param name="ms_levels" argument="-algorithm:ms_levels" type="text" optional="true" value="" label="List of MS levels for which the peak picking is applied" help="If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes (space separated list, in order to allow for spaces in list items surround them by single quotes)">
109 <remove value="&quot;"/> 51 <expand macro="list_integer_valsan">
110 </valid> 52 <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if 1 <= int(_)])
111 </sanitizer> 53 ]]></validator>
54 </expand>
112 </param> 55 </param>
113 </repeat> 56 <param name="report_FWHM" argument="-algorithm:report_FWHM" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help=""/>
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) "/> 57 <param name="report_FWHM_unit" argument="-algorithm:report_FWHM_unit" display="radio" type="select" optional="false" label="Unit of FWHM" help="Either absolute in the unit of input, 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)"> 58 <option value="relative" selected="true">relative</option>
116 <option value="relative" selected="true">relative</option> 59 <option value="absolute">absolute</option>
117 <option value="absolute">absolute</option> 60 <expand macro="list_string_san"/>
118 </param> 61 </param>
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) "/> 62 <section name="SignalToNoise" title="" help="" expanded="false">
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) "/> 63 <param name="max_intensity" argument="-algorithm:SignalToNoise:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="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_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) "/> 64 <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
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) "> 65 <param name="auto_max_percentile" argument="-algorithm:SignalToNoise:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
123 <option value="true" selected="true">true</option> 66 <param name="auto_mode" argument="-algorithm:SignalToNoise:auto_mode" type="integer" optional="true" min="-1" max="1" 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=""/>
124 <option value="false">false</option> 67 <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
125 </param> 68 <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
126 <expand macro="advanced_options"> 69 <param name="min_required_elements" argument="-algorithm:SignalToNoise:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
127 <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) "> 70 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
71 <param name="write_log_messages" argument="-algorithm:SignalToNoise:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help=""/>
72 </section>
73 </section>
74 <expand macro="adv_opts_macro">
75 <param name="processOption" argument="-processOption" display="radio" type="select" optional="false" 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="">
128 <option value="inmemory" selected="true">inmemory</option> 76 <option value="inmemory" selected="true">inmemory</option>
129 <option value="lowmemory">lowmemory</option> 77 <option value="lowmemory">lowmemory</option>
78 <expand macro="list_string_san"/>
130 </param> 79 </param>
131 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
132 <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"/> 81 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
133 <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"/> 82 <expand macro="list_string_san"/>
134 <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"/> 83 </param>
135 <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"/>
136 <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) "/>
137 <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) "/>
138 <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) "/>
139 <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) "/>
140 </expand> 84 </expand>
85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
87 </param>
141 </inputs> 88 </inputs>
142 <outputs> 89 <outputs>
143 <data name="param_out" format="mzml"/> 90 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
91 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
92 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
93 </data>
144 </outputs> 94 </outputs>
145 <help>Finds mass spectrometric peaks in profile mass spectra. 95 <tests>
96 <expand macro="autotest_PeakPickerHiRes"/>
97 <expand macro="manutest_PeakPickerHiRes"/>
98 </tests>
99 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
146 100
147 101
148 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PeakPickerHiRes.html</help> 102 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PeakPickerHiRes.html]]></help>
103 <expand macro="references"/>
149 </tool> 104 </tool>