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comparison MassTraceExtractor.xml @ 0:87171d7b6ff8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 10:19:56 -0500
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children 50fc3706dbc1
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-1:000000000000 0:87171d7b6ff8
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.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.1.0">
5 <description>Detects mass traces in centroided LC-MS data.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MassTraceExtractor</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MassTraceExtractor
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_out_type:
22 -out_type
23 #if " " in str($param_out_type):
24 "$param_out_type"
25 #else
26 $param_out_type
27 #end if
28 #end if
29 #if $param_algorithm_common_noise_threshold_int:
30 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
31 #end if
32 #if $param_algorithm_common_chrom_peak_snr:
33 -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
34 #end if
35 #if $param_algorithm_common_chrom_fwhm:
36 -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
37 #end if
38 #if $param_algorithm_mtd_mass_error_ppm:
39 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
40 #end if
41 #if $param_algorithm_mtd_reestimate_mt_sd:
42 -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd
43 #end if
44 #if $param_algorithm_mtd_quant_method:
45 -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method
46 #end if
47 #if $param_algorithm_epd_width_filtering:
48 -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering
49 #end if
50 #if $param_algorithm_epd_enabled:
51 -algorithm:epd:enabled $param_algorithm_epd_enabled
52 #end if
53 #if $adv_opts.adv_opts_selector=='advanced':
54 #if $adv_opts.param_force:
55 -force
56 #end if
57 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
58 -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion
59 #end if
60 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
61 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
62 #end if
63 #if $adv_opts.param_algorithm_mtd_min_sample_rate:
64 -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
65 #end if
66 #if $adv_opts.param_algorithm_mtd_min_trace_length:
67 -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
68 #end if
69 #if $adv_opts.param_algorithm_mtd_max_trace_length:
70 -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
71 #end if
72 #if $adv_opts.param_algorithm_epd_min_fwhm:
73 -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
74 #end if
75 #if $adv_opts.param_algorithm_epd_max_fwhm:
76 -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
77 #end if
78 #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
79 -algorithm:epd:masstrace_snr_filtering
80 #end if
81 #end if
82 </command>
83 <inputs>
84 <param name="param_in" type="data" format="mzml" optional="False" label="input centroided mzML file" help="(-in) "/>
85 <param name="param_out_type" display="radio" type="select" optional="True" label="output file type -- default: determined from file extension or content" help="(-out_type) ">
86 <option value="featureXML">featureXML</option>
87 <option value="consensusXML">consensusXML</option>
88 </param>
89 <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/>
90 <param name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help="(-chrom_peak_snr) "/>
91 <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/>
92 <param name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help="(-mass_error_ppm) "/>
93 <param name="param_algorithm_mtd_reestimate_mt_sd" display="radio" type="select" optional="False" value="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help="(-reestimate_mt_sd) ">
94 <option value="true" selected="true">true</option>
95 <option value="false">false</option>
96 </param>
97 <param name="param_algorithm_mtd_quant_method" display="radio" type="select" optional="False" value="area" label="Method of quantification for mass traces" help="(-quant_method) For LC data 'area' is recommended, 'median' for direct injection data">
98 <option value="area" selected="true">area</option>
99 <option value="median">median</option>
100 </param>
101 <param name="param_algorithm_epd_width_filtering" display="radio" type="select" optional="False" value="fixed" label="Enable filtering of unlikely peak widths" help="(-width_filtering) The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
102 <option value="off">off</option>
103 <option value="fixed" selected="true">fixed</option>
104 <option value="auto">auto</option>
105 </param>
106 <param name="param_algorithm_epd_enabled" display="radio" type="select" optional="False" value="true" label="Enables/disables the chromatographic peak detection of mass traces" help="(-enabled) ">
107 <option value="true" selected="true">true</option>
108 <option value="false">false</option>
109 </param>
110 <expand macro="advanced_options">
111 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
112 <param name="param_algorithm_mtd_trace_termination_criterion" display="radio" type="select" optional="False" value="outlier" label="Termination criterion for the extension of mass traces" help="(-trace_termination_criterion) In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
113 <option value="outlier" selected="true">outlier</option>
114 <option value="sample_rate">sample_rate</option>
115 </param>
116 <param name="param_algorithm_mtd_trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help="(-trace_termination_outliers) "/>
117 <param name="param_algorithm_mtd_min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help="(-min_sample_rate) "/>
118 <param name="param_algorithm_mtd_min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help="(-min_trace_length) "/>
119 <param name="param_algorithm_mtd_max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="(-max_trace_length) Set to a negative value to disable maximal length check during mass trace detection"/>
120 <param name="param_algorithm_epd_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-min_fwhm) Ignored if parameter width_filtering is off or auto"/>
121 <param name="param_algorithm_epd_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-max_fwhm) Ignored if parameter width_filtering is off or auto"/>
122 <param name="param_algorithm_epd_masstrace_snr_filtering" display="radio" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering" falsevalue="" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing" help="(-masstrace_snr_filtering) "/>
123 </expand>
124 </inputs>
125 <outputs>
126 <data name="param_out" format="featurexml"/>
127 </outputs>
128 <help>Detects mass traces in centroided LC-MS data.
129
130
131 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html</help>
132 </tool>