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comparison MassTraceExtractor.xml @ 0:3d84209d3178 draft

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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="1.12.0">
3 <description>Detects mass traces in centroided LC-MS data.</description>
4 <macros>
5 <token name="@EXECUTABLE@">MassTraceExtractor</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>MassTraceExtractor
11
12 -in ${param_in}
13 -out ${param_out}
14 -out_type ${param_out_type}
15 -threads \${GALAXY_SLOTS:-24}
16 -algorithm:common:noise_threshold_int ${param_noise_threshold_int}
17 -algorithm:common:chrom_peak_snr ${param_chrom_peak_snr}
18 -algorithm:common:chrom_fwhm ${param_chrom_fwhm}
19 -algorithm:mtd:mass_error_ppm ${param_mass_error_ppm}
20 ${param_reestimate_mt_sd}
21 -algorithm:epd:width_filtering ${param_width_filtering}
22 ${param_enabled}
23 #if $adv_opts.adv_opts_selector=='advanced':
24 -algorithm:mtd:trace_termination_criterion ${adv_opts.param_trace_termination_criterion}
25 -algorithm:mtd:trace_termination_outliers ${adv_opts.param_trace_termination_outliers}
26 -algorithm:mtd:min_sample_rate ${adv_opts.param_min_sample_rate}
27 -algorithm:mtd:min_trace_length ${adv_opts.param_min_trace_length}
28 -algorithm:mtd:max_trace_length ${adv_opts.param_max_trace_length}
29 -algorithm:epd:min_fwhm ${adv_opts.param_min_fwhm}
30 -algorithm:epd:max_fwhm ${adv_opts.param_max_fwhm}
31 ${adv_opts.param_masstrace_snr_filtering}
32 #end if
33 </command>
34 <inputs>
35 <param name="param_in" type="data" format="mzML" optional="False" label="input centroided mzML file" help="(-in)"/>
36 <param name="param_out_type" type="select" optional="True" label="output file type -- default: determined from file extension or content" help="(-out_type)">
37 <option value="featureXML">featureXML</option>
38 <option value="consensusXML">consensusXML</option>
39 </param>
40 <param name="param_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise." help="(-noise_threshold_int)"/>
41 <param name="param_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have." help="(-chrom_peak_snr)"/>
42 <param name="param_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)." help="(-chrom_fwhm)"/>
43 <param name="param_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)." help="(-mass_error_ppm)"/>
44 <param name="param_reestimate_mt_sd" type="boolean" truevalue="-algorithm:mtd:reestimate_mt_sd true" falsevalue="-algorithm:mtd:reestimate_mt_sd false" checked="true" optional="True" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage." help="(-reestimate_mt_sd)"/>
45 <param name="param_width_filtering" type="select" optional="True" value="fixed" label="Enable filtering of unlikely peak widths. 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." help="(-width_filtering)">
46 <option value="off">off</option>
47 <option value="fixed">fixed</option>
48 <option value="auto">auto</option>
49 </param>
50 <param name="param_enabled" type="boolean" truevalue="-algorithm:epd:enabled true" falsevalue="-algorithm:epd:enabled false" checked="true" optional="True" label="Enables/disables the chromatographic peak detection of mass traces" help="(-enabled)"/>
51 <expand macro="advanced_options">
52 <param name="param_trace_termination_criterion" type="select" optional="True" value="outlier" label="Termination criterion for the extension of mass traces. 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." help="(-trace_termination_criterion)">
53 <option value="outlier">outlier</option>
54 <option value="sample_rate">sample_rate</option>
55 </param>
56 <param name="param_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)"/>
57 <param name="param_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)"/>
58 <param name="param_min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)." help="(-min_trace_length)"/>
59 <param name="param_max_trace_length" type="float" value="300.0" label="Minimum expected length of a mass trace (in seconds)." help="(-max_trace_length)"/>
60 <param name="param_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto." help="(-min_fwhm)"/>
61 <param name="param_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto." help="(-max_fwhm)"/>
62 <param name="param_masstrace_snr_filtering" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering true" falsevalue="-algorithm:epd:masstrace_snr_filtering false" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing." help="(-masstrace_snr_filtering)"/>
63 </expand>
64 </inputs>
65 <outputs>
66 <data name="param_out" label="output featureXML file with mass traces" format="consensusXML">
67 <change_format>
68 <when input="param_out_type" value="featureXML" format="featureXML"/>
69 </change_format>
70 </data>
71 </outputs>
72 <help>**What it does**
73
74 Detects mass traces in centroided LC-MS data.
75
76
77 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html
78
79 @REFERENCES@
80 </help>
81 </tool>