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comparison MassTraceExtractor.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="MassTraceExtractor" name="MassTraceExtractor" 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>Detects mass traces in centroided LC-MS data.</description> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <macros> 4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.0.0">
5 <token name="@EXECUTABLE@">MassTraceExtractor</token> 5 <description>Detects mass traces in centroided LC-MS data.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">MassTraceExtractor</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>MassTraceExtractor 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MassTraceExtractor
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -out_type ${param_out_type} 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_out:
16 -algorithm:common:noise_threshold_int ${param_noise_threshold_int} 19 -out $param_out
17 -algorithm:common:chrom_peak_snr ${param_chrom_peak_snr} 20 #end if
18 -algorithm:common:chrom_fwhm ${param_chrom_fwhm} 21 #if $param_out_type:
19 -algorithm:mtd:mass_error_ppm ${param_mass_error_ppm} 22 -out_type
20 ${param_reestimate_mt_sd} 23 #if &quot; &quot; in str($param_out_type):
21 -algorithm:epd:width_filtering ${param_width_filtering} 24 &quot;$param_out_type&quot;
22 ${param_enabled} 25 #else
26 $param_out_type
27 #end if
28 #end if
29 -threads \${GALAXY_SLOTS:-24}
30 #if $param_algorithm_common_noise_threshold_int:
31 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
32 #end if
33 #if $param_algorithm_common_chrom_peak_snr:
34 -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
35 #end if
36 #if $param_algorithm_common_chrom_fwhm:
37 -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
38 #end if
39 #if $param_algorithm_mtd_mass_error_ppm:
40 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
41 #end if
42 #if $param_algorithm_mtd_reestimate_mt_sd:
43 -algorithm:mtd:reestimate_mt_sd
44 #end if
45 #if $param_algorithm_epd_width_filtering:
46 -algorithm:epd:width_filtering
47 #if &quot; &quot; in str($param_algorithm_epd_width_filtering):
48 &quot;$param_algorithm_epd_width_filtering&quot;
49 #else
50 $param_algorithm_epd_width_filtering
51 #end if
52 #end if
53 #if $param_algorithm_epd_enabled:
54 -algorithm:epd:enabled
55 #end if
23 #if $adv_opts.adv_opts_selector=='advanced': 56 #if $adv_opts.adv_opts_selector=='advanced':
24 -algorithm:mtd:trace_termination_criterion ${adv_opts.param_trace_termination_criterion} 57 #if $adv_opts.param_force:
25 -algorithm:mtd:trace_termination_outliers ${adv_opts.param_trace_termination_outliers} 58 -force
26 -algorithm:mtd:min_sample_rate ${adv_opts.param_min_sample_rate} 59 #end if
27 -algorithm:mtd:min_trace_length ${adv_opts.param_min_trace_length} 60 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
28 -algorithm:mtd:max_trace_length ${adv_opts.param_max_trace_length} 61 -algorithm:mtd:trace_termination_criterion
29 -algorithm:epd:min_fwhm ${adv_opts.param_min_fwhm} 62 #if &quot; &quot; in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
30 -algorithm:epd:max_fwhm ${adv_opts.param_max_fwhm} 63 &quot;$adv_opts.param_algorithm_mtd_trace_termination_criterion&quot;
31 ${adv_opts.param_masstrace_snr_filtering} 64 #else
65 $adv_opts.param_algorithm_mtd_trace_termination_criterion
66 #end if
67 #end if
68 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
69 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
70 #end if
71 #if $adv_opts.param_algorithm_mtd_min_sample_rate:
72 -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
73 #end if
74 #if $adv_opts.param_algorithm_mtd_min_trace_length:
75 -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
76 #end if
77 #if $adv_opts.param_algorithm_mtd_max_trace_length:
78 -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
79 #end if
80 #if $adv_opts.param_algorithm_epd_min_fwhm:
81 -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
82 #end if
83 #if $adv_opts.param_algorithm_epd_max_fwhm:
84 -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
85 #end if
86 #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
87 -algorithm:epd:masstrace_snr_filtering
88 #end if
32 #end if 89 #end if
33 </command> 90 </command>
34 <inputs> 91 <inputs>
35 <param name="param_in" type="data" format="mzML" optional="False" label="input centroided mzML file" help="(-in)"/> 92 <param format="mzml" help="(-in) " label="input centroided mzML file" name="param_in" optional="False" type="data"/>
36 <param name="param_out_type" type="select" optional="True" label="output file type -- default: determined from file extension or content" help="(-out_type)"> 93 <param help="(-out_type) " label="output file type -- default: determined from file extension or content" name="param_out_type" optional="True" type="select">
37 <option value="featureXML">featureXML</option> 94 <option value="featureXML">featureXML</option>
38 <option value="consensusXML">consensusXML</option> 95 <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> 96 </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)"/> 97 <param help="(-noise_threshold_int) " label="Intensity threshold below which peaks are regarded as noise" name="param_algorithm_common_noise_threshold_int" type="float" value="10.0"/>
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)"/> 98 <param help="(-chrom_peak_snr) " label="Minimum signal-to-noise a mass trace should have" name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0"/>
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)"/> 99 <param help="(-chrom_fwhm) " label="Expected chromatographic peak width (in seconds)" name="param_algorithm_common_chrom_fwhm" type="float" value="5.0"/>
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)"/> 100 <param help="(-mass_error_ppm) " label="Allowed mass deviation (in ppm)" name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0"/>
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)"/> 101 <param checked="true" falsevalue="" help="(-reestimate_mt_sd) " label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" name="param_algorithm_mtd_reestimate_mt_sd" optional="True" truevalue="-algorithm:mtd:reestimate_mt_sd" type="boolean"/>
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)"/> 102 <param 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" label="Enable filtering of unlikely peak widths" name="param_algorithm_epd_width_filtering" optional="True" type="select" value="fixed">
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)"/> 103 <option value="off">off</option>
63 </expand> 104 <option value="fixed">fixed</option>
64 </inputs> 105 <option value="auto">auto</option>
65 <outputs> 106 </param>
66 <data name="param_out" label="output featureXML file with mass traces" format="consensusXML"> 107 <param checked="true" falsevalue="" help="(-enabled) " label="Enables/disables the chromatographic peak detection of mass traces" name="param_algorithm_epd_enabled" optional="True" truevalue="-algorithm:epd:enabled" type="boolean"/>
67 <change_format> 108 <expand macro="advanced_options">
68 <when input="param_out_type" value="featureXML" format="featureXML"/> 109 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
69 </change_format> 110 <param 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" label="Termination criterion for the extension of mass traces" name="param_algorithm_mtd_trace_termination_criterion" optional="True" type="select" value="outlier">
70 </data> 111 <option value="outlier">outlier</option>
71 </outputs> 112 <option value="sample_rate">sample_rate</option>
72 <help>**What it does** 113 </param>
73 114 <param help="(-trace_termination_outliers) " label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" name="param_algorithm_mtd_trace_termination_outliers" type="integer" value="5"/>
74 Detects mass traces in centroided LC-MS data. 115 <param help="(-min_sample_rate) " label="Minimum fraction of scans along the mass trace that must contain a peak" name="param_algorithm_mtd_min_sample_rate" type="float" value="0.5"/>
116 <param help="(-min_trace_length) " label="Minimum expected length of a mass trace (in seconds)" name="param_algorithm_mtd_min_trace_length" type="float" value="5.0"/>
117 <param help="(-max_trace_length) " label="Maximum expected length of a mass trace (in seconds)" name="param_algorithm_mtd_max_trace_length" type="float" value="300.0"/>
118 <param help="(-min_fwhm) Ignored if parameter width_filtering is off or auto" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" name="param_algorithm_epd_min_fwhm" type="float" value="3.0"/>
119 <param help="(-max_fwhm) Ignored if parameter width_filtering is off or auto" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" name="param_algorithm_epd_max_fwhm" type="float" value="60.0"/>
120 <param checked="false" falsevalue="" help="(-masstrace_snr_filtering) " label="Apply post-filtering by signal-to-noise ratio after smoothing" name="param_algorithm_epd_masstrace_snr_filtering" optional="True" truevalue="-algorithm:epd:masstrace_snr_filtering" type="boolean"/>
121 </expand>
122 </inputs>
123 <outputs>
124 <data format="xml" name="param_out"/>
125 </outputs>
126 <help>Detects mass traces in centroided LC-MS data.
75 127
76 128
77 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html 129 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html</help>
78 130 </tool>
79 @REFERENCES@
80 </help>
81 </tool>