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annotate MassTraceExtractor.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.0.0">
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5 <description>Detects mass traces in centroided LC-MS data.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MassTraceExtractor</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>MassTraceExtractor
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_out_type:
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22 -out_type
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23 #if &quot; &quot; in str($param_out_type):
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24 &quot;$param_out_type&quot;
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25 #else
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26 $param_out_type
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27 #end if
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28 #end if
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29 -threads \${GALAXY_SLOTS:-24}
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30 #if $param_algorithm_common_noise_threshold_int:
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31 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
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32 #end if
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33 #if $param_algorithm_common_chrom_peak_snr:
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34 -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
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35 #end if
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36 #if $param_algorithm_common_chrom_fwhm:
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37 -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
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38 #end if
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39 #if $param_algorithm_mtd_mass_error_ppm:
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40 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
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41 #end if
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42 #if $param_algorithm_mtd_reestimate_mt_sd:
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43 -algorithm:mtd:reestimate_mt_sd
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44 #end if
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45 #if $param_algorithm_epd_width_filtering:
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46 -algorithm:epd:width_filtering
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47 #if &quot; &quot; in str($param_algorithm_epd_width_filtering):
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48 &quot;$param_algorithm_epd_width_filtering&quot;
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49 #else
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50 $param_algorithm_epd_width_filtering
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51 #end if
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52 #end if
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53 #if $param_algorithm_epd_enabled:
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54 -algorithm:epd:enabled
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55 #end if
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56 #if $adv_opts.adv_opts_selector=='advanced':
4
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57 #if $adv_opts.param_force:
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58 -force
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59 #end if
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60 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
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61 -algorithm:mtd:trace_termination_criterion
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62 #if &quot; &quot; in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
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63 &quot;$adv_opts.param_algorithm_mtd_trace_termination_criterion&quot;
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64 #else
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65 $adv_opts.param_algorithm_mtd_trace_termination_criterion
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66 #end if
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67 #end if
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68 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
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69 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
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70 #end if
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71 #if $adv_opts.param_algorithm_mtd_min_sample_rate:
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72 -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
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73 #end if
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74 #if $adv_opts.param_algorithm_mtd_min_trace_length:
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75 -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
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76 #end if
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77 #if $adv_opts.param_algorithm_mtd_max_trace_length:
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78 -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
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79 #end if
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80 #if $adv_opts.param_algorithm_epd_min_fwhm:
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81 -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
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82 #end if
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83 #if $adv_opts.param_algorithm_epd_max_fwhm:
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84 -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
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85 #end if
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86 #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
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87 -algorithm:epd:masstrace_snr_filtering
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88 #end if
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89 #end if
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90 </command>
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91 <inputs>
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92 <param format="mzml" help="(-in) " label="input centroided mzML file" name="param_in" optional="False" type="data"/>
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93 <param help="(-out_type) " label="output file type -- default: determined from file extension or content" name="param_out_type" optional="True" type="select">
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94 <option value="featureXML">featureXML</option>
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95 <option value="consensusXML">consensusXML</option>
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96 </param>
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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"/>
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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"/>
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99 <param help="(-chrom_fwhm) " label="Expected chromatographic peak width (in seconds)" name="param_algorithm_common_chrom_fwhm" type="float" value="5.0"/>
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100 <param help="(-mass_error_ppm) " label="Allowed mass deviation (in ppm)" name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0"/>
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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"/>
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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">
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103 <option value="off">off</option>
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104 <option value="fixed">fixed</option>
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105 <option value="auto">auto</option>
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106 </param>
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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"/>
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108 <expand macro="advanced_options">
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109 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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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">
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111 <option value="outlier">outlier</option>
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112 <option value="sample_rate">sample_rate</option>
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113 </param>
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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"/>
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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"/>
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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"/>
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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"/>
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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"/>
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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"/>
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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"/>
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121 </expand>
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122 </inputs>
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123 <outputs>
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124 <data format="xml" name="param_out"/>
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125 </outputs>
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126 <help>Detects mass traces in centroided LC-MS data.
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127
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128
4
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129 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html</help>
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130 </tool>