Mercurial > repos > galaxyp > openms_featurefindermetabo

annotate FeatureFinderMetabo.xml @ 13:00080bb4299e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:38:53 +0000
parents 21dc135961b5
children 2451315543f9
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderMetabo</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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22 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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23 mkdir out_chrom &&
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24 #end if
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26 ## Main program call
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28 set -o pipefail &&
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29 @EXECUTABLE@ -write_ctd ./ &&
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30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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32 -in
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33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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34 -out
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35 'out/output.${gxy2omsext("featurexml")}'
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36 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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37 -out_chrom
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38 'out_chrom/output.${gxy2omsext("mzml")}'
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39 #end if
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40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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41 | tee '$stdout'
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42 #end if
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44 ## Postprocessing
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45 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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46 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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47 && mv 'out_chrom/output.${gxy2omsext("mzml")}' '$out_chrom'
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48 #end if
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49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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50 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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51 #end if]]></command>
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52 <configfiles>
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53 <inputs name="args_json" data_style="paths"/>
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54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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55 </configfiles>
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56 <inputs>
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57 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/>
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58 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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59 <section name="common" title="Common parameters for all other subsections" help="" expanded="false">
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60 <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
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61 <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" optional="true" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
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62 <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
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63 </section>
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64 <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false">
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65 <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
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66 <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
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67 <param name="quant_method" argument="-algorithm:mtd:quant_method" display="radio" type="select" optional="false" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
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68 <option value="area" selected="true">area</option>
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69 <option value="median">median</option>
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70 <option value="max_height">max_height</option>
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71 <expand macro="list_string_san"/>
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72 </param>
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73 <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" display="radio" type="select" optional="false" label="Termination criterion for the extension of mass traces" help="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">
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74 <option value="outlier" selected="true">outlier</option>
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75 <option value="sample_rate">sample_rate</option>
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76 <expand macro="list_string_san"/>
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77 </param>
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78 <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
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79 <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
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80 <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" optional="true" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
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81 <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
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82 </section>
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83 <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false">
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84 <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/>
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85 <param name="width_filtering" argument="-algorithm:epd:width_filtering" display="radio" type="select" optional="false" label="Enable filtering of unlikely peak widths" help="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">
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86 <option value="off">off</option>
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87 <option value="fixed" selected="true">fixed</option>
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88 <option value="auto">auto</option>
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89 <expand macro="list_string_san"/>
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90 </param>
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91 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
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92 <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
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93 <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/>
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94 </section>
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95 <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false">
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96 <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" optional="true" value="10.0" label="RT range where to look for coeluting mass traces" help=""/>
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97 <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" optional="true" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/>
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98 <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" optional="true" value="1" label="Lowest charge state to conside" help=""/>
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99 <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="true" value="3" label="Highest charge state to conside" help=""/>
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100 <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/>
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101 <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/>
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102 <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" display="radio" type="select" optional="false" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
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103 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
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104 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
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105 <option value="peptides">peptides</option>
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106 <option value="none">none</option>
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107 <expand macro="list_string_san"/>
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108 </param>
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109 <param name="mz_scoring_13C" argument="-algorithm:ffm:mz_scoring_13C" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
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110 <param name="use_smoothed_intensities" argument="-algorithm:ffm:use_smoothed_intensities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use LOWESS intensities instead of raw intensities" help=""/>
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111 <param name="report_convex_hulls" argument="-algorithm:ffm:report_convex_hulls" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help=""/>
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112 <param name="remove_single_traces" argument="-algorithm:ffm:remove_single_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassembled traces (single traces)" help=""/>
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113 <param name="mz_scoring_by_elements" argument="-algorithm:ffm:mz_scoring_by_elements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the m/z range of the assumed elements to detect isotope peaks" help="A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'"/>
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114 <param name="elements" argument="-algorithm:ffm:elements" type="text" optional="true" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help="">
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115 <expand macro="list_string_san"/>
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116 </param>
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117 </section>
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118 </section>
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119 <expand macro="adv_opts_macro">
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120 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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121 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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122 <expand macro="list_string_san"/>
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123 </param>
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124 </expand>
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125 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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126 <option value="out_chrom_FLAG">out_chrom (Optional mzML file with chromatograms)</option>
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127 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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128 </param>
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129 </inputs>
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130 <outputs>
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131 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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132 <data name="out_chrom" label="${tool.name} on ${on_string}: out_chrom" format="mzml">
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133 <filter>OPTIONAL_OUTPUTS is not None and "out_chrom_FLAG" in OPTIONAL_OUTPUTS</filter>
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134 </data>
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135 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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136 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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137 </data>
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138 </outputs>
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139 <tests>
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140 <expand macro="autotest_FeatureFinderMetabo"/>
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141 <expand macro="manutest_FeatureFinderMetabo"/>
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142 </tests>
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143 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
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144
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145
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146 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderMetabo.html]]></help>
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147 <expand macro="references"/>
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148 </tool>