Mercurial > repos > galaxyp > openms_accuratemasssearch

annotate AccurateMassSearch.xml @ 15:06df83a2ada5 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 18:30:22 +0000
parents 5e756121804a
children
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8c50e8e50ea5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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: [Utilities]-->
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4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Match MS signals to molecules from a database by mass.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">AccurateMassSearch</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($in.ext)' &&
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21 mkdir out &&
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22 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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23 mkdir out_annotation &&
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24 #end if
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25 #if $positive_adducts:
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26 mkdir positive_adducts &&
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27 ln -s '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' &&
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28 #end if
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29 #if $negative_adducts:
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30 mkdir negative_adducts &&
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31 ln -s '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' &&
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32 #end if
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33 #if $db.mapping:
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34 mkdir db.mapping &&
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35 ${ ' '.join(["ln -s '%s' 'db.mapping/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _]) }
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36 #end if
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37 #if $db.struct:
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38 mkdir db.struct &&
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39 ${ ' '.join(["ln -s '%s' 'db.struct/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _]) }
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8c50e8e50ea5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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40 #end if
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42 ## Main program call
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44 set -o pipefail &&
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45 @EXECUTABLE@ -write_ctd ./ &&
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46 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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47 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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48 -in
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49 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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50 -out
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51 'out/output.${gxy2omsext("mztab")}'
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52 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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53 -out_annotation
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54 'out_annotation/output.${in.ext}'
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55 #end if
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56 #if $positive_adducts:
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57 -positive_adducts
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58 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)'
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59 #end if
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60 #if $negative_adducts:
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61 -negative_adducts
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62 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)'
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63 #end if
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64 #if $db.mapping:
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65 -db:mapping
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66 ${' '.join(["'db.mapping/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])}
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67 #end if
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68 #if $db.struct:
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69 -db:struct
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70 ${' '.join(["'db.struct/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])}
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71 #end if
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72 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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73 | tee '$stdout'
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74 #end if
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75
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76 ## Postprocessing
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77 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
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78 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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79 && mv 'out_annotation/output.${in.ext}' '$out_annotation'
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80 #end if
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81 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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82 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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83 #end if]]></command>
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84 <configfiles>
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85 <inputs name="args_json" data_style="paths"/>
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86 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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87 </configfiles>
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88 <inputs>
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89 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/>
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90 <param name="positive_adducts" argument="-positive_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential positive adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/>
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91 <param name="negative_adducts" argument="-negative_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential negative adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/>
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92 <section name="db" title="Database files which contain the identifications" help="" expanded="false">
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93 <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
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94 <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
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95 </section>
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96 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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97 <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="true" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
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98 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" display="radio" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
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99 <option value="ppm" selected="true">ppm</option>
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100 <option value="Da">Da</option>
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101 <expand macro="list_string_san"/>
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102 </param>
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103 <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
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104 <option value="positive" selected="true">positive</option>
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105 <option value="negative">negative</option>
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106 <option value="auto">auto</option>
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107 <expand macro="list_string_san"/>
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108 </param>
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109 <param name="isotopic_similarity" argument="-algorithm:isotopic_similarity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help=""/>
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110 <param name="use_feature_adducts" argument="-algorithm:use_feature_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to filter AMS candidates mismatching available feature adduct annotation" help=""/>
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111 <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep features that did not yield any DB hit" help=""/>
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112 <section name="mzTab" title="" help="" expanded="false">
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113 <param name="exportIsotopeIntensities" argument="-algorithm:mzTab:exportIsotopeIntensities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[featureXML input only] Export column with available isotope trace intensities (opt_global_MTint)" help=""/>
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114 </section>
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115 </section>
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116 <expand macro="adv_opts_macro">
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117 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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118 <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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119 <expand macro="list_string_san"/>
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120 </param>
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121 </expand>
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122 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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123 <option value="out_annotation_FLAG">out_annotation (A copy of the input file, annotated with matching hits from the database)</option>
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124 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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125 </param>
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126 </inputs>
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127 <outputs>
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128 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
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129 <data name="out_annotation" label="${tool.name} on ${on_string}: out_annotation" format_source="in" metadata_source="in">
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130 <filter>OPTIONAL_OUTPUTS is not None and "out_annotation_FLAG" in OPTIONAL_OUTPUTS</filter>
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131 </data>
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132 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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133 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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134 </data>
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135 </outputs>
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136 <tests>
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137 <expand macro="autotest_AccurateMassSearch"/>
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138 <expand macro="manutest_AccurateMassSearch"/>
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139 </tests>
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140 <help><![CDATA[Match MS signals to molecules from a database by mass.
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141
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142
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143 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_AccurateMassSearch.html]]></help>
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144 <expand macro="references"/>
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145 </tool>