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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.0.0">
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3 <description>Find potential HMDB ids within the given mass error window.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">AccurateMassSearch</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>AccurateMassSearch
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_out_annotation:
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19 -out_annotation $param_out_annotation
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20 #end if
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21 #if $param_positive_adducts_file:
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22 -positive_adducts_file $param_positive_adducts_file
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23 #end if
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24 #if $param_negative_adducts_file:
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25 -negative_adducts_file $param_negative_adducts_file
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26 #end if
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27 -threads \${GALAXY_SLOTS:-24}
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28 #if $param_db_mapping:
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29 -db:mapping $param_db_mapping
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30 #end if
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31 #if $param_db_struct:
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32 -db:struct $param_db_struct
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33 #end if
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34 #if $param_algorithm_mass_error_value:
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35 -algorithm:mass_error_value $param_algorithm_mass_error_value
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36 #end if
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37 #if $param_algorithm_mass_error_unit:
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38 -algorithm:mass_error_unit
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39 #if " " in str($param_algorithm_mass_error_unit):
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40 "$param_algorithm_mass_error_unit"
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41 #else
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42 $param_algorithm_mass_error_unit
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43 #end if
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44 #end if
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45 #if $param_algorithm_ionization_mode:
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46 -algorithm:ionization_mode
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47 #if " " in str($param_algorithm_ionization_mode):
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48 "$param_algorithm_ionization_mode"
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49 #else
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50 $param_algorithm_ionization_mode
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51 #end if
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52 #end if
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53 #if $param_algorithm_isotopic_similarity:
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54 -algorithm:isotopic_similarity
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55 #end if
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56 #if $param_algorithm_report_mode:
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57 -algorithm:report_mode
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58 #if " " in str($param_algorithm_report_mode):
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59 "$param_algorithm_report_mode"
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60 #else
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61 $param_algorithm_report_mode
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62 #end if
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63 #end if
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64 #if $param_algorithm_keep_unidentified_masses:
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65 -algorithm:keep_unidentified_masses
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66 #end if
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67 #if $adv_opts.adv_opts_selector=='advanced':
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68 #if $adv_opts.param_force:
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69 -force
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70 #end if
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71 #end if
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72 </command>
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73 <inputs>
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74 <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="featureXML or consensusXML file" help="(-in) "/>
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75 <param name="param_positive_adducts_file" type="data" format="tabular" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts_file) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
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76 <param name="param_negative_adducts_file" type="data" format="tabular" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts_file) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
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77 <param name="param_db_mapping" type="data" format="tabular" optional="False" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file, containing three tab-separated columns of mass, formula, identifie" help="(-mapping) 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"/>
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78 <param name="param_db_struct" type="data" format="tabular" optional="False" value="CHEMISTRY/HMDB2StructMapping.tsv" label="Database input file, containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="(-struct) 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"/>
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79 <param name="param_algorithm_mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search" help="(-mass_error_value) "/>
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80 <param name="param_algorithm_mass_error_unit" type="select" optional="True" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
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81 <option value="ppm">ppm</option>
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82 <option value="Da">Da</option>
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83 </param>
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84 <param name="param_algorithm_ionization_mode" type="select" optional="True" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) 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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85 <option value="positive">positive</option>
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86 <option value="negative">negative</option>
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87 <option value="auto">auto</option>
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88 </param>
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89 <param name="param_algorithm_isotopic_similarity" type="boolean" truevalue="-algorithm:isotopic_similarity" falsevalue="" checked="false" optional="True" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help="(-isotopic_similarity) "/>
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90 <param name="param_algorithm_report_mode" type="select" optional="True" value="all" label="Results are reported in one of several modes: Either (all) matching hits, the (top3) scoring hits, or the (best) scoring hit" help="(-report_mode) ">
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91 <option value="all">all</option>
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92 <option value="top3">top3</option>
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93 <option value="best">best</option>
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94 </param>
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95 <param name="param_algorithm_keep_unidentified_masses" type="boolean" truevalue="-algorithm:keep_unidentified_masses" falsevalue="" checked="false" optional="True" label="Keep features that did not yield any DB hit" help="(-keep_unidentified_masses) "/>
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96 <expand macro="advanced_options">
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97 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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98 </expand>
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99 </inputs>
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100 <outputs>
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101 <data name="param_out" format="tabular"/>
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102 <data name="param_out_annotation" metadata_source="param_in" format="input"/>
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103 </outputs>
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104 <help>**What it does**
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105
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106 Find potential HMDB ids within the given mass error window.
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107
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108
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109 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help>
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110 <expand macro="references"/>
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111 </tool>
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