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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: [Utilities]-->
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4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.0.0">
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5 <description>Find potential HMDB ids within the given mass error window.</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 </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>AccurateMassSearch
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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_annotation:
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22 -out_annotation $param_out_annotation
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23 #end if
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24 #if $param_positive_adducts_file:
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25 -positive_adducts_file $param_positive_adducts_file
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26 #end if
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27 #if $param_negative_adducts_file:
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28 -negative_adducts_file $param_negative_adducts_file
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29 #end if
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30 -threads \${GALAXY_SLOTS:-24}
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31 #if $param_db_mapping:
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32 -db:mapping $param_db_mapping
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33 #end if
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34 #if $param_db_struct:
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35 -db:struct $param_db_struct
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36 #end if
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37 #if $param_algorithm_mass_error_value:
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38 -algorithm:mass_error_value $param_algorithm_mass_error_value
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39 #end if
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40 #if $param_algorithm_mass_error_unit:
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41 -algorithm:mass_error_unit
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42 #if &quot; &quot; in str($param_algorithm_mass_error_unit):
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43 &quot;$param_algorithm_mass_error_unit&quot;
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44 #else
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45 $param_algorithm_mass_error_unit
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46 #end if
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47 #end if
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48 #if $param_algorithm_ionization_mode:
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49 -algorithm:ionization_mode
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50 #if &quot; &quot; in str($param_algorithm_ionization_mode):
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51 &quot;$param_algorithm_ionization_mode&quot;
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52 #else
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53 $param_algorithm_ionization_mode
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54 #end if
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55 #end if
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56 #if $param_algorithm_isotopic_similarity:
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57 -algorithm:isotopic_similarity
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58 #end if
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59 #if $param_algorithm_keep_unidentified_masses:
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60 -algorithm:keep_unidentified_masses
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61 #end if
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62 #if $param_algorithm_mzTab_exportIsotopeIntensities:
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63 -algorithm:mzTab:exportIsotopeIntensities $param_algorithm_mzTab_exportIsotopeIntensities
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64 #end if
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65 #if $adv_opts.adv_opts_selector=='advanced':
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66 #if $adv_opts.param_force:
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67 -force
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68 #end if
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69 #end if
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70 </command>
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71 <inputs>
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72 <param format="xml,consensusxml" help="(-in) " label="featureXML or consensusXML file" name="param_in" optional="False" type="data"/>
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73 <param format="tabular" 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" label="This file contains the list of potential positive adducts that will be looked for in the database" name="param_positive_adducts_file" optional="False" type="data" value="CHEMISTRY/PositiveAdducts.tsv"/>
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74 <param format="tabular" 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" label="This file contains the list of potential negative adducts that will be looked for in the database" name="param_negative_adducts_file" optional="False" type="data" value="CHEMISTRY/NegativeAdducts.tsv"/>
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75 <param format="tabular" 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" label="Database input file, containing three tab-separated columns of mass, formula, identifie" name="param_db_mapping" optional="False" type="data" value="CHEMISTRY/HMDBMappingFile.tsv"/>
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76 <param format="tabular" 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" label="Database input file, containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" name="param_db_struct" optional="False" type="data" value="CHEMISTRY/HMDB2StructMapping.tsv"/>
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77 <param help="(-mass_error_value) " label="Tolerance allowed for accurate mass search" name="param_algorithm_mass_error_value" type="float" value="5.0"/>
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78 <param help="(-mass_error_unit) " label="Unit of mass error (ppm or Da)" name="param_algorithm_mass_error_unit" optional="True" type="select" value="ppm">
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79 <option value="ppm">ppm</option>
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80 <option value="Da">Da</option>
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81 </param>
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82 <param 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" label="Positive or negative ionization mode?" name="param_algorithm_ionization_mode" optional="True" type="select" value="positive">
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83 <option value="positive">positive</option>
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84 <option value="negative">negative</option>
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85 <option value="auto">auto</option>
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86 </param>
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87 <param checked="false" falsevalue="" help="(-isotopic_similarity) " label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" name="param_algorithm_isotopic_similarity" optional="True" truevalue="-algorithm:isotopic_similarity" type="boolean"/>
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88 <param checked="false" falsevalue="" help="(-keep_unidentified_masses) " label="Keep features that did not yield any DB hit" name="param_algorithm_keep_unidentified_masses" optional="True" truevalue="-algorithm:keep_unidentified_masses" type="boolean"/>
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89 <param help="(-exportIsotopeIntensities) '0' to deactivate, '1' for monoisotopic peak, etc. If a feature does not have a certain isotope, 'null' will be reported" label="[featureXML input only] Number of extra columns in mzTab output, which provide intensities up to the x'th isotope" min="0" name="param_algorithm_mzTab_exportIsotopeIntensities" optional="True" type="integer" value="0"/>
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90 <expand macro="advanced_options">
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91 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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92 </expand>
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93 </inputs>
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94 <outputs>
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95 <data format="tabular" name="param_out"/>
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96 <data format="input" metadata_source="param_in" name="param_out_annotation"/>
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97 </outputs>
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98 <help>Find potential HMDB ids within the given mass error window.
0
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99
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100
4
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101 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help>
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102 </tool>