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<?xml version='1.0' encoding='UTF-8'?>
<tool id="AccurateMassSearch" name="AccurateMassSearch" version="1.12.0">
  <description>Find potential HMDB ids within the given mass error window.</description>
  <macros>
    <token name="@EXECUTABLE@">AccurateMassSearch</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>AccurateMassSearch

-in ${param_in}
-out ${param_out}
-out_annotation ${param_out_annotation}
-positive_adducts_file ${param_positive_adducts_file}
-negative_adducts_file ${param_negative_adducts_file}
-threads \${GALAXY_SLOTS:-24} 
-db:mapping ${param_mapping}
-db:struct ${param_struct}
-algorithm:mass_error_value ${param_mass_error_value}
-algorithm:mass_error_unit ${param_mass_error_unit}
-algorithm:ionization_mode ${param_ionization_mode}
${param_isotopic_similarity}
-algorithm:report_mode ${param_report_mode}
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="featureXML or consensusXML file" help="(-in)"/>
    <param name="param_positive_adducts_file" type="data" format="" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database. 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." help="(-positive_adducts_file)"/>
    <param name="param_negative_adducts_file" type="data" format="" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database. 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." help="(-negative_adducts_file)"/>
    <param name="param_mapping" type="data" format="" optional="False" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file, containing three tab-separated columns of mass, formula, identifier. 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." help="(-mapping)"/>
    <param name="param_struct" type="data" format="" 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. 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." help="(-struct)"/>
    <param name="param_mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search." help="(-mass_error_value)"/>
    <param name="param_mass_error_unit" type="select" optional="True" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit)">
      <option value="ppm">ppm</option>
      <option value="Da">Da</option>
    </param>
    <param name="param_ionization_mode" type="select" optional="True" value="positive" label="Positive or negative 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." help="(-ionization_mode)">
      <option value="positive">positive</option>
      <option value="negative">negative</option>
      <option value="auto">auto</option>
    </param>
    <param name="param_isotopic_similarity" type="boolean" truevalue="-algorithm:isotopic_similarity true" falsevalue="-algorithm:isotopic_similarity false" 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)"/>
    <param name="param_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)">
      <option value="all">all</option>
      <option value="top3">top3</option>
      <option value="best">best</option>
    </param>
  </inputs>
  <outputs>
    <data name="param_out" label="mzTab file" format="tabular"/>
    <data name="param_out_annotation" label="The input file, annotated with matching hits from the database." format="consensusXML">
      <change_format>
        <when input="param_out_type" value="featureXML" format="featureXML"/>
      </change_format>
    </data>
  </outputs>
  <help>**What it does**

Find potential HMDB ids within the given mass error window.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html

@REFERENCES@
</help>
</tool>