view AccurateMassSearch.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?xml version="1.0" encoding="UTF-8"?>
  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
  <!--Proposed Tool Section: [Utilities]-->
  <tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.0.0">
    <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="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>AccurateMassSearch

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_annotation:
  -out_annotation $param_out_annotation
#end if
#if $param_positive_adducts_file:
  -positive_adducts_file $param_positive_adducts_file
#end if
#if $param_negative_adducts_file:
  -negative_adducts_file $param_negative_adducts_file
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_db_mapping:
  -db:mapping $param_db_mapping
#end if
#if $param_db_struct:
  -db:struct $param_db_struct
#end if
#if $param_algorithm_mass_error_value:
  -algorithm:mass_error_value $param_algorithm_mass_error_value
#end if
#if $param_algorithm_mass_error_unit:
  -algorithm:mass_error_unit
  #if &quot; &quot; in str($param_algorithm_mass_error_unit):
    &quot;$param_algorithm_mass_error_unit&quot;
  #else
    $param_algorithm_mass_error_unit
  #end if
#end if
#if $param_algorithm_ionization_mode:
  -algorithm:ionization_mode
  #if &quot; &quot; in str($param_algorithm_ionization_mode):
    &quot;$param_algorithm_ionization_mode&quot;
  #else
    $param_algorithm_ionization_mode
  #end if
#end if
#if $param_algorithm_isotopic_similarity:
  -algorithm:isotopic_similarity
#end if
#if $param_algorithm_keep_unidentified_masses:
  -algorithm:keep_unidentified_masses
#end if
#if $param_algorithm_mzTab_exportIsotopeIntensities:
  -algorithm:mzTab:exportIsotopeIntensities $param_algorithm_mzTab_exportIsotopeIntensities
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml,consensusxml" help="(-in) " label="featureXML or consensusXML file" name="param_in" optional="False" type="data"/>
      <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"/>
      <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"/>
      <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"/>
      <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"/>
      <param help="(-mass_error_value) " label="Tolerance allowed for accurate mass search" name="param_algorithm_mass_error_value" type="float" value="5.0"/>
      <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">
        <option value="ppm">ppm</option>
        <option value="Da">Da</option>
      </param>
      <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">
        <option value="positive">positive</option>
        <option value="negative">negative</option>
        <option value="auto">auto</option>
      </param>
      <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"/>
      <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"/>
      <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"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="tabular" name="param_out"/>
      <data format="input" metadata_source="param_in" name="param_out_annotation"/>
    </outputs>
    <help>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</help>
  </tool>