annotate AccurateMassSearch.xml @ 5:de301ea3e22a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

<?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="2.2.0">
  <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
-db:mapping
  #for token in $param_db_mapping:
    $token
  #end for
-db:struct
  #for token in $param_db_struct:
    $token
  #end for
#if $param_algorithm_mass_error_value:
  -algorithm:mass_error_value $param_algorithm_mass_error_value
#end if
#if $param_algorithm_mass_error_unit:
  -algorithm:mass_error_unit
  #if " " in str($param_algorithm_mass_error_unit):
    "$param_algorithm_mass_error_unit"
  #else
    $param_algorithm_mass_error_unit
  #end if
#end if
#if $param_algorithm_ionization_mode:
  -algorithm:ionization_mode
  #if " " in str($param_algorithm_ionization_mode):
    "$param_algorithm_ionization_mode"
  #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 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="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"/>
    <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"/>
    <param name="param_db_mapping" type="data" format="tabular" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file(s), 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">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_db_struct" type="data" format="tabular" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDB2StructMapping.tsv" label="Database input file(s), 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">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_mass_error_value" type="float" value="5.0" label="Tolerance allowed for accurate mass search" help="(-mass_error_value) "/>
    <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
      <option value="ppm" selected="true">ppm</option>
      <option value="Da">Da</option>
    </param>
    <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" 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">
      <option value="positive" selected="true">positive</option>
      <option value="negative">negative</option>
      <option value="auto">auto</option>
    </param>
    <param name="param_algorithm_isotopic_similarity" display="radio" 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) "/>
    <param name="param_algorithm_keep_unidentified_masses" display="radio" 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) "/>
    <param name="param_algorithm_mzTab_exportIsotopeIntensities" type="integer" min="0" optional="True" value="0" label="[featureXML input only] Number of extra columns in mzTab output, which provide intensities up to the x'th isotope" help="(-exportIsotopeIntensities) '0' to deactivate, '1' for monoisotopic peak, etc. If a feature does not have a certain isotope, 'null' will be reported"/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
    <data name="param_out_annotation" metadata_source="param_in" format="input"/>
  </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>