annotate SpectraSTSearchAdapter.xml @ 2:409583e6aec8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d4b74e94ddabaccec6b1c5f9540d074c39207600

<?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="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="2.2.0.1">
  <description>Interface to the SEARCH Mode of the SpectraST executable</description>
  <macros>
    <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpectraSTSearchAdapter

-spectra_files
  #for token in $param_spectra_files:
    $token
  #end for

#if $rep_param_output_files:
-output_files
  #for token in $rep_param_output_files:
    #if " " in str(token):
      "$token.param_output_files"
    #else
      $token.param_output_files
    #end if
  #end for
#end if
#if $param_library_file:
  -library_file $param_library_file
#end if
#if $param_sequence_database_file:
  -sequence_database_file $param_sequence_database_file
#end if
#if $param_sequence_database_type:
  -sequence_database_type
  #if " " in str($param_sequence_database_type):
    "$param_sequence_database_type"
  #else
    $param_sequence_database_type
  #end if
#end if
#if $param_search_file:
  -search_file $param_search_file
#end if
#if $param_params_file:
  -params_file $param_params_file
#end if
#if $param_precursor_mz_tolerance:
  -precursor_mz_tolerance $param_precursor_mz_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_use_isotopically_averaged_mass:
  -use_isotopically_averaged_mass
#end if
    #if $adv_opts.param_use_all_charge_states:
  -use_all_charge_states
#end if
    #if $adv_opts.param_user_mod_file:
  -user_mod_file $adv_opts.param_user_mod_file
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_spectra_files" type="data" format="mzml,mzxml,mzData,dta,msp" multiple="true" optional="False" size="30" label="File names(s) of spectra to be searched" help="(-spectra_files) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_library_file" type="data" format="splib" optional="False" label="Specify library file" help="(-library_file) "/>
    <param name="param_sequence_database_file" type="data" format="fasta" optional="True" label="The sequence database" help="(-sequence_database_file) "/>
    <param name="param_sequence_database_type" display="radio" type="select" optional="False" value="AA" label="Specify type of sequence database" help="(-sequence_database_type) ">
      <option value="DNA">DNA</option>
      <option value="AA" selected="true">AA</option>
    </param>
    <param name="param_search_file" type="data" format="txt,dat" optional="True" label="Only search a subset of the query spectra in the search file" help="(-search_file) "/>
    <param name="param_params_file" type="data" format="params" optional="True" label="Read search options from file" help="(-params_file) All options set in the file will be overridden by command-line options, if specified"/>
    <param name="param_precursor_mz_tolerance" type="float" min="0.0" optional="True" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="(-precursor_mz_tolerance) Monoisotopic mass is assumed"/>
    <expand macro="advanced_options">
      <param name="param_use_isotopically_averaged_mass" display="radio" type="boolean" truevalue="-use_isotopically_averaged_mass" falsevalue="" checked="false" optional="True" label="Use isotopically averaged mass instead of monoisotopic mass" help="(-use_isotopically_averaged_mass) "/>
      <param name="param_use_all_charge_states" display="radio" type="boolean" truevalue="-use_all_charge_states" falsevalue="" checked="false" optional="True" label="Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrum" help="(-use_all_charge_states) "/>
      <param name="param_user_mod_file" type="data" format="txt" label="Specify name of user-defined modifications file" help="(-user_mod_file) Default is &quot;spectrast.usermods&quot;"/>
      <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_output_files" format="txt"/>
  </outputs>
  <help>Interface to the SEARCH Mode of the SpectraST executable


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpectraSTSearchAdapter.html</help>
</tool>