<?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: [Targeted Experiments]-->
  <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.0.0">
    <description>Generates decoys according to different models for a specific TraML</description>
    <macros>
      <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>OpenSwathDecoyGenerator

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_method:
  -method     &quot;$param_method&quot;
#end if
#if $param_decoy_tag:
  -decoy_tag     &quot;$param_decoy_tag&quot;
#end if
#if $param_theoretical:
  -theoretical
#end if
#if $param_mz_threshold:
  -mz_threshold $param_mz_threshold
#end if
#if $param_exclude_similar:
  -exclude_similar
#end if
#if $param_similarity_threshold:
  -similarity_threshold $param_similarity_threshold
#end if
#if $param_append:
  -append
#end if
#if $param_remove_CNterm_mods:
  -remove_CNterm_mods
#end if
#if $param_remove_unannotated:
  -remove_unannotated
#end if
#if $param_enable_losses:
  -enable_losses
#end if
#if $param_identity_threshold:
  -identity_threshold $param_identity_threshold
#end if
#if $param_max_attempts:
  -max_attempts $param_max_attempts
#end if
#if $param_mz_shift:
  -mz_shift $param_mz_shift
#end if
#if $param_precursor_mass_shift:
  -precursor_mass_shift $param_precursor_mass_shift
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="traml" help="(-in) " label="input file ('traML')" name="param_in" optional="False" type="data"/>
      <param help="(-method) " label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" name="param_method" size="30" type="text" value="shuffle">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-decoy_tag) " label="decoy tag" name="param_decoy_tag" size="30" type="text" value="DECOY_">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param checked="false" falsevalue="" help="(-theoretical) " label="set this flag if only annotated transitions should be used and be corrected to the theoretical mz" name="param_theoretical" optional="True" truevalue="-theoretical" type="boolean"/>
      <param help="(-mz_threshold) " label="MZ threshold in Thomson for fragment ion annotation" name="param_mz_threshold" type="float" value="0.05"/>
      <param checked="false" falsevalue="" help="(-exclude_similar) If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded" label="set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded" name="param_exclude_similar" optional="True" truevalue="-exclude_similar" type="boolean"/>
      <param help="(-similarity_threshold) Suggested value: 0.05" label="Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton" name="param_similarity_threshold" type="float" value="-1.0"/>
      <param checked="false" falsevalue="" help="(-append) " label="set this flag if non-decoy TraML should be appended to the output" name="param_append" optional="True" truevalue="-append" type="boolean"/>
      <param checked="false" falsevalue="" help="(-remove_CNterm_mods) " label="set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method)" name="param_remove_CNterm_mods" optional="True" truevalue="-remove_CNterm_mods" type="boolean"/>
      <param checked="false" falsevalue="" help="(-remove_unannotated) " label="set this flag if target assays with unannotated ions should be ignored from decoy generation" name="param_remove_unannotated" optional="True" truevalue="-remove_unannotated" type="boolean"/>
      <param checked="false" falsevalue="" help="(-enable_losses) " label="set this flag if fragment ions should also be annotated with neutral losses" name="param_enable_losses" optional="True" truevalue="-enable_losses" type="boolean"/>
      <param help="(-identity_threshold) " label="shuffle: identity threshold for the shuffle algorithm" name="param_identity_threshold" type="float" value="0.7"/>
      <param help="(-max_attempts) " label="shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm" name="param_max_attempts" type="integer" value="10"/>
      <param help="(-mz_shift) " label="shift: MZ shift in Thomson for shift decoy method" name="param_mz_shift" type="float" value="20.0"/>
      <param help="(-precursor_mass_shift) " label="Mass shift to apply to the precursor ion" name="param_precursor_mass_shift" type="float" value="0.0"/>
      <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="traml" name="param_out"/>
    </outputs>
    <help>Generates decoys according to different models for a specific TraML


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