<?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="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="2.2.0">
  <description>Generates assays according to different models for a specific TraML</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathAssayGenerator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathAssayGenerator

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_min_transitions:
  -min_transitions $param_min_transitions
#end if
#if $param_max_transitions:
  -max_transitions $param_max_transitions
#end if
#if $param_allowed_fragment_types:
  -allowed_fragment_types     "$param_allowed_fragment_types"
#end if
#if $param_allowed_fragment_charges:
  -allowed_fragment_charges     "$param_allowed_fragment_charges"
#end if
#if $param_enable_detection_specific_losses:
  -enable_detection_specific_losses
#end if
#if $param_enable_detection_unspecific_losses:
  -enable_detection_unspecific_losses
#end if
#if $param_enable_identification_specific_losses:
  -enable_identification_specific_losses
#end if
#if $param_enable_identification_unspecific_losses:
  -enable_identification_unspecific_losses
#end if
#if $param_enable_identification_ms2_precursors:
  -enable_identification_ms2_precursors
#end if
#if $param_enable_ms1_uis_scoring:
  -enable_ms1_uis_scoring
#end if
#if $param_enable_ms2_uis_scoring:
  -enable_ms2_uis_scoring
#end if
#if $param_max_num_alternative_localizations:
  -max_num_alternative_localizations $param_max_num_alternative_localizations
#end if
#if $param_enable_reannotation:
  -enable_reannotation
#end if
#if $param_precursor_mz_threshold:
  -precursor_mz_threshold $param_precursor_mz_threshold
#end if
#if $param_precursor_lower_mz_limit:
  -precursor_lower_mz_limit $param_precursor_lower_mz_limit
#end if
#if $param_precursor_upper_mz_limit:
  -precursor_upper_mz_limit $param_precursor_upper_mz_limit
#end if
#if $param_product_mz_threshold:
  -product_mz_threshold $param_product_mz_threshold
#end if
#if $param_product_lower_mz_limit:
  -product_lower_mz_limit $param_product_lower_mz_limit
#end if
#if $param_product_upper_mz_limit:
  -product_upper_mz_limit $param_product_upper_mz_limit
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_swath_windows_file:
  -swath_windows_file $adv_opts.param_swath_windows_file
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/>
    <param name="param_min_transitions" type="integer" value="6" label="minimal number of transitions" help="(-min_transitions) "/>
    <param name="param_max_transitions" type="integer" value="6" label="maximal number of transitions" help="(-max_transitions) "/>
    <param name="param_allowed_fragment_types" type="text" size="30" value="b,y" label="allowed fragment types" help="(-allowed_fragment_types) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_allowed_fragment_charges" type="text" size="30" value="1,2,3,4" label="allowed fragment charge states" help="(-allowed_fragment_charges) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_enable_detection_specific_losses" display="radio" type="boolean" truevalue="-enable_detection_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help="(-enable_detection_specific_losses) "/>
    <param name="param_enable_detection_unspecific_losses" display="radio" type="boolean" truevalue="-enable_detection_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help="(-enable_detection_unspecific_losses) "/>
    <param name="param_enable_identification_specific_losses" display="radio" type="boolean" truevalue="-enable_identification_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for identification fragment ions should be allowed" help="(-enable_identification_specific_losses) "/>
    <param name="param_enable_identification_unspecific_losses" display="radio" type="boolean" truevalue="-enable_identification_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help="(-enable_identification_unspecific_losses) "/>
    <param name="param_enable_identification_ms2_precursors" display="radio" type="boolean" truevalue="-enable_identification_ms2_precursors" falsevalue="" checked="false" optional="True" label="set this flag if MS2-level precursor ions for identification should be allowed to enable extraction of the precursor signal from the fragment ion data (MS2-level)" help="(-enable_identification_ms2_precursors) This may help in identification if the MS1 signal is weak"/>
    <param name="param_enable_ms1_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms1_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS1-UIS assays for UIS scoring should be generated" help="(-enable_ms1_uis_scoring) "/>
    <param name="param_enable_ms2_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms2_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS2-UIS assays for UIS scoring should be generated" help="(-enable_ms2_uis_scoring) "/>
    <param name="param_max_num_alternative_localizations" type="integer" value="20" label="maximum number of site-localization permutations" help="(-max_num_alternative_localizations) "/>
    <param name="param_enable_reannotation" display="radio" type="boolean" truevalue="-enable_reannotation" falsevalue="" checked="false" optional="True" label="set this flag if reannotation of fragment ions should be allowed" help="(-enable_reannotation) "/>
    <param name="param_precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help="(-precursor_mz_threshold) "/>
    <param name="param_precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help="(-precursor_lower_mz_limit) "/>
    <param name="param_precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help="(-precursor_upper_mz_limit) "/>
    <param name="param_product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help="(-product_mz_threshold) "/>
    <param name="param_product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help="(-product_lower_mz_limit) "/>
    <param name="param_product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help="(-product_upper_mz_limit) "/>
    <expand macro="advanced_options">
      <param name="param_swath_windows_file" type="data" format="txt" optional="True" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
      <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="traml"/>
  </outputs>
  <help>Generates assays according to different models for a specific TraML


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