<?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: [File Handling]-->
  <tool id="FileConverter" name="FileConverter" version="2.0.0">
    <description>Converts between different MS file formats.</description>
    <macros>
      <token name="@EXECUTABLE@">FileConverter</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>FileConverter

#if $param_in:
  -in $param_in
#end if
#if $param_UID_postprocessing:
  -UID_postprocessing
  #if &quot; &quot; in str($param_UID_postprocessing):
    &quot;$param_UID_postprocessing&quot;
  #else
    $param_UID_postprocessing
  #end if
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_type:
  -out_type
  #if &quot; &quot; in str($param_out_type):
    &quot;$param_out_type&quot;
  #else
    $param_out_type
  #end if
#end if
#if $param_write_mzML_index:
  -write_mzML_index
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_TIC_DTA2D:
  -TIC_DTA2D
#end if
    #if $adv_opts.param_MGF_compact:
  -MGF_compact
#end if
    #if $adv_opts.param_process_lowmemory:
  -process_lowmemory
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml,mzml,mzxml,tabular,txt,consensusxml" help="(-in) " label="Input file to convert" name="param_in" optional="False" type="data"/>
      <param help="(-UID_postprocessing) &lt;br&gt;'none' keeps current IDs even if invalid. &lt;br&gt;'ensure' keeps current IDs but reassigns invalid ones. &lt;br&gt;'reassign' assigns new unique IDs" label="unique ID post-processing for output data" name="param_UID_postprocessing" optional="True" type="select" value="ensure">
        <option value="none">none</option>
        <option value="ensure">ensure</option>
        <option value="reassign">reassign</option>
      </param>
      <param help="(-out_type) " label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" name="param_out_type" optional="True" type="select">
        <option value="mzData">mzData</option>
        <option value="mzXML">mzXML</option>
        <option value="mzML">mzML</option>
        <option value="dta2d">dta2d</option>
        <option value="mgf">mgf</option>
        <option value="featureXML">featureXML</option>
        <option value="consensusXML">consensusXML</option>
        <option value="edta">edta</option>
        <option value="csv">csv</option>
      </param>
      <param checked="false" falsevalue="" help="(-write_mzML_index) " label="Add an index to the file when writing mzML files (default: no index)" name="param_write_mzML_index" optional="True" truevalue="-write_mzML_index" type="boolean"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-TIC_DTA2D) " label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" name="param_TIC_DTA2D" optional="True" truevalue="-TIC_DTA2D" type="boolean"/>
        <param checked="false" falsevalue="" help="(-MGF_compact) " label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" name="param_MGF_compact" optional="True" truevalue="-MGF_compact" type="boolean"/>
        <param checked="false" falsevalue="" help="(-process_lowmemory) &lt;br&gt;Note: this flag will prevent conversion from spectra to chromatograms" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" name="param_process_lowmemory" optional="True" truevalue="-process_lowmemory" type="boolean"/>
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
        <data name="param_out" metadata_source="param_in" format="mgf">
        <change_format>
            <when input="param_out_type" value="mzData" format="mzData" />
            <when input="param_out_type" value="mzXML" format="mzXML" />
            <when input="param_out_type" value="mzML" format="mzML" />
            <when input="param_out_type" value="dta2d" format="dta2d" />
            <when input="param_out_type" value="featureXML" format="featureXML" />
            <when input="param_out_type" value="consensusXML" format="consensusXML" />
            <when input="param_out_type" value="edta" format="edta" />
            <when input="param_out_type" value="csv" format="csv" />
        </change_format>
    </data>
    </outputs>
    <help>Converts between different MS file formats.


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