annotate FileConverter.xml @ 16:8b6336c903ef draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [File Converter]-->
<tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Converts between different MS file formats</description>
  <macros>
    <token name="@EXECUTABLE@">FileConverter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${out_type}'

## Postprocessing
&& mv 'out/output.${out_type}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw data sets(s)"/>
    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
      <option value="consensusXML">consensusxml</option>
      <option value="csv">csv</option>
      <option value="dta2d">dta2d</option>
      <option value="edta">edta</option>
      <option value="featureXML">featurexml</option>
      <option value="mgf">mgf</option>
      <option value="mzData">mzdata</option>
      <option value="mzML">mzml</option>
      <option value="mzXML">mzxml</option>
      <option value="oms">sqlite (oms)</option>
      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
      <expand macro="list_string_san" name="out_type"/>
    </param>
    <expand macro="adv_opts_macro">
      <param argument="-UID_postprocessing" type="select" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
        <option value="none">none</option>
        <option value="ensure" selected="true">ensure</option>
        <option value="reassign">reassign</option>
        <expand macro="list_string_san" name="UID_postprocessing"/>
      </param>
      <param argument="-TIC_DTA2D" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help=""/>
      <param argument="-MGF_compact" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help=""/>
      <param argument="-force_MaxQuant_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help=""/>
      <param argument="-force_TPP_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help=""/>
      <param argument="-convert_to_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data" help=""/>
      <param argument="-change_im_format" type="select" label="[mzML output only] How to store ion mobility scans (none: no change in format; multiple_spectra: store each IM frame as multiple scans (one per drift time value); concatenated: store whole frame as single scan with IM values in a FloatDataArray" help="">
        <option value="none" selected="true">none</option>
        <option value="concatenated">concatenated</option>
        <option value="multiple_spectra">multiple_spectra</option>
        <option value="mixed">mixed</option>
        <expand macro="list_string_san" name="change_im_format"/>
      </param>
      <param argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/>
      <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data)" help=""/>
      <param argument="-lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
      <param argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" 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)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
      <param argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/>
      <param argument="-no_zlib_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables zlib compression for raw file conversion" help="Enables compatibility with some tools that do not support compressed input files, e.g. X!Tandem"/>
      <param argument="-include_noise" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include noise data in mzML output" help=""/>
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml">
      <change_format>
        <when input="out_type" value="csv" format="csv"/>
        <when input="out_type" value="dta2d" format="dta2d"/>
        <when input="out_type" value="edta" format="edta"/>
        <when input="out_type" value="featureXML" format="featurexml"/>
        <when input="out_type" value="mgf" format="mgf"/>
        <when input="out_type" value="mzData" format="mzdata"/>
        <when input="out_type" value="mzML" format="mzml"/>
        <when input="out_type" value="mzXML" format="mzxml"/>
        <when input="out_type" value="oms" format="sqlite"/>
      </change_format>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_FileConverter_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_1_input.mzData"/>
      <output name="out" value="FileConverter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
      <output name="out" value="FileConverter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_3_input.featureXML"/>
      <output name="out" value="FileConverter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_4 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_4_input.mzXML"/>
      <output name="out" value="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_5 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_5_input.mzML"/>
      <output name="out" value="FileConverter_5_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
      <param name="out_type" value="mzXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_6 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_6_input.mzML"/>
      <output name="out" value="FileConverter_6_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
      <param name="out_type" value="mzXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_7 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_7_input.consensusXML"/>
      <output name="out" value="FileConverter_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_8 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_8_input.mzML"/>
      <output name="out" value="FileConverter_8_output.mzData" compare="sim_size" delta_frac="0.7" ftype="mzdata"/>
      <param name="out_type" value="mzData"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_9 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_9_input.consensusXML"/>
      <output name="out" value="FileConverter_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_10 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
      <output name="out" value="FileConverter_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_11 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_11_input.peplist"/>
      <output name="out" value="FileConverter_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_12 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
      <output name="out" value="FileConverter_12_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_13 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
      <output name="out" value="FileConverter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_14 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_9_output.featureXML"/>
      <output name="out" value="FileConverter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_15 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
      <output name="out" value="FileConverter_15_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_16 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
      <output name="out" value="FileConverter_16_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_17 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_17_input.consensusXML"/>
      <output name="out" value="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
      <param name="out_type" value="csv"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_18 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_17_input.consensusXML"/>
      <output name="out" value="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
      <param name="out_type" value="csv"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_19 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output name="out" value="FileConverter_19_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_20 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_20_input.featureXML"/>
      <output name="out" value="FileConverter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_21 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_4_input.mzXML"/>
      <output name="out" value="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_23 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_23_input.mzML"/>
      <output name="out" value="FileConverter_23_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_24 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="true"/>
        <param name="lossy_mass_accuracy" value="0.0001"/>
        <param name="process_lowmemory" value="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output name="out" value="FileConverter_24_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_25 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="true"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output name="out" value="FileConverter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_26 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="true"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output name="out" value="FileConverter_26_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
      <param name="out_type" value="mzXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_26-2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="true"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_26_output.mzXML"/>
      <output name="out" value="FileConverter_26-2_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
      <param name="out_type" value="mzXML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_27 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="true"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_27_input.mzML"/>
      <output name="out" value="FileConverter_27_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_28 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="true"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_28_input.mzML"/>
      <output name="out" value="FileConverter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_29 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="true"/>
        <param name="lossy_mass_accuracy" value="1e-05"/>
        <param name="process_lowmemory" value="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
      <output name="out" value="FileConverter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_29_back -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_29_output.mzML"/>
      <output name="out" value="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_30 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="multiple_spectra"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_30_input.mzML"/>
      <output name="out" value="FileConverter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_31 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="concatenated"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_30_output.mzML"/>
      <output name="out" value="FileConverter_31_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileConverter_32 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileConverter_32_input.mzML"/>
      <output name="out" value="FileConverter_32_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_32_File_Conversion -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="IDFileConverter_32_output.tmp"/>
      <output name="out" value="IDFileConverter_32_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
      <param name="out_type" value="mgf"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_IDFileConverter_33_File_Conversion -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="IDFileConverter_33_output.tmp"/>
      <output name="out" value="IDFileConverter_33_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
      <param name="out_type" value="mgf"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_CometAdapter_2_prepare -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="true"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="CometAdapter_2_in.mzML"/>
      <output name="out" value="CometAdapter_2_prepared.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_THERMORAWFILEPARSER_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="ginkgotoxin-ms-switching.raw"/>
      <output name="out" value="ginkgotoxin-ms-switching_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_SpectrastSearchAdapter_0_prepare -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="force_TPP_compatibility" value="true"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="no_zlib_compression" value="false"/>
        <param name="include_noise" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="spectra_spectrast.mzXML"/>
      <output name="out" value="SpectrastAdapter_1_hack.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <test expect_num_outputs="1">
      <param name="in" value="FileConverter_1_input.mzData"/>
      <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
    </test>
  </tests>
  <help><![CDATA[Converts between different MS file formats.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileConverter.html]]></help>
  <expand macro="references"/>
</tool>