comparison msconvert_macros.xml @ 11:052798dd73dd draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"

10:06747cba5685

<macros>
  <token name="@VERSION@">3.0.19052</token>
  <token name="@FULL_VERSION@">@VERSION@-089e81090</token>

  <xml name="msconvertCommand">
    <command detect_errors="exit_code">
<![CDATA[
    #import re
    #set $ext = $input.ext

      #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
      #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
      ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
    #end if


    CAN_SUDO=\$(sudo -n -l 2> /dev/null; echo \$?) &&
    if [ "\$CAN_SUDO" -eq "0" ]; then
        uid=`id -u` &&
        gid=`id -g` &&    
        WINE="wine64_anyuser";
    else
        WINE="wine64" &&
        ## create a writable copy of wine prefix (since copying fails for some html
        ## stderr and exit code is swallowed)
        export WINEPREFIX=\$(mktemp -d) &&
        (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true);
    fi
    &&
    \$WINE msconvert ${inputmask}

    --outdir outputs

        --gzip
      #end if

      #if $general_options.multi_run_output.do_multi_run_output == 'false':
        --outfile '${os.path.splitext($basename)[0]}'
        && 
        if [ "\$CAN_SUDO" -eq "0" ]; then
            sudo chown \$uid:\$gid 'outputs/${os.path.splitext($basename)[0]}.${output_type}' && 
            sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}';
        else
          mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}';
        fi
      #else
        && ls -la outputs/
      #end if

      #if $data_processing.precursor_refinement.use_mzrefinement
      && if [ "\$CAN_SUDO" -ne "0" ]; then
        mv '$output_refinement_name' '$output_refinement';
      fi
      #end if
]]>
    </command>
  </xml>

  </xml>


  <xml name="msconvert_tests">
    <test>
      <param name="input" value="small.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="cwt" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />
    </test>
    <test>
      <param name="input" value="small.RAW" ftype="thermo.raw" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="vendor" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="small-peakpicking-vendor-allMS.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="ThyroglobMRM000003.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="combineIonMobilitySpectra" value="true" />
      <param name="do_scan_summing" value="true" />
      <output name="output" file="ThyroglobMRM000003.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="MassLynxTest.raw.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <output name="output" file="MassLynxTest.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="AgilentMassHunterTest.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="BrukerBafTest.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="vendor" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="BrukerBafTest.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="0" />
      <output name="output" file="SciexTest-HPINalone.mzML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="0" />
      <param name="indices_0|from" value="0" />
      <param name="indices_0|to" value="499" />
      <param name="srmAsSpectra" value="true" />
      <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="1" />
      <param name="indices_0|from" value="0" />
      <param name="indices_0|to" value="499" />
      <param name="srmAsSpectra" value="true" />
      <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="true" />
      <param name="run_index_set_0|from" value="0" />
      <param name="run_index_set_0|to" value="1" />
      <output_collection name="multi_run_output_list" type="list">
        <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" />
        <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" />
      </output_collection>
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="true" />
      <output_collection name="multi_run_output_list" type="list">
        <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" />
        <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" />
      </output_collection>
    </test>

    <!-- this data file only has profile MS1, so the result is the same -->
    <test>
      <param name="input" value="small.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="cwt" />
      <param name="pick_peaks_ms_levels" value="1" />
      <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mz5" />
      <param name="mz_encoding" value="64" />
      <param name="intensity_encoding" value="64" />
      <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="mz_encoding" value="32" />
      <param name="intensity_encoding" value="32" />
      <output name="output" file="small-zlib-32.mzXML" lines_diff="6" />
    </test>
    <!-- TODO: how to test gzipped output?
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzXML" />

      <param name="gzip_compression" value="true" />
      <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
    </test>-->

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-numpressLP.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearSlof" />
      <output name="output" file="small-numpressLS.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinear" />
      <output name="output" file="small-numpressL.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressPic" />
      <output name="output" file="small-numpressP.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressSlof" />
      <output name="output" file="small-numpressS.mzML" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="Rpal_01.mz5" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="use_mzrefinement" value="true" />
      <param name="input_ident" value="Rpal_01.pepXML" />
      <param name="thresholdScore" value="mvh" />
      <param name="thresholdValue" value="40-" />
      <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
      <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="charge_state_calculation_method" value="predictor" />
      <param name="predictor_overrideExistingCharge" value="true" />
      <param name="minMultipleCharge" value="2" />
      <param name="maxMultipleCharge" value="5" />
      <param name="singleChargeFractionTIC" value="0.95" />
      <param name="maxKnownCharge" value="8" />
      <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="charge_state_calculation_method" value="turbocharger" />
      <param name="minCharge" value="1" />

      <param name="precursorsBefore" value="1" />
      <param name="precursorsAfter" value="1" />
      <param name="halfIsoWidth" value="1.5" />
      <param name="defaultMinCharge" value="1" />
      <param name="defaultMaxCharge" value="5" />
      <output name="output" file="small-turbocharger.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_etd_filtering" value="true" />
      <param name="remove_precursor" value="true" />
      <param name="remove_charge_reduced" value="true" />
      <param name="remove_neutral_loss" value="false" />
      <param name="blanket_removal" value="false" />
      <param name="matching_tolerance" value="50" />
      <param name="matching_tolerance_units" value="ppm" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="thresholds_0|threshold_type" value="count" />
      <param name="thresholds_0|value" value="100" />
      <param name="thresholds_0|orientation" value="most-intense" />
      <param name="thresholds_1|threshold_type" value="absolute" />
      <param name="thresholds_1|value" value="1" />
      <param name="thresholds_1|orientation" value="most-intense" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-threshold.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_mzwindow_filter" value="true" />
      <param name="mz_window_from" value="420" />
      <param name="mz_window_to" value="840" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-mzWindow.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="denoise" value="true" />
      <param name="num_peaks" value="10" />
      <param name="window_width" value="40" />
      <param name="relax" value="false" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-denoise.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="ms2deisotope" value="true" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-deisotope.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="activation" value="CID" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-activation.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="indices_0|from" value="2" />
      <param name="indices_0|to" value="4" />
      <param name="indices_1|from" value="10" />
      <param name="indices_1|to" value="10" />
      <param name="indices_2|from" value="13" />
      <param name="indices_2|to" value="15" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-index-filter.mzML" lines_diff="32" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="strip_it" value="true" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-strip-it.mzML" lines_diff="100" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_ms_level_filter" value="true" />
      <param name="ms_level_from" value="2" />
      <param name="ms_level_to" value="2" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="polarity" value="positive" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="analyzer" value="IT" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="scan_numbers_0|from" value="3" />
      <param name="scan_numbers_0|to" value="5" />
      <param name="scan_numbers_1|from" value="11" />
      <param name="scan_numbers_1|to" value="11" />
      <param name="scan_numbers_2|from" value="14" />
      <param name="scan_numbers_2|to" value="16" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->
    </test>
    <!--<test>
      <param name="input" value="small.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />

11:052798dd73dd

<macros>
  <token name="@VERSION@">3.0.20287</token>
  <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>
  <xml name="msconvertCommand">
    <command detect_errors="exit_code">
<![CDATA[
    #import re
    #set $ext = $input.ext

      #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
      #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
      ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
    #end if

    CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null; echo $?) &&
    if [ "\$CAN_SUDO" -eq "0" ]; then
      uid=`id -u` &&
      gid=`id -g` &&    
      WINE="wine64_anyuser";
    else
      WINE="wine64" &&
      ## create a writable copy of wine prefix (since copying fails for some html
      ## stderr and exit code is swallowed)
      export WINEPREFIX=\$(mktemp -d) &&
      (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true);
    fi
    &&
    \$WINE msconvert ${inputmask}

    --outdir outputs

        --gzip
      #end if

      #if $general_options.multi_run_output.do_multi_run_output == 'false':
        --outfile '${os.path.splitext($basename)[0]}'
      #end if
      && 
      if [ "\$CAN_SUDO" -eq "0" ]; then
        sudo chown -R \$uid:\$gid './';
      fi
      #if $general_options.multi_run_output.do_multi_run_output == 'false':
        && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
      #else
        ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
        ## TODO this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
        #if $output_type == 'mzML' or $output_type == 'mzXML'
          && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
          ## a newline is needed after `#echo ...` therefore the `;'` on the next line
;'
        #end if
      #end if

      #if $data_processing.precursor_refinement.use_mzrefinement
        && mv '$output_refinement_name' '$output_refinement';
      #end if
]]>
    </command>
  </xml>

  </xml>


  <xml name="msconvert_tests">
    <test>
      <param name="input" value="small.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="cwt" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
    </test>
    <test>
      <param name="input" value="small.RAW" ftype="thermo.raw" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="vendor" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="combineIonMobilitySpectra" value="true" />
      <param name="do_scan_summing" value="true" />
      <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="vendor" />
      <param name="pick_peaks_ms_levels" value="1-" />
      <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="0" />
      <output name="output" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="0" />
      <param name="indices_0|from" value="0" />
      <param name="indices_0|to" value="499" />
      <param name="srmAsSpectra" value="true" />
      <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="do_multi_run_output" value="false" />
      <param name="runIndexSet" value="1" />
      <param name="indices_0|from" value="0" />
      <param name="indices_0|to" value="499" />
      <param name="srmAsSpectra" value="true" />
      <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="true" />
      <param name="run_index_set_0|from" value="0" />
      <param name="run_index_set_0|to" value="1" />
      <output_collection name="multi_run_output_list" type="list">
        <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
        <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
      </output_collection>
    </test>
    <test>
      <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_multi_run_output" value="true" />
      <output_collection name="multi_run_output_list" type="list">
        <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
        <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
      </output_collection>
    </test>

    <!-- this data file only has profile MS1, so the result is the same -->
    <test>
      <param name="input" value="small.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="cwt" />
      <param name="pick_peaks_ms_levels" value="1" />
      <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mz5" />
      <param name="mz_encoding" value="64" />
      <param name="intensity_encoding" value="64" />
      <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzXML" />
      <param name="mz_encoding" value="32" />
      <param name="intensity_encoding" value="32" />
      <output name="output" file="small-zlib-32.mzXML" ftype="mzxml" lines_diff="6" />
    </test>
    <!-- TODO: how to test gzipped output?
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
      <param name="output_type" value="mzXML" />

      <param name="gzip_compression" value="true" />
      <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
    </test>-->

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-numpressLP.mzML" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearSlof" />
      <output name="output" file="small-numpressLS.mzML" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinear" />
      <output name="output" file="small-numpressL.mzML" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressPic" />
      <output name="output" file="small-numpressP.mzML" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressSlof" />
      <output name="output" file="small-numpressS.mzML" ftype="mzml" lines_diff="114" />
    </test>

    <test>
      <param name="input" value="Rpal_01.mz5" ftype="mz5" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="use_mzrefinement" value="true" />
      <param name="input_ident" value="Rpal_01.pepXML" />
      <param name="thresholdScore" value="mvh" />
      <param name="thresholdValue" value="40-" />
      <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" />
      <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
    </test>

    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="charge_state_calculation_method" value="predictor" />
      <param name="predictor_overrideExistingCharge" value="true" />
      <param name="minMultipleCharge" value="2" />
      <param name="maxMultipleCharge" value="5" />
      <param name="singleChargeFractionTIC" value="0.95" />
      <param name="maxKnownCharge" value="8" />
      <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />
      <param name="charge_state_calculation_method" value="turbocharger" />
      <param name="minCharge" value="1" />

      <param name="precursorsBefore" value="1" />
      <param name="precursorsAfter" value="1" />
      <param name="halfIsoWidth" value="1.5" />
      <param name="defaultMinCharge" value="1" />
      <param name="defaultMaxCharge" value="5" />
      <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" />
    </test>
    <test>
      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_etd_filtering" value="true" />
      <param name="remove_precursor" value="true" />
      <param name="remove_charge_reduced" value="true" />
      <param name="remove_neutral_loss" value="false" />
      <param name="blanket_removal" value="false" />
      <param name="matching_tolerance" value="50" />
      <param name="matching_tolerance_units" value="ppm" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="thresholds_0|threshold_type" value="count" />
      <param name="thresholds_0|value" value="100" />
      <param name="thresholds_0|orientation" value="most-intense" />
      <param name="thresholds_1|threshold_type" value="absolute" />
      <param name="thresholds_1|value" value="1" />
      <param name="thresholds_1|orientation" value="most-intense" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-threshold.mzML" lines_diff="114" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_mzwindow_filter" value="true" />
      <param name="mz_window_from" value="420" />
      <param name="mz_window_to" value="840" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-mzWindow.mzML" lines_diff="114" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="denoise" value="true" />
      <param name="num_peaks" value="10" />
      <param name="window_width" value="40" />
      <param name="relax" value="false" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-denoise.mzML" lines_diff="114" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="ms2deisotope" value="true" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="activation" value="CID" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="indices_0|from" value="2" />
      <param name="indices_0|to" value="4" />
      <param name="indices_1|from" value="10" />
      <param name="indices_1|to" value="10" />
      <param name="indices_2|from" value="13" />
      <param name="indices_2|to" value="15" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="strip_it" value="true" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="do_ms_level_filter" value="true" />
      <param name="ms_level_from" value="2" />
      <param name="ms_level_to" value="2" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="polarity" value="positive" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="analyzer" value="IT" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />
    </test>
    <test>
      <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
      <param name="license_agreement" value="true" />
      <param name="output_type" value="mzML" />
      <param name="scan_numbers_0|from" value="3" />
      <param name="scan_numbers_0|to" value="5" />
      <param name="scan_numbers_1|from" value="11" />
      <param name="scan_numbers_1|to" value="11" />
      <param name="scan_numbers_2|from" value="14" />
      <param name="scan_numbers_2|to" value="16" />
      <param name="binary_compression" value="numpressLinearPic" />
      <output name="output" file="small-index-filter.mzML" lines_diff="86" ftype="mzml"/> <!-- the scan numbers here produce the same output as the index test above -->
    </test>
    <!--<test>
      <param name="input" value="small.mzML" />
      <param name="output_type" value="mzML" />
      <param name="binary_compression" value="numpressLinearPic" />