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comparison msconvert_macros.xml @ 18:331a50e8fd2f draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
author galaxyp
date Mon, 10 Mar 2025 07:48:32 +0000
parents ab6c14374bc0
children
comparison
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17:ab6c14374bc0 18:331a50e8fd2f
1 <macros> 1 <macros>
2 <token name="@VERSION@">3.0.20287</token> 2 <token name="@VERSION@">3.0.20287</token>
3 <token name="@FULL_VERSION@">@VERSION@-769529fa4</token> 3 <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>
4 <token name="@PROFILE_VERSION@">24.2</token>
4 <xml name="msconvertCommand"> 5 <xml name="msconvertCommand">
5 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
6 <![CDATA[ 7 <![CDATA[
7 #import re 8 #import re
8 #set $ext = $input.ext 9 #set $ext = $input.ext
59 $general_options.simAsSpectra 60 $general_options.simAsSpectra
60 $general_options.srmAsSpectra 61 $general_options.srmAsSpectra
61 $general_options.acceptZeroLengthSpectra 62 $general_options.acceptZeroLengthSpectra
62 $general_options.ignoreUnknownInstrumentError 63 $general_options.ignoreUnknownInstrumentError
63 64
64 #if $general_options.scan_summing.do_scan_summing: 65 #if $general_options.scan_summing.do_scan_summing == "true":
65 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" 66 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
66 #end if 67 #end if
67 68
68 #if $general_options.multi_run_output.do_multi_run_output == "true": 69 #if $general_options.multi_run_output.do_multi_run_output == "true":
69 #if len($general_options.multi_run_output.run_index_set) > 0 70 #if len($general_options.multi_run_output.run_index_set) > 0
79 80
80 ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests 81 ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests
81 --stripLocationFromSourceFiles 82 --stripLocationFromSourceFiles
82 83
83 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) 84 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
84 #if $data_processing.peak_picking.pick_peaks 85 #if $data_processing.peak_picking.pick_peaks == "true"
85 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" 86 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
86 #end if 87 #end if
87 88
88 #if $data_processing.precursor_refinement.use_mzrefinement == "true" 89 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
89 --filter "mzRefiner $input_ident_name 90 --filter "mzRefiner $input_ident_name
114 115
115 #for threshold_entry in $data_processing.thresholds 116 #for threshold_entry in $data_processing.thresholds
116 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" 117 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
117 #end for 118 #end for
118 119
119 #if $data_processing.filter_mz_windows.do_mzwindow_filter 120 #if $data_processing.filter_mz_windows.do_mzwindow_filter == "true"
120 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" 121 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
121 #end if 122 #end if
122 123
123 #if $data_processing.etd_filtering.do_etd_filtering 124 #if $data_processing.etd_filtering.do_etd_filtering == "true"
124 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor 125 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
125 $data_processing.etd_filtering.remove_charge_reduced 126 $data_processing.etd_filtering.remove_charge_reduced
126 $data_processing.etd_filtering.remove_neutral_loss 127 $data_processing.etd_filtering.remove_neutral_loss
127 $data_processing.etd_filtering.blanket_removal 128 $data_processing.etd_filtering.blanket_removal
128 $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units" 129 $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"
129 #end if 130 #end if
130 131
131 #if $data_processing.ms2denoise.denoise 132 #if $data_processing.ms2denoise.denoise == "true"
132 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" 133 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
133 #end if 134 #end if
134 135
135 #if str($data_processing.ms2deisotope) == "true" 136 #if str($data_processing.ms2deisotope) == "true"
136 --filter "MS2Deisotope" 137 --filter "MS2Deisotope"
137 #end if 138 #end if
138 139
139 #if $data_processing.demultiplex.demultiplex_on 140 #if $data_processing.demultiplex.demultiplex_on == "true"
140 --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize" 141 --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize"
141 #end if 142 #end if
142 143
143 ## SCAN INCLUSION/EXCLUSION FILTERS 144 ## SCAN INCLUSION/EXCLUSION FILTERS
144 #if str($filtering.activation) != "false" 145 #if str($filtering.activation) != "false"
163 164
164 #if $filtering.strip_it.value 165 #if $filtering.strip_it.value
165 --filter "stripIT" 166 --filter "stripIT"
166 #end if 167 #end if
167 168
168 #if $filtering.filter_ms_levels.do_ms_level_filter 169 #if $filtering.filter_ms_levels.do_ms_level_filter == "true"
169 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" 170 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
170 #end if 171 #end if
171 172
172 #if str($filtering.polarity) != "false" 173 #if str($filtering.polarity) != "false"
173 --filter "polarity $filtering.polarity" 174 --filter "polarity $filtering.polarity"
204 --numpressPic 205 --numpressPic
205 #else if $binary_compression == "numpressSlof" 206 #else if $binary_compression == "numpressSlof"
206 --numpressSlof 207 --numpressSlof
207 #end if 208 #end if
208 209
209 #if $settings.gzip_compression 210 #if $settings.gzip_compression == "true"
210 --gzip 211 --gzip
211 #end if 212 #end if
212 213
213 #if $general_options.multi_run_output.do_multi_run_output == 'false': 214 #if $general_options.multi_run_output.do_multi_run_output == 'false':
214 --outfile '${os.path.splitext($basename)[0]}' 215 --outfile '${os.path.splitext($basename)[0]}'
251 252
252 <section name="data_processing" title="Data Processing Filters"> 253 <section name="data_processing" title="Data Processing Filters">
253 <conditional name="peak_picking"> 254 <conditional name="peak_picking">
254 <param type="select" name="pick_peaks" label="Apply peak picking?"> 255 <param type="select" name="pick_peaks" label="Apply peak picking?">
255 <option value="true">Yes</option> 256 <option value="true">Yes</option>
256 <option value="false">No</option> 257 <option value="false" selected="true">No</option>
257 </param> 258 </param>
258 <when value="false" /> 259 <when value="false" />
259 <when value="true"> 260 <when value="true">
260 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> 261 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
261 <option value="1">MS1 Only (1)</option> 262 <option value="1">MS1 Only (1)</option>
343 </repeat> 344 </repeat>
344 345
345 <conditional name="filter_mz_windows"> 346 <conditional name="filter_mz_windows">
346 <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help=""> 347 <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help="">
347 <option value="true">Yes</option> 348 <option value="true">Yes</option>
348 <option value="false">No</option> 349 <option value="false" selected="true">No</option>
349 </param> 350 </param>
350 <when value="false" /> 351 <when value="false" />
351 <when value="true"> 352 <when value="true">
352 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" /> 353 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
353 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" /> 354 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
355 </conditional> 356 </conditional>
356 357
357 <conditional name="etd_filtering"> 358 <conditional name="etd_filtering">
358 <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?"> 359 <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?">
359 <option value="true">Yes</option> 360 <option value="true">Yes</option>
360 <option value="false">No</option> 361 <option value="false" selected="true">No</option>
361 </param> 362 </param>
362 <when value="false" /> 363 <when value="false" />
363 <when value="true"> 364 <when value="true">
364 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor"> 365 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
365 <option value="true" selected="true">yes</option> 366 <option value="true" selected="true">yes</option>
386 </conditional> 387 </conditional>
387 388
388 <conditional name="ms2denoise"> 389 <conditional name="ms2denoise">
389 <param name="denoise" type="select" label="De-noise MS2 with moving window filter"> 390 <param name="denoise" type="select" label="De-noise MS2 with moving window filter">
390 <option value="true">Yes</option> 391 <option value="true">Yes</option>
391 <option value="false">No</option> 392 <option value="false" selected="true">No</option>
392 </param> 393 </param>
393 <when value="true"> 394 <when value="true">
394 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" /> 395 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
395 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" /> 396 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
396 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" /> 397 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
401 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> 402 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
402 403
403 <conditional name="demultiplex"> 404 <conditional name="demultiplex">
404 <param name="demultiplex_on" type="select" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)"> 405 <param name="demultiplex_on" type="select" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)">
405 <option value="true">Yes</option> 406 <option value="true">Yes</option>
406 <option value="false">No</option> 407 <option value="false" selected="true">No</option>
407 </param> 408 </param>
408 <when value="true"> 409 <when value="true">
409 <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" /> 410 <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
410 <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance"> 411 <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
411 <option value="MZ">mz</option> 412 <option value="MZ">mz</option>
461 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> 462 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
462 463
463 <conditional name="filter_ms_levels"> 464 <conditional name="filter_ms_levels">
464 <param name="do_ms_level_filter" type="select" label="Filter MS Levels"> 465 <param name="do_ms_level_filter" type="select" label="Filter MS Levels">
465 <option value="true">Yes</option> 466 <option value="true">Yes</option>
466 <option value="false">No</option> 467 <option value="false" selected="true">No</option>
467 </param> 468 </param>
468 <when value="false" /> 469 <when value="false" />
469 <when value="true"> 470 <when value="true">
470 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" /> 471 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
471 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" /> 472 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
492 <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." /> 493 <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />
493 494
494 <conditional name="scan_summing"> 495 <conditional name="scan_summing">
495 <param name="do_scan_summing" type="select" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR"> 496 <param name="do_scan_summing" type="select" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR">
496 <option value="true">Yes</option> 497 <option value="true">Yes</option>
497 <option value="false">No</option> 498 <option value="false" selected="true">No</option>
498 </param> 499 </param>
499 <when value="false" /> 500 <when value="false" />
500 <when value="true"> 501 <when value="true">
501 <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." /> 502 <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." />
502 <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." /> 503 <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." />
510 <param argument="--ignoreUnknownInstrumentError" type="boolean" truevalue="--ignoreUnknownInstrumentError" falsevalue="" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" /> 511 <param argument="--ignoreUnknownInstrumentError" type="boolean" truevalue="--ignoreUnknownInstrumentError" falsevalue="" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
511 512
512 <conditional name="multi_run_output"> 513 <conditional name="multi_run_output">
513 <param name="do_multi_run_output" type="select" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)"> 514 <param name="do_multi_run_output" type="select" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)">
514 <option value="true">Yes</option> 515 <option value="true">Yes</option>
515 <option value="false">No</option> 516 <option value="false" selected="true">No</option>
516 </param> 517 </param>
517 <when value="false"> 518 <when value="false">
518 <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" /> 519 <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
519 </when> 520 </when>
520 <when value="true"> 521 <when value="true">
549 </xml> 550 </xml>
550 551
551 <xml name="msconvertOutput"> 552 <xml name="msconvertOutput">
552 <outputs> 553 <outputs>
553 <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" > 554 <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" >
554 <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter> 555 <filter>general_options['multi_run_output']['do_multi_run_output'] == "false"</filter>
555 <change_format> 556 <change_format>
556 <when input="output_type" value="mz5" format="mz5" /> 557 <when input="output_type" value="mz5" format="mz5" />
557 <when input="output_type" value="mzXML" format="mzxml" /> 558 <when input="output_type" value="mzXML" format="mzxml" />
558 <when input="output_type" value="ms2" format="ms2" /> 559 <when input="output_type" value="ms2" format="ms2" />
559 <when input="output_type" value="mgf" format="mgf" /> 560 <when input="output_type" value="mgf" format="mgf" />
570 </xml> 571 </xml>
571 572
572 573
573 <xml name="msconvert_tests"> 574 <xml name="msconvert_tests">
574 <test expect_num_outputs="1"> 575 <test expect_num_outputs="1">
575 <param name="input" value="small.mzML" ftype="mzml" />
576 <param name="license_agreement" value="true" />
577 <param name="output_type" value="mzML" />
578 <param name="pick_peaks" value="true" />
579 <param name="pick_peaks_algorithm" value="cwt" />
580 <param name="pick_peaks_ms_levels" value="1-" />
581 <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
582 </test>
583 <test expect_num_outputs="1">
584 <param name="input" value="small.RAW" ftype="thermo.raw" /> 576 <param name="input" value="small.RAW" ftype="thermo.raw" />
585 <param name="license_agreement" value="true" /> 577 <param name="license_agreement" value="true" />
586 <param name="output_type" value="mzML" /> 578 <param name="output_type" value="mzML" />
587 <param name="pick_peaks" value="true" /> 579 <param name="data_processing|peak_picking|pick_peaks" value="true" />
588 <param name="pick_peaks_algorithm" value="vendor" /> 580 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="vendor" />
589 <param name="pick_peaks_ms_levels" value="1-" /> 581 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1-" />
590 <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" /> 582 <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" />
591 </test> 583 </test>
592 <test expect_num_outputs="1"> 584 <test expect_num_outputs="1">
593 <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" /> 585 <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" />
594 <param name="license_agreement" value="true" /> 586 <param name="license_agreement" value="true" />
595 <param name="output_type" value="mzML" /> 587 <param name="output_type" value="mzML" />
596 <param name="combineIonMobilitySpectra" value="true" /> 588 <param name="general_options|combineIonMobilitySpectra" value="true" />
597 <param name="do_scan_summing" value="true" /> 589 <param name="general_options|scan_summing|do_scan_summing" value="true" />
598 <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" /> 590 <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" />
599 </test> 591 </test>
600 <test expect_num_outputs="1"> 592 <test expect_num_outputs="1">
601 <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" /> 593 <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
602 <param name="license_agreement" value="true" /> 594 <param name="license_agreement" value="true" />
611 </test> 603 </test>
612 <test expect_num_outputs="1"> 604 <test expect_num_outputs="1">
613 <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" /> 605 <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" />
614 <param name="license_agreement" value="true" /> 606 <param name="license_agreement" value="true" />
615 <param name="output_type" value="mzML" /> 607 <param name="output_type" value="mzML" />
616 <param name="pick_peaks" value="true" /> 608 <param name="data_processing|peak_picking|pick_peaks" value="true" />
617 <param name="pick_peaks_algorithm" value="vendor" /> 609 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="vendor" />
618 <param name="pick_peaks_ms_levels" value="1-" /> 610 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1-" />
619 <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" /> 611 <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" />
620 </test> 612 </test>
621 <test expect_num_outputs="1"> 613 <test expect_num_outputs="1">
622 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> 614 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
623 <param name="license_agreement" value="true" /> 615 <param name="license_agreement" value="true" />
624 <param name="output_type" value="mzML" /> 616 <param name="output_type" value="mzXML" />
625 <param name="do_multi_run_output" value="false" /> 617 <param name="general_options|multi_run_output|do_multi_run_output" value="false" />
626 <param name="runIndexSet" value="0" /> 618 <param name="general_options|multi_run_output|runIndexSet" value="1" />
627 <output name="output" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> 619 <param name="filtering|indices_0|from" value="0" />
620 <param name="filtering|indices_0|to" value="499" />
621 <param name="general_options|srmAsSpectra" value="true" />
622 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
628 </test> 623 </test>
629 <test expect_num_outputs="1"> 624 <test expect_num_outputs="1">
630 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> 625 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
631 <param name="license_agreement" value="true" /> 626 <param name="license_agreement" value="true" />
632 <param name="output_type" value="mzXML" /> 627 <param name="output_type" value="mzML" />
633 <param name="do_multi_run_output" value="false" /> 628 <param name="general_options|multi_run_output|do_multi_run_output" value="true" />
634 <param name="runIndexSet" value="0" /> 629 <param name="general_options|multi_run_output|run_index_set_0|from" value="0" />
635 <param name="indices_0|from" value="0" /> 630 <param name="general_options|multi_run_output|run_index_set_0|to" value="1" />
636 <param name="indices_0|to" value="499" />
637 <param name="srmAsSpectra" value="true" />
638 <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
639 </test>
640 <test expect_num_outputs="1">
641 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
642 <param name="license_agreement" value="true" />
643 <param name="output_type" value="mzXML" />
644 <param name="do_multi_run_output" value="false" />
645 <param name="runIndexSet" value="1" />
646 <param name="indices_0|from" value="0" />
647 <param name="indices_0|to" value="499" />
648 <param name="srmAsSpectra" value="true" />
649 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
650 </test>
651 <test expect_num_outputs="1">
652 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
653 <param name="license_agreement" value="true" />
654 <param name="output_type" value="mzML" />
655 <param name="do_multi_run_output" value="true" />
656 <param name="run_index_set_0|from" value="0" />
657 <param name="run_index_set_0|to" value="1" />
658 <output_collection name="multi_run_output_list" type="list"> 631 <output_collection name="multi_run_output_list" type="list">
659 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> 632 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
660 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" /> 633 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
661 </output_collection> 634 </output_collection>
662 </test> 635 </test>
663 <test expect_num_outputs="1"> 636 <test expect_num_outputs="1">
664 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" /> 637 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
665 <param name="license_agreement" value="true" /> 638 <param name="license_agreement" value="true" />
666 <param name="output_type" value="mzML" /> 639 <param name="output_type" value="mzML" />
667 <param name="do_multi_run_output" value="true" /> 640 <param name="general_options|multi_run_output|do_multi_run_output" value="true" />
668 <output_collection name="multi_run_output_list" type="list"> 641 <output_collection name="multi_run_output_list" type="list">
669 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" /> 642 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
670 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" /> 643 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
671 </output_collection> 644 </output_collection>
672 </test> 645 </test>
673 646
674 <!-- this data file only has profile MS1, so the result is the same --> 647 <!-- this data file only has profile MS1, so the result is the same -->
675 <test expect_num_outputs="1"> 648 <test expect_num_outputs="1">
676 <param name="input" value="small.mzML" ftype="mzml" />
677 <param name="license_agreement" value="true" />
678 <param name="output_type" value="mzML" />
679 <param name="pick_peaks" value="true" />
680 <param name="pick_peaks_algorithm" value="cwt" />
681 <param name="pick_peaks_ms_levels" value="1" />
682 <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
683 </test>
684 <test expect_num_outputs="1">
685 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> 649 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
686 <param name="license_agreement" value="true" /> 650 <param name="license_agreement" value="true" />
687 <param name="output_type" value="mz5" /> 651 <param name="output_type" value="mz5" />
688 <param name="mz_encoding" value="64" /> 652 <param name="settings|mz_encoding" value="64" />
689 <param name="intensity_encoding" value="64" /> 653 <param name="settings|intensity_encoding" value="64" />
690 <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" /> 654 <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" />
691 </test>
692 <test expect_num_outputs="1">
693 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
694 <param name="license_agreement" value="true" />
695 <param name="output_type" value="mzXML" />
696 <param name="mz_encoding" value="32" />
697 <param name="intensity_encoding" value="32" />
698 <output name="output" file="small-zlib-32.mzXML" ftype="mzxml" lines_diff="6" />
699 </test> 655 </test>
700 <!-- TODO: how to test gzipped output? 656 <!-- TODO: how to test gzipped output?
701 <test> 657 <test>
702 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 658 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
703 <param name="output_type" value="mzXML" /> 659 <param name="output_type" value="mzXML" />
704 <param name="mz_encoding" value="32" /> 660 <param name="mz_encoding" value="32" />
705 <param name="intensity_encoding" value="32" /> 661 <param name="intensity_encoding" value="32" />
706 <param name="binary_compression" value="false" /> 662 <param name="settings|binary_compression" value="false" />
707 <param name="gzip_compression" value="true" /> 663 <param name="gzip_compression" value="true" />
708 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" /> 664 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
709 </test> 665 </test>
710 <test> 666 <test>
711 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 667 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
712 <param name="output_type" value="mzML" /> 668 <param name="output_type" value="mzML" />
713 <param name="mz_encoding" value="32" /> 669 <param name="mz_encoding" value="32" />
714 <param name="intensity_encoding" value="32" /> 670 <param name="intensity_encoding" value="32" />
715 <param name="binary_compression" value="false" /> 671 <param name="settings|binary_compression" value="false" />
716 <param name="gzip_compression" value="true" /> 672 <param name="gzip_compression" value="true" />
717 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" /> 673 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
718 </test>--> 674 </test>-->
719 675 <test expect_num_outputs="2">
720 <test expect_num_outputs="1">
721 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
722 <param name="license_agreement" value="true" />
723 <param name="output_type" value="mzML" />
724 <param name="binary_compression" value="numpressLinearPic" />
725 <output name="output" file="small-numpressLP.mzML" ftype="mzml" lines_diff="114" />
726 </test>
727
728 <test expect_num_outputs="1">
729 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
730 <param name="license_agreement" value="true" />
731 <param name="output_type" value="mzML" />
732 <param name="binary_compression" value="numpressLinearSlof" />
733 <output name="output" file="small-numpressLS.mzML" ftype="mzml" lines_diff="114" />
734 </test>
735
736 <test expect_num_outputs="1">
737 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
738 <param name="license_agreement" value="true" />
739 <param name="output_type" value="mzML" />
740 <param name="binary_compression" value="numpressLinear" />
741 <output name="output" file="small-numpressL.mzML" ftype="mzml" lines_diff="114" />
742 </test>
743
744 <test expect_num_outputs="1">
745 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
746 <param name="license_agreement" value="true" />
747 <param name="output_type" value="mzML" />
748 <param name="binary_compression" value="numpressPic" />
749 <output name="output" file="small-numpressP.mzML" ftype="mzml" lines_diff="114" />
750 </test>
751
752 <test expect_num_outputs="1">
753 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
754 <param name="license_agreement" value="true" />
755 <param name="output_type" value="mzML" />
756 <param name="binary_compression" value="numpressSlof" />
757 <output name="output" file="small-numpressS.mzML" ftype="mzml" lines_diff="114" />
758 </test>
759
760 <test expect_num_outputs="1">
761 <param name="input" value="Rpal_01.mz5" ftype="mz5" /> 676 <param name="input" value="Rpal_01.mz5" ftype="mz5" />
762 <param name="license_agreement" value="true" /> 677 <param name="license_agreement" value="true" />
763 <param name="output_type" value="mzML" /> 678 <param name="output_type" value="mzML" />
764 <param name="binary_compression" value="numpressLinearPic" /> 679 <param name="settings|binary_compression" value="numpressLinearPic" />
765 <param name="use_mzrefinement" value="true" /> 680 <param name="data_processing|precursor_refinement|use_mzrefinement" value="true" />
766 <param name="input_ident" value="Rpal_01.pepXML" /> 681 <param name="data_processing|precursor_refinement|input_ident" value="Rpal_01.pepXML" />
767 <param name="thresholdScore" value="mvh" /> 682 <param name="data_processing|precursor_refinement|thresholdScore" value="mvh" />
768 <param name="thresholdValue" value="40-" /> 683 <param name="data_processing|precursor_refinement|thresholdValue" value="40-" />
769 <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" /> 684 <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" />
770 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" /> 685 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
771 </test> 686 </test>
772 687 <test expect_num_outputs="1">
688 <param name="input" value="small.mzML" ftype="mzml" />
689 <param name="license_agreement" value="true" />
690 <param name="output_type" value="mzML" />
691
692 <param name="data_processing|peak_picking|pick_peaks" value="true" />
693 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="cwt" />
694 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1" />
695
696 <param name="data_processing|thresholds_0|threshold_type" value="count" />
697 <param name="data_processing|thresholds_0|value" value="100" />
698 <param name="data_processing|thresholds_0|orientation" value="most-intense" />
699 <param name="data_processing|thresholds_1|threshold_type" value="absolute" />
700 <param name="data_processing|thresholds_1|value" value="1" />
701 <param name="data_processing|thresholds_1|orientation" value="most-intense" />
702
703 <param name="data_processing|filter_mz_windows|do_mzwindow_filter" value="true" />
704 <param name="data_processing|filter_mz_windows|mz_window_from" value="420" />
705 <param name="data_processing|filter_mz_windows|mz_window_to" value="840" />
706
707 <param name="filtering|indices_0|from" value="0" />
708 <param name="filtering|indices_0|to" value="20" />
709 <param name="filtering|indices_1|from" value="41" />
710 <param name="filtering|indices_1|to" value="41" />
711
712 <param name="filtering|filter_ms_levels|do_ms_level_filter" value="true" />
713 <param name="filtering|filter_ms_levels|ms_level_from" value="2" />
714 <param name="filtering|filter_ms_levels|ms_level_to" value="2" />
715
716 <param name="filtering|scan_numbers_0|from" value="5" />
717 <param name="filtering|scan_numbers_0|to" value="25" />
718 <param name="filtering|scan_numbers_1|from" value="40" />
719 <param name="filtering|scan_numbers_1|to" value="40" />
720
721 <param name="data_processing|ms2deisotope" value="true" />
722
723 <param name="data_processing|ms2denoise|denoise" value="true" />
724 <param name="data_processing|ms2denoise|num_peaks" value="10" />
725 <param name="data_processing|ms2denoise|window_width" value="40" />
726 <param name="data_processing|ms2denoise|relax" value="false" />
727
728 <param name="data_processing|charge_state_calculation|charge_state_calculation_method" value="predictor" />
729 <param name="data_processing|charge_state_calculation|predictor_overrideExistingCharge" value="true" />
730 <param name="data_processing|charge_state_calculation|minMultipleCharge" value="2" />
731 <param name="data_processing|charge_state_calculation|maxMultipleCharge" value="5" />
732 <param name="data_processing|charge_state_calculation|singleChargeFractionTIC" value="0.95" />
733 <param name="data_processing|charge_state_calculation|maxKnownCharge" value="8" />
734
735 <param name="settings|mz_encoding" value="32" />
736 <param name="settings|intensity_encoding" value="32" />
737
738 <param name="settings|binary_compression" value="numpressLinearPic" />
739 <output name="output" file="small-composite-test.mzML" ftype="mzml" />
740 </test>
773 <test expect_num_outputs="1"> 741 <test expect_num_outputs="1">
774 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> 742 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
775 <param name="license_agreement" value="true" /> 743 <param name="license_agreement" value="true" />
776 <param name="output_type" value="mzML" /> 744 <param name="output_type" value="mzML" />
777 <param name="binary_compression" value="numpressLinearPic" /> 745 <param name="settings|binary_compression" value="numpressLinearPic" />
778 <param name="charge_state_calculation_method" value="predictor" /> 746 <param name="data_processing|charge_state_calculation|charge_state_calculation_method" value="turbocharger" />
779 <param name="predictor_overrideExistingCharge" value="true" /> 747 <param name="data_processing|charge_state_calculation|minCharge" value="1" />
780 <param name="minMultipleCharge" value="2" /> 748 <param name="data_processing|charge_state_calculation|maxCharge" value="5" />
781 <param name="maxMultipleCharge" value="5" /> 749 <param name="data_processing|charge_state_calculation|precursorsBefore" value="1" />
782 <param name="singleChargeFractionTIC" value="0.95" /> 750 <param name="data_processing|charge_state_calculation|precursorsAfter" value="1" />
783 <param name="maxKnownCharge" value="8" /> 751 <param name="data_processing|charge_state_calculation|halfIsoWidth" value="1.5" />
784 <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" /> 752 <param name="data_processing|charge_state_calculation|defaultMinCharge" value="1" />
753 <param name="data_processing|charge_state_calculation|defaultMaxCharge" value="5" />
754 <param name="filtering|strip_it" value="true" />
755 <output name="output" file="small-composite-test-2.mzML" ftype="mzml" />
785 </test> 756 </test>
786 <test expect_num_outputs="1"> 757 <test expect_num_outputs="1">
787 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" /> 758 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
788 <param name="license_agreement" value="true" /> 759 <param name="license_agreement" value="true" />
789 <param name="output_type" value="mzML" /> 760 <param name="output_type" value="mzML" />
790 <param name="binary_compression" value="numpressLinearPic" /> 761 <param name="filtering|activation" value="CID" />
791 <param name="charge_state_calculation_method" value="turbocharger" /> 762 <param name="settings|binary_compression" value="numpressLinearPic" />
792 <param name="minCharge" value="1" /> 763 <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
793 <param name="maxCharge" value="5" /> 764 </test>
794 <param name="precursorsBefore" value="1" /> 765 <test expect_num_outputs="1">
795 <param name="precursorsAfter" value="1" /> 766 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
796 <param name="halfIsoWidth" value="1.5" /> 767 <param name="license_agreement" value="true" />
797 <param name="defaultMinCharge" value="1" /> 768 <param name="output_type" value="mzML" />
798 <param name="defaultMaxCharge" value="5" /> 769 <param name="filtering|polarity" value="positive" />
799 <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" /> 770 <param name="settings|binary_compression" value="numpressLinearPic" />
771 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
800 </test> 772 </test>
801 <test expect_num_outputs="1"> 773 <test expect_num_outputs="1">
802 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" /> 774 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />
803 <param name="license_agreement" value="true" /> 775 <param name="license_agreement" value="true" />
804 <param name="output_type" value="mzML" /> 776 <param name="output_type" value="mzML" />
805 <param name="do_etd_filtering" value="true" /> 777 <param name="data_processing|etd_filtering|do_etd_filtering" value="true" />
806 <param name="remove_precursor" value="true" /> 778 <param name="data_processing|etd_filtering|remove_precursor" value="true" />
807 <param name="remove_charge_reduced" value="true" /> 779 <param name="data_processing|etd_filtering|remove_charge_reduced" value="true" />
808 <param name="remove_neutral_loss" value="false" /> 780 <param name="data_processing|etd_filtering|remove_neutral_loss" value="false" />
809 <param name="blanket_removal" value="false" /> 781 <param name="data_processing|etd_filtering|blanket_removal" value="false" />
810 <param name="matching_tolerance" value="50" /> 782 <param name="data_processing|etd_filtering|matching_tolerance" value="50" />
811 <param name="matching_tolerance_units" value="ppm" /> 783 <param name="data_processing|etd_filtering|matching_tolerance_units" value="PPM" />
812 <param name="binary_compression" value="numpressLinearPic" /> 784 <param name="settings|binary_compression" value="numpressLinearPic" />
813 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" /> 785 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
814 </test>
815 <test expect_num_outputs="1">
816 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
817 <param name="license_agreement" value="true" />
818 <param name="output_type" value="mzML" />
819 <param name="thresholds_0|threshold_type" value="count" />
820 <param name="thresholds_0|value" value="100" />
821 <param name="thresholds_0|orientation" value="most-intense" />
822 <param name="thresholds_1|threshold_type" value="absolute" />
823 <param name="thresholds_1|value" value="1" />
824 <param name="thresholds_1|orientation" value="most-intense" />
825 <param name="binary_compression" value="numpressLinearPic" />
826 <output name="output" file="small-threshold.mzML" lines_diff="114" ftype="mzml" />
827 </test>
828 <test expect_num_outputs="1">
829 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
830 <param name="license_agreement" value="true" />
831 <param name="output_type" value="mzML" />
832 <param name="do_mzwindow_filter" value="true" />
833 <param name="mz_window_from" value="420" />
834 <param name="mz_window_to" value="840" />
835 <param name="binary_compression" value="numpressLinearPic" />
836 <output name="output" file="small-mzWindow.mzML" lines_diff="114" ftype="mzml" />
837 </test>
838 <test expect_num_outputs="1">
839 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
840 <param name="license_agreement" value="true" />
841 <param name="output_type" value="mzML" />
842 <param name="denoise" value="true" />
843 <param name="num_peaks" value="10" />
844 <param name="window_width" value="40" />
845 <param name="relax" value="false" />
846 <param name="binary_compression" value="numpressLinearPic" />
847 <output name="output" file="small-denoise.mzML" lines_diff="114" ftype="mzml" />
848 </test>
849 <test expect_num_outputs="1">
850 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
851 <param name="license_agreement" value="true" />
852 <param name="output_type" value="mzML" />
853 <param name="ms2deisotope" value="true" />
854 <param name="binary_compression" value="numpressLinearPic" />
855 <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" />
856 </test>
857 <test expect_num_outputs="1">
858 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
859 <param name="license_agreement" value="true" />
860 <param name="output_type" value="mzML" />
861 <param name="activation" value="CID" />
862 <param name="binary_compression" value="numpressLinearPic" />
863 <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
864 </test>
865 <test expect_num_outputs="1">
866 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
867 <param name="license_agreement" value="true" />
868 <param name="output_type" value="mzML" />
869 <param name="indices_0|from" value="2" />
870 <param name="indices_0|to" value="4" />
871 <param name="indices_1|from" value="10" />
872 <param name="indices_1|to" value="10" />
873 <param name="indices_2|from" value="13" />
874 <param name="indices_2|to" value="15" />
875 <param name="binary_compression" value="numpressLinearPic" />
876 <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" />
877 </test>
878 <test expect_num_outputs="1">
879 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
880 <param name="license_agreement" value="true" />
881 <param name="output_type" value="mzML" />
882 <param name="strip_it" value="true" />
883 <param name="binary_compression" value="numpressLinearPic" />
884 <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />
885 </test>
886 <test expect_num_outputs="1">
887 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
888 <param name="license_agreement" value="true" />
889 <param name="output_type" value="mzML" />
890 <param name="do_ms_level_filter" value="true" />
891 <param name="ms_level_from" value="2" />
892 <param name="ms_level_to" value="2" />
893 <param name="binary_compression" value="numpressLinearPic" />
894 <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />
895 </test>
896 <test expect_num_outputs="1">
897 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
898 <param name="license_agreement" value="true" />
899 <param name="output_type" value="mzML" />
900 <param name="polarity" value="positive" />
901 <param name="binary_compression" value="numpressLinearPic" />
902 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
903 </test>
904 <test expect_num_outputs="1">
905 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
906 <param name="license_agreement" value="true" />
907 <param name="output_type" value="mzML" />
908 <param name="analyzer" value="IT" />
909 <param name="binary_compression" value="numpressLinearPic" />
910 <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />
911 </test>
912 <test expect_num_outputs="1">
913 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
914 <param name="license_agreement" value="true" />
915 <param name="output_type" value="mzML" />
916 <param name="scan_numbers_0|from" value="3" />
917 <param name="scan_numbers_0|to" value="5" />
918 <param name="scan_numbers_1|from" value="11" />
919 <param name="scan_numbers_1|to" value="11" />
920 <param name="scan_numbers_2|from" value="14" />
921 <param name="scan_numbers_2|to" value="16" />
922 <param name="binary_compression" value="numpressLinearPic" />
923 <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 -->
924 </test> 786 </test>
925 <!--<test> 787 <!--<test>
926 <param name="input" value="small.mzML" /> 788 <param name="input" value="small.mzML" />
927 <param name="output_type" value="mzML" /> 789 <param name="output_type" value="mzML" />
928 <param name="binary_compression" value="numpressLinearPic" /> 790 <param name="settings|binary_compression" value="numpressLinearPic" />
929 <output name="output" file="small-deisotope-poisson.mzML" /> 791 <output name="output" file="small-deisotope-poisson.mzML" />
930 </test>--> 792 </test>-->
931 </xml> 793 </xml>
932 <xml name="citations"> 794 <xml name="citations">
933 <citations> 795 <citations>